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Ma Q, Wang X, Appels R, Zhang D, Zhang X, Zou L, Hu X. Large flour aggregates containing ordered B + V starch crystals significantly improved the digestion resistance of starch in pretreated multigrain flour. Int J Biol Macromol 2024; 264:130719. [PMID: 38460625 DOI: 10.1016/j.ijbiomac.2024.130719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 03/05/2024] [Accepted: 03/06/2024] [Indexed: 03/11/2024]
Abstract
The starch digestibility of flour is influenced by both physicochemical treatment and flour particle size, but the interactive effect of these two factors is still unclear. In this study, the effect of pullulanase debranching, combined with heat-moisture treatment (P-HMT), on starch digestibility of multi-grain flours (including oat, buckwheat and wheat) differing in particle size was investigated. The results showed that the larger-size flour always resulted in a higher resistant starch (RS) content either in natural or treated multi-grain flour (NMF or PHF). P-HMT doubled the RS content in NMFs and the large-size PHF yielded the highest RS content (78.43 %). In NMFs, the cell wall integrity and flour particle size were positively related to starch anti-digestibility. P-HMT caused the destruction of cell walls and starch granules, as well as the formation of rigid flour aggregates with B + V starch crystallite. The largest flour aggregates with the most ordered B + V starch were found in large-size PHF, which contributed to its highest RS yield, while the medium- and small-size PHFs with smaller aggregates were sensitive to P-HMT, resulting in the lower ordered starch but stronger interactions between starch and free lipid or monomeric proteins, eventually leading to their lower RS but higher SDS yield.
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Affiliation(s)
- Qianying Ma
- College of Food Engineering and Nutritional Science, Shaanxi Normal University, No. 620 West Chang'an Avenue, Chang'an District, Xi'an 710119, China
| | - Xiaolong Wang
- College of Food Engineering and Nutritional Science, Shaanxi Normal University, No. 620 West Chang'an Avenue, Chang'an District, Xi'an 710119, China.
| | - Rudi Appels
- Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, VIC 3010, Australia
| | - Di Zhang
- College of Food Engineering and Nutritional Science, Shaanxi Normal University, No. 620 West Chang'an Avenue, Chang'an District, Xi'an 710119, China
| | - Xinyu Zhang
- College of Food Engineering and Nutritional Science, Shaanxi Normal University, No. 620 West Chang'an Avenue, Chang'an District, Xi'an 710119, China
| | - Liang Zou
- School of Food and Biological Engineering, Chengdu University, Chengdu 610106, Sichuan, China
| | - Xinzhong Hu
- College of Food Engineering and Nutritional Science, Shaanxi Normal University, No. 620 West Chang'an Avenue, Chang'an District, Xi'an 710119, China
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2
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Bashmil YM, Dunshea FR, Appels R, Suleria HAR. Bioaccessibility of Phenolic Compounds, Resistant Starch, and Dietary Fibers from Australian Green Banana during In Vitro Digestion and Colonic Fermentation. Molecules 2024; 29:1535. [PMID: 38611814 PMCID: PMC11013930 DOI: 10.3390/molecules29071535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Revised: 03/22/2024] [Accepted: 03/27/2024] [Indexed: 04/14/2024] Open
Abstract
Green bananas contain a substantial amount of resistant starch (RS), dietary fiber (DF), and phytochemicals, which exhibit potent antioxidant capabilities, primarily attributable to the abundance of polyphenols. The objective of this study was to assess the variations in the contents and bioaccessibility of RS, DF, and phenolic compounds in three types of Australian green bananas (Cavendish "Musa acuminata", Ladyfinger "Musa paradisiaca L.", and Ducasse "Musa balbisiana"), along with their antioxidant capacities, and the production of short-chain fatty acids (SCFAs) following in vitro simulated gastrointestinal digestion and colonic fermentation. The studied cultivars exhibited significant levels of RS, with Ladyfinger showing the greatest (49%). However, Ducasse bananas had the greatest DF concentration (38.73%). Greater TPC levels for Ladyfinger (2.32 mg GAE/g), as well as TFC and TTC (0.06 mg QE/g and 3.2 mg CE/g, respectively) in Cavendish, together with strong antioxidant capacities (DPPH, 0.89 mg TE/g in Cavendish), have been detected after both intestinal phase and colonic fermentation at 12 and 24 h. The bioaccessibility of most phenolic compounds from bananas was high after gastric and small intestinal digestion. Nevertheless, a significant proportion of kaempferol (31% in Cavendish) remained detectable in the residue after colonic fermentation. The greatest production of SCFAs in all banana cultivars was observed after 24 h of fermentation, except valeric acid, which exhibited the greatest output after 12 h of fermentation. In conclusion, the consumption of whole green bananas may have an advantageous effect on bowel health and offer antioxidant characteristics.
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Affiliation(s)
- Yasmeen M. Bashmil
- Department of Food and Nutrition, Faculty of Human Sciences and Design, King Abdulaziz University, Jeddah 21589, Saudi Arabia;
- School of Agriculture, Food and Ecosystem Sciences, Faculty of Science, The University of Melbourne, Parkville, VIC 3010, Australia; (F.R.D.); (R.A.)
| | - Frank R. Dunshea
- School of Agriculture, Food and Ecosystem Sciences, Faculty of Science, The University of Melbourne, Parkville, VIC 3010, Australia; (F.R.D.); (R.A.)
- Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Rudi Appels
- School of Agriculture, Food and Ecosystem Sciences, Faculty of Science, The University of Melbourne, Parkville, VIC 3010, Australia; (F.R.D.); (R.A.)
| | - Hafiz A. R. Suleria
- School of Agriculture, Food and Ecosystem Sciences, Faculty of Science, The University of Melbourne, Parkville, VIC 3010, Australia; (F.R.D.); (R.A.)
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3
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Zare T, Paril JF, Barnett EM, Kaur P, Appels R, Ebert B, Roessner U, Fournier-Level A. Comparative genomics points to tandem duplications of SAD gene clusters as drivers of increased α-linolenic (ω-3) content in S. hispanica seeds. Plant Genome 2024; 17:e20430. [PMID: 38339968 DOI: 10.1002/tpg2.20430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 11/28/2023] [Accepted: 01/02/2024] [Indexed: 02/12/2024]
Abstract
Salvia hispanica L. (chia) is a source of abundant ω-3 polyunsaturated fatty acids (ω-3-PUFAs) that are highly beneficial to human health. The genomic basis for this accrued ω-3-PUFA content in this emerging crop was investigated through the assembly and comparative analysis of a chromosome-level reference genome for S. hispanica. The highly contiguous 321.5-Mbp genome assembly covering all six chromosomes enabled the identification of 32,922 protein-coding genes. Two whole-genome duplications (WGD) events were identified in the S. hispanica lineage. However, these WGD events could not be linked to the high α-linolenic acid (ALA, ω-3) accumulation in S. hispanica seeds based on phylogenomics. Instead, our analysis supports the hypothesis that evolutionary expansion through tandem duplications of specific lipid gene families, particularly the stearoyl-acyl carrier protein desaturase (ShSAD) gene family, is the main driver of the abundance of ω-3-PUFAs in S. hispanica seeds. The insights gained from the genomic analysis of S. hispanica will help establish a molecular breeding target that can be leveraged through genome editing techniques to increase ω-3 content in oil crops.
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Affiliation(s)
- Tannaz Zare
- School of BioSciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Jeff F Paril
- School of BioSciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Emma M Barnett
- School of BioSciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Parwinder Kaur
- School of Agriculture and Environment, The University of Western Australia, Perth, Western Australia, Australia
| | - Rudi Appels
- School of Agriculture, Food and Ecosystem Sciences, University of Melbourne, Parkville, Victoria, Australia
| | - Berit Ebert
- School of Biology and Biotechnology, Ruhr-Universitat Bochum, Bochum, Germany
| | - Ute Roessner
- Research School of Biology, The Australian National University, Canberra, Australian Capital Territory, Australia
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Khan N, Zhang J, Islam S, Appels R, Dell B. Wheat Water-Soluble Carbohydrate Remobilisation under Water Deficit by 1-FEH w3. Curr Issues Mol Biol 2023; 45:6634-6650. [PMID: 37623238 PMCID: PMC10453044 DOI: 10.3390/cimb45080419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 08/03/2023] [Accepted: 08/08/2023] [Indexed: 08/26/2023] Open
Abstract
Fructan 1-exohydrolase (1-FEH) is one of the major enzymes in water-soluble carbohydrate (WSC) remobilisation for grains in wheat. We investigated the functional role of 1-FEH w1, w2, and w3 isoforms in WSC remobilisation under post-anthesis water deficit using mutation lines derived from the Australian wheat variety Chara. F1 seeds, developed by backcrossing the 1-FEH w1, w2, and w3 mutation lines with Chara, were genotyped using the Infinium 90K SNP iSelect platform to characterise the mutated region. Putative deletions were identified in FEH mutation lines encompassing the FEH genomic regions. Mapping analysis demonstrated that mutations affected significantly longer regions than the target FEH gene regions. Functional roles of the non-target genes were carried out utilising bioinformatics and confirmed that the non-target genes were unlikely to confound the effects considered to be due to the influence of 1-FEH gene functions. Glasshouse experiments revealed that the 1-FEH w3 mutation line had a slower degradation and remobilisation of fructans than the 1-FEH w2 and w1 mutation lines and Chara, which reduced grain filling and grain yield. Thus, 1-FEH w3 plays a vital role in reducing yield loss under drought. This insight into the distinct role of the 1-FEH isoforms provides new gene targets for water-deficit-tolerant wheat breeding.
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Affiliation(s)
- Nusrat Khan
- Centre for Crop and Food Innovation, Food Futures Institute, Murdoch University, 90 South Street, Murdoch, WA 6163, Australia; (N.K.); (J.Z.); (S.I.)
- Department of Plant Sciences, North Dakota State University, Fargo, ND 58102, USA
| | - Jingjuan Zhang
- Centre for Crop and Food Innovation, Food Futures Institute, Murdoch University, 90 South Street, Murdoch, WA 6163, Australia; (N.K.); (J.Z.); (S.I.)
| | - Shahidul Islam
- Centre for Crop and Food Innovation, Food Futures Institute, Murdoch University, 90 South Street, Murdoch, WA 6163, Australia; (N.K.); (J.Z.); (S.I.)
- Department of Plant Sciences, North Dakota State University, Fargo, ND 58102, USA
| | - Rudi Appels
- Faculty of Science, University of Melbourne, Parkville, VIC 3010, Australia;
| | - Bernard Dell
- Centre for Crop and Food Innovation, Food Futures Institute, Murdoch University, 90 South Street, Murdoch, WA 6163, Australia; (N.K.); (J.Z.); (S.I.)
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Zhao J, Xie Y, Kong C, Lu Z, Jia H, Ma Z, Zhang Y, Cui D, Ru Z, Wang Y, Appels R, Jia J, Zhang X. Centromere repositioning and shifts in wheat evolution. Plant Commun 2023:100556. [PMID: 36739481 PMCID: PMC10398676 DOI: 10.1016/j.xplc.2023.100556] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 01/07/2023] [Accepted: 02/01/2023] [Indexed: 06/18/2023]
Abstract
The centromere is the region of a chromosome that directs its separation and plays an important role in cell division and reproduction of organisms. Elucidating the dynamics of centromeres is an alternative strategy for exploring the evolution of wheat. Here, we comprehensively analyzed centromeres from the de novo-assembled common wheat cultivar Aikang58 (AK58), Chinese Spring (CS), and all sequenced diploid and tetraploid ancestors by chromatin immunoprecipitation sequencing, whole-genome bisulfite sequencing, RNA sequencing, assay for transposase-accessible chromatin using sequencing, and comparative genomics. We found that centromere-associated sequences were concentrated during tetraploidization and hexaploidization. Centromeric repeats of wheat (CRWs) have undergone expansion during wheat evolution, with strong interweaving between the A and B subgenomes post tetraploidization. We found that CENH3 prefers to bind with younger CRWs, as directly supported by immunocolocalization on two chromosomes (1A and 2A) of wild emmer wheat with dicentromeric regions, only one of which bound with CENH3. In a comparison of AK58 with CS, obvious centromere repositioning was detected on chromosomes 1B, 3D, and 4D. The active centromeres showed a unique combination of lower CG but higher CHH and CHG methylation levels. We also found that centromeric chromatin was more open than pericentromeric chromatin, with higher levels of gene expression but lower gene density. Frequent introgression between tetraploid and hexaploid wheat also had a strong influence on centromere position on the same chromosome. This study also showed that active wheat centromeres were genetically and epigenetically determined.
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Affiliation(s)
- Jing Zhao
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs/Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China; Nanjing Agricultural University, Nanjing 210095, Jiangsu, China
| | - Yilin Xie
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Chuizheng Kong
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs/Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Zefu Lu
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs/Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Haiyan Jia
- Nanjing Agricultural University, Nanjing 210095, Jiangsu, China
| | - Zhengqiang Ma
- Nanjing Agricultural University, Nanjing 210095, Jiangsu, China
| | - Yijing Zhang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Dangqun Cui
- Agronomy College/National Key Laboratory of Wheat and Maize Crop Science/Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou 450046, China
| | - Zhengang Ru
- Henan Institute of Science and Technology, Xinxiang 453003, China
| | - Yuquan Wang
- Henan Institute of Science and Technology, Xinxiang 453003, China
| | - Rudi Appels
- Agriculture Victoria Research, Department of Economic Development, Jobs, Transport and Resources, AgriBio, Bundoora, VIC 3083, Australia
| | - Jizeng Jia
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs/Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China; Agronomy College/National Key Laboratory of Wheat and Maize Crop Science/Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou 450046, China.
| | - Xueyong Zhang
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs/Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China; Nanjing Agricultural University, Nanjing 210095, Jiangsu, China.
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6
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Zou X, Wang X, Li L, Peng P, Ma Q, Hu X, Appels R. Effects of Composition and Strength of Wheat Gluten on Starch Structure, Digestion Properties and the Underlying Mechanism. Foods 2022; 11:foods11213432. [PMID: 36360045 PMCID: PMC9655948 DOI: 10.3390/foods11213432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 10/21/2022] [Accepted: 10/26/2022] [Indexed: 12/01/2022] Open
Abstract
To understand the effect of gluten on starch digestion characteristics, the structural characteristics of protein, starch, and starch digestion attributes were explored by using flours of four wheat near-isogenic lines. Protein and starch fractions from the four flours were used to form so-called recombinant flours where glutenin and gliadin protein fractions, in different ratios, were combined with starch and heated in a water slurry at 80 °C for 5 min. We found that starch digestibility of the recombinant flours could be reproducibly modified by altering the long- and short-range molecular order of starch through varying the attributes of the gluten protein by virtue of the gluten strength as well as the proportions of glutenin and gliadins. The gluten composition changes of strong-gluten flour did not improve the starch digestion resistibility, however, for the moderate- and weak-gluten flours, the proportional increase of glutenin improved the resistance of starch to digestion through the increased long- and short-range molecular order of starch. The resistance of starch to digestion could also be enhanced with increasing gliadin, and was associated with the modified short-range molecular order of starch. We propose that flour mixtures can be optimized for specified product quality by manipulating the amounts of both gliadin and glutenin.
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Affiliation(s)
- Xiaoyang Zou
- College of Food Engineering and Nutritional Science, Shaanxi Normal University, No. 620 West Chang’an Avenue, Chang’an District, Xi’an 710119, China
| | - Xiaolong Wang
- College of Food Engineering and Nutritional Science, Shaanxi Normal University, No. 620 West Chang’an Avenue, Chang’an District, Xi’an 710119, China
- Correspondence: (X.W.); (R.A.)
| | - Liang Li
- Shaanxi Surea Group Co., Ltd., Xi’an 710003, China
| | - Pai Peng
- College of Food Engineering and Nutritional Science, Shaanxi Normal University, No. 620 West Chang’an Avenue, Chang’an District, Xi’an 710119, China
| | - Qianying Ma
- College of Food Engineering and Nutritional Science, Shaanxi Normal University, No. 620 West Chang’an Avenue, Chang’an District, Xi’an 710119, China
| | - Xinzhong Hu
- College of Food Engineering and Nutritional Science, Shaanxi Normal University, No. 620 West Chang’an Avenue, Chang’an District, Xi’an 710119, China
| | - Rudi Appels
- Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, VIC 3010, Australia
- Correspondence: (X.W.); (R.A.)
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7
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Hussain B, Akpınar BA, Alaux M, Algharib AM, Sehgal D, Ali Z, Aradottir GI, Batley J, Bellec A, Bentley AR, Cagirici HB, Cattivelli L, Choulet F, Cockram J, Desiderio F, Devaux P, Dogramaci M, Dorado G, Dreisigacker S, Edwards D, El-Hassouni K, Eversole K, Fahima T, Figueroa M, Gálvez S, Gill KS, Govta L, Gul A, Hensel G, Hernandez P, Crespo-Herrera LA, Ibrahim A, Kilian B, Korzun V, Krugman T, Li Y, Liu S, Mahmoud AF, Morgounov A, Muslu T, Naseer F, Ordon F, Paux E, Perovic D, Reddy GVP, Reif JC, Reynolds M, Roychowdhury R, Rudd J, Sen TZ, Sukumaran S, Ozdemir BS, Tiwari VK, Ullah N, Unver T, Yazar S, Appels R, Budak H. Capturing Wheat Phenotypes at the Genome Level. Front Plant Sci 2022; 13:851079. [PMID: 35860541 PMCID: PMC9289626 DOI: 10.3389/fpls.2022.851079] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/09/2022] [Accepted: 05/19/2022] [Indexed: 06/15/2023]
Abstract
Recent technological advances in next-generation sequencing (NGS) technologies have dramatically reduced the cost of DNA sequencing, allowing species with large and complex genomes to be sequenced. Although bread wheat (Triticum aestivum L.) is one of the world's most important food crops, efficient exploitation of molecular marker-assisted breeding approaches has lagged behind that achieved in other crop species, due to its large polyploid genome. However, an international public-private effort spanning 9 years reported over 65% draft genome of bread wheat in 2014, and finally, after more than a decade culminated in the release of a gold-standard, fully annotated reference wheat-genome assembly in 2018. Shortly thereafter, in 2020, the genome of assemblies of additional 15 global wheat accessions was released. As a result, wheat has now entered into the pan-genomic era, where basic resources can be efficiently exploited. Wheat genotyping with a few hundred markers has been replaced by genotyping arrays, capable of characterizing hundreds of wheat lines, using thousands of markers, providing fast, relatively inexpensive, and reliable data for exploitation in wheat breeding. These advances have opened up new opportunities for marker-assisted selection (MAS) and genomic selection (GS) in wheat. Herein, we review the advances and perspectives in wheat genetics and genomics, with a focus on key traits, including grain yield, yield-related traits, end-use quality, and resistance to biotic and abiotic stresses. We also focus on reported candidate genes cloned and linked to traits of interest. Furthermore, we report on the improvement in the aforementioned quantitative traits, through the use of (i) clustered regularly interspaced short-palindromic repeats/CRISPR-associated protein 9 (CRISPR/Cas9)-mediated gene-editing and (ii) positional cloning methods, and of genomic selection. Finally, we examine the utilization of genomics for the next-generation wheat breeding, providing a practical example of using in silico bioinformatics tools that are based on the wheat reference-genome sequence.
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Affiliation(s)
- Babar Hussain
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
- Department of Biotechnology, Faculty of Life Sciences, University of Central Punjab, Lahore, Pakistan
| | | | - Michael Alaux
- Université Paris-Saclay, INRAE, URGI, Versailles, France
| | - Ahmed M. Algharib
- Department of Environment and Bio-Agriculture, Faculty of Agriculture, Al-Azhar University, Cairo, Egypt
| | - Deepmala Sehgal
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
| | - Zulfiqar Ali
- Institute of Plant Breeding and Biotechnology, MNS University of Agriculture, Multan, Pakistan
| | - Gudbjorg I. Aradottir
- Department of Pathology, The National Institute of Agricultural Botany, Cambridge, United Kingdom
| | - Jacqueline Batley
- School of Biological Sciences and Institute of Agriculture, University of Western Australia, Perth, WA, Australia
| | - Arnaud Bellec
- French Plant Genomic Resource Center, INRAE-CNRGV, Castanet Tolosan, France
| | - Alison R. Bentley
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
| | - Halise B. Cagirici
- Crop Improvement and Genetics Research, USDA, Agricultural Research Service, Albany, CA, United States
| | - Luigi Cattivelli
- Council for Agricultural Research and Economics-Research Centre for Genomics and Bioinformatics, Fiorenzuola d’Arda, Italy
| | - Fred Choulet
- French National Research Institute for Agriculture, Food and the Environment, INRAE, GDEC, Clermont-Ferrand, France
| | - James Cockram
- The John Bingham Laboratory, The National Institute of Agricultural Botany, Cambridge, United Kingdom
| | - Francesca Desiderio
- Council for Agricultural Research and Economics-Research Centre for Genomics and Bioinformatics, Fiorenzuola d’Arda, Italy
| | - Pierre Devaux
- Research & Innovation, Florimond Desprez Group, Cappelle-en-Pévèle, France
| | - Munevver Dogramaci
- USDA, Agricultural Research Service, Edward T. Schafer Agricultural Research Center, Fargo, ND, United States
| | - Gabriel Dorado
- Department of Bioquímica y Biología Molecular, Campus Rabanales C6-1-E17, Campus de Excelencia Internacional Agroalimentario (ceiA3), Universidad de Córdoba, Córdoba, Spain
| | | | - David Edwards
- University of Western Australia, Perth, WA, Australia
| | - Khaoula El-Hassouni
- State Plant Breeding Institute, The University of Hohenheim, Stuttgart, Germany
| | - Kellye Eversole
- International Wheat Genome Sequencing Consortium (IWGSC), Bethesda, MD, United States
| | - Tzion Fahima
- Institute of Evolution and Department of Environmental and Evolutionary Biology, University of Haifa, Haifa, Israel
| | - Melania Figueroa
- Commonwealth Scientific and Industrial Research Organization, Agriculture and Food, Canberra, ACT, Australia
| | - Sergio Gálvez
- Department of Languages and Computer Science, ETSI Informática, Campus de Teatinos, Universidad de Málaga, Andalucía Tech, Málaga, Spain
| | - Kulvinder S. Gill
- Department of Crop Science, Washington State University, Pullman, WA, United States
| | - Liubov Govta
- Institute of Evolution and Department of Environmental and Evolutionary Biology, University of Haifa, Haifa, Israel
| | - Alvina Gul
- Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
| | - Goetz Hensel
- Center of Plant Genome Engineering, Heinrich-Heine-Universität, Düsseldorf, Germany
- Division of Molecular Biology, Centre of Region Haná for Biotechnological and Agriculture Research, Czech Advanced Technology and Research Institute, Palacký University, Olomouc, Czechia
| | - Pilar Hernandez
- Institute for Sustainable Agriculture (IAS-CSIC), Consejo Superior de Investigaciones Científicas (CSIC), Córdoba, Spain
| | | | - Amir Ibrahim
- Crop and Soil Science, Texas A&M University, College Station, TX, United States
| | | | | | - Tamar Krugman
- Institute of Evolution and Department of Environmental and Evolutionary Biology, University of Haifa, Haifa, Israel
| | - Yinghui Li
- Institute of Evolution and Department of Environmental and Evolutionary Biology, University of Haifa, Haifa, Israel
| | - Shuyu Liu
- Crop and Soil Science, Texas A&M University, College Station, TX, United States
| | - Amer F. Mahmoud
- Department of Plant Pathology, Faculty of Agriculture, Assiut University, Assiut, Egypt
| | - Alexey Morgounov
- Food and Agriculture Organization of the United Nations, Riyadh, Saudi Arabia
| | - Tugdem Muslu
- Molecular Biology, Genetics and Bioengineering, Sabanci University, Istanbul, Turkey
| | - Faiza Naseer
- Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
| | - Frank Ordon
- Institute for Resistance Research and Stress Tolerance, Julius Kühn Institute, Quedlinburg, Germany
| | - Etienne Paux
- French National Research Institute for Agriculture, Food and the Environment, INRAE, GDEC, Clermont-Ferrand, France
| | - Dragan Perovic
- Institute for Resistance Research and Stress Tolerance, Julius Kühn Institute, Quedlinburg, Germany
| | - Gadi V. P. Reddy
- USDA-Agricultural Research Service, Southern Insect Management Research Unit, Stoneville, MS, United States
| | - Jochen Christoph Reif
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Matthew Reynolds
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
| | - Rajib Roychowdhury
- Institute of Evolution and Department of Environmental and Evolutionary Biology, University of Haifa, Haifa, Israel
| | - Jackie Rudd
- Crop and Soil Science, Texas A&M University, College Station, TX, United States
| | - Taner Z. Sen
- Crop Improvement and Genetics Research, USDA, Agricultural Research Service, Albany, CA, United States
| | | | | | | | - Naimat Ullah
- Institute of Biological Sciences (IBS), Gomal University, D. I. Khan, Pakistan
| | - Turgay Unver
- Ficus Biotechnology, Ostim Teknopark, Ankara, Turkey
| | - Selami Yazar
- General Directorate of Research, Ministry of Agriculture, Ankara, Turkey
| | | | - Hikmet Budak
- Montana BioAgriculture, Inc., Missoula, MT, United States
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8
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Beasley JT, Bonneau JP, Moreno-Moyano LT, Callahan DL, Howell KS, Tako E, Taylor J, Glahn RP, Appels R, Johnson AAT. Multi-year field evaluation of nicotianamine biofortified bread wheat. Plant J 2022; 109:1168-1182. [PMID: 34902177 DOI: 10.1111/tpj.15623] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 11/27/2021] [Indexed: 06/14/2023]
Abstract
Conventional breeding efforts for iron (Fe) and zinc (Zn) biofortification of bread wheat (Triticum aestivum L.) have been hindered by a lack of genetic variation for these traits and a negative correlation between grain Fe and Zn concentrations and yield. We have employed genetic engineering to constitutively express (CE) the rice (Oryza sativa) nicotianamine synthase 2 (OsNAS2) gene and upregulate biosynthesis of two metal chelators - nicotianamine (NA) and 2'-deoxymugineic acid (DMA) - in bread wheat, resulting in increased Fe and Zn concentrations in wholemeal and white flour. Here we describe multi-location confined field trial (CFT) evaluation of a low-copy transgenic CE-OsNAS2 wheat event (CE-1) over 3 years and demonstrate higher concentrations of NA, DMA, Fe, and Zn in CE-1 wholemeal flour, white flour, and white bread and higher Fe bioavailability in CE-1 white flour relative to a null segregant (NS) control. Multi-environment models of agronomic and grain nutrition traits revealed a negative correlation between grain yield and grain Fe, Zn, and total protein concentrations, yet no correlation between grain yield and grain NA and DMA concentrations. White flour Fe bioavailability was positively correlated with white flour NA concentration, suggesting that NA-chelated Fe should be targeted in wheat Fe biofortification efforts.
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Affiliation(s)
- Jesse T Beasley
- School of BioSciences, The University of Melbourne, Melbourne, Victoria, 3010, Australia
| | - Julien P Bonneau
- School of BioSciences, The University of Melbourne, Melbourne, Victoria, 3010, Australia
| | - Laura T Moreno-Moyano
- School of BioSciences, The University of Melbourne, Melbourne, Victoria, 3010, Australia
| | - Damien L Callahan
- School of Life and Environmental Sciences, Deakin University, Melbourne, Victoria, 3125, Australia
| | - Kate S Howell
- School of Agriculture and Food, The University of Melbourne, Melbourne, Victoria, 3010, Australia
| | - Elad Tako
- Department of Food Science, Cornell University, Stocking Hall, Ithaca, NY, 14853-7201, USA
| | - Julian Taylor
- School of Agriculture, Food and Wine, University of Adelaide, Glen Osmond, South Australia, 5064, Australia
| | - Raymond P Glahn
- Robert W. Holley Center for Agriculture and Health, USDA-ARS, Ithaca, NY, 14853, USA
| | - Rudi Appels
- School of Agriculture and Food, The University of Melbourne, Melbourne, Victoria, 3010, Australia
| | - Alexander A T Johnson
- School of BioSciences, The University of Melbourne, Melbourne, Victoria, 3010, Australia
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9
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Appels R, Wang P, Islam S. Integrating Wheat Nucleolus Structure and Function: Variation in the Wheat Ribosomal RNA and Protein Genes. Front Plant Sci 2021; 12:686586. [PMID: 35003148 PMCID: PMC8739226 DOI: 10.3389/fpls.2021.686586] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Accepted: 11/08/2021] [Indexed: 06/13/2023]
Abstract
We review the coordinated production and integration of the RNA (ribosomal RNA, rRNA) and protein (ribosomal protein, RP) components of wheat cytoplasmic ribosomes in response to changes in genetic constitution, biotic and abiotic stresses. The components examined are highly conserved and identified with reference to model systems such as human, Arabidopsis, and rice, but have sufficient levels of differences in their DNA and amino acid sequences to form fingerprints or gene haplotypes that provide new markers to associate with phenotype variation. Specifically, it is argued that populations of ribosomes within a cell can comprise distinct complements of rRNA and RPs to form units with unique functionalities. The unique functionalities of ribosome populations within a cell can become central in situations of stress where they may preferentially translate mRNAs coding for proteins better suited to contributing to survival of the cell. In model systems where this concept has been developed, the engagement of initiation factors and elongation factors to account for variation in the translation machinery of the cell in response to stresses provided the precedents. The polyploid nature of wheat adds extra variation at each step of the synthesis and assembly of the rRNAs and RPs which can, as a result, potentially enhance its response to changing environments and disease threats.
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Affiliation(s)
- Rudi Appels
- AgriBio, Centre for AgriBioscience, La Trobe University, Bundoora, VIC, Australia
- Faculty of Veterinary and Agricultural Science, Melbourne, VIC, Australia
| | - Penghao Wang
- School of Veterinary and Life Sciences, Murdoch University, Murdoch, WA, Australia
| | - Shahidul Islam
- Centre for Crop Innovation, Food Futures Institute, Murdoch University, Murdoch, WA, Australia
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10
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Abstract
Background Lessons learned and experiences gained ask for enhancing the response even during a crisis. We present the application of the in-action review (IAR) of Dutch ports and airports, based on methods developed by the World Health Organization (WHO) and the European Centre for Disease Control (ECDC). Methods We performed two separate IARs among Dutch airports (5/5) and ports (15/16) respectively. 1) A questionnaire among participants was used to decide upon most urgent matters to discuss during a 4-hour online meeting. 2) a 4-hour, interactive, online meeting was held among local representatives of points of entry, regional public health professionals, safety professionals, the national institute of public health and the ministry of health. Best practices, lessons, barriers and actions on different topics were first prepared in small groups, and discussed and finalized in plenary sessions. Follow-up of actions was performed during the consecutive 6 weeks at the moment of writing. A questionnaire among participants evaluated satisfaction and impact of the IAR among participants. Results Main items for the online meetings were the implementation of measures, and regional and supra-regional collaboration. Most urgent actions formulated were a better integration of local needs into national policy making, and enhancing contacts among different points of entry. Implemented actions include the integration of local public health authorities involved at airports into an existing meeting structure at the national level; and an inter-port meeting structure that was developed leading to 3-weekly meetings to discuss upcoming challenges and exchange practices and advice. Conclusions This is to our best knowledge the first time that an in-action review has been performed specifically for the point of entry setting. Performing IARs, online with operational partners led to quick wins and a better network during the COVID-19 pandemic.
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Affiliation(s)
- D de Rooij
- National Coordination Center for Infectious Disease Response, RIVM, Bilthoven, Netherlands
- Athena Institute, Free University, Amsterdam, Netherlands
| | - M van de Watering
- National Coordination Center for Infectious Disease Response, RIVM, Bilthoven, Netherlands
| | - R van Dijk
- National Coordination Center for Infectious Disease Response, RIVM, Bilthoven, Netherlands
| | - R Appels
- National Coordination Center for Infectious Disease Response, RIVM, Bilthoven, Netherlands
| | - T Veenstra
- National Coordination Center for Infectious Disease Response, RIVM, Bilthoven, Netherlands
| | - C Swaan
- National Coordination Center for Infectious Disease Response, RIVM, Bilthoven, Netherlands
| | - A Timen
- National Coordination Center for Infectious Disease Response, RIVM, Bilthoven, Netherlands
- Athena Institute, Free University, Amsterdam, Netherlands
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11
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Wang X, Peng P, Appels R, Tian L, Zou X. Macromolecular networks interactions in wheat flour dough matrices during sequential thermal-mechanical treatment. Food Chem 2021; 366:130543. [PMID: 34284193 DOI: 10.1016/j.foodchem.2021.130543] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 07/02/2021] [Accepted: 07/04/2021] [Indexed: 11/04/2022]
Abstract
Differences in Mixolab measurements of dough processing were examined using, as a base, flour from pure breeding, isogenic, wheat lines carrying either the high molecular weight glutenin subunits 5 + 10 or 2 + 12. Before dough pasting, subunits 5 + 10 tend to form a stable gluten network relying mainly on disulfide bonds and hydrogen bonds, but 2 + 12 flour was prone to generating fragile protein aggregates dominated by disulfide bonds and hydrophobicity. During dough pasting, a broader protein network rich in un-extractable polymeric proteins, disulfide bonds and β-sheets was formed in the dough with subunits 5 + 10, thus resulting in an extensive and compact protein-starch complex which was characterized by high thermal stability and low starch gelatinization, while in the dough of the 2 + 12 line, a porous protein-starch gel with fragmented protein aggregates was controlled by the combination of disulfide bonds, hydrophobicity and hydrogen bonds that facilitated the formation of antiparallel β-sheets.
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Affiliation(s)
- Xiaolong Wang
- College of Food Engineering and Nutritional Science, Shaanxi Normal University, Xi'an 710162, Shaanxi, China.
| | - Pai Peng
- College of Food Engineering and Nutritional Science, Shaanxi Normal University, Xi'an 710162, Shaanxi, China
| | - Rudi Appels
- School of Agriculture and Food, University of Melbourne, Parkville 3010, Australia
| | - Linpei Tian
- College of Food Engineering and Nutritional Science, Shaanxi Normal University, Xi'an 710162, Shaanxi, China
| | - Xiaoyang Zou
- College of Food Engineering and Nutritional Science, Shaanxi Normal University, Xi'an 710162, Shaanxi, China
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12
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Zhu T, Wang L, Rimbert H, Rodriguez JC, Deal KR, De Oliveira R, Choulet F, Keeble‐Gagnère G, Tibbits J, Rogers J, Eversole K, Appels R, Gu YQ, Mascher M, Dvorak J, Luo M. Optical maps refine the bread wheat Triticum aestivum cv. Chinese Spring genome assembly. Plant J 2021; 107:303-314. [PMID: 33893684 PMCID: PMC8360199 DOI: 10.1111/tpj.15289] [Citation(s) in RCA: 174] [Impact Index Per Article: 58.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 04/12/2021] [Accepted: 04/19/2021] [Indexed: 05/09/2023]
Abstract
Until recently, achieving a reference-quality genome sequence for bread wheat was long thought beyond the limits of genome sequencing and assembly technology, primarily due to the large genome size and > 80% repetitive sequence content. The release of the chromosome scale 14.5-Gb IWGSC RefSeq v1.0 genome sequence of bread wheat cv. Chinese Spring (CS) was, therefore, a milestone. Here, we used a direct label and stain (DLS) optical map of the CS genome together with a prior nick, label, repair and stain (NLRS) optical map, and sequence contigs assembled with Pacific Biosciences long reads, to refine the v1.0 assembly. Inconsistencies between the sequence and maps were reconciled and gaps were closed. Gap filling and anchoring of 279 unplaced scaffolds increased the total length of pseudomolecules by 168 Mb (excluding Ns). Positions and orientations were corrected for 233 and 354 scaffolds, respectively, representing 10% of the genome sequence. The accuracy of the remaining 90% of the assembly was validated. As a result of the increased contiguity, the numbers of transposable elements (TEs) and intact TEs have increased in IWGSC RefSeq v2.1 compared with v1.0. In total, 98% of the gene models identified in v1.0 were mapped onto this new assembly through development of a dedicated approach implemented in the MAGAAT pipeline. The numbers of high-confidence genes on pseudomolecules have increased from 105 319 to 105 534. The reconciled assembly enhances the utility of the sequence for genetic mapping, comparative genomics, gene annotation and isolation, and more general studies on the biology of wheat.
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Affiliation(s)
- Tingting Zhu
- Department of Plant SciencesUniversity of CaliforniaDavisCA95616USA
| | - Le Wang
- Department of Plant SciencesUniversity of CaliforniaDavisCA95616USA
| | - Hélène Rimbert
- GDECUniversité Clermont AuvergneINRAEClermont‐Ferrand63000France
| | | | - Karin R. Deal
- Department of Plant SciencesUniversity of CaliforniaDavisCA95616USA
| | | | - Frédéric Choulet
- GDECUniversité Clermont AuvergneINRAEClermont‐Ferrand63000France
| | | | - Josquin Tibbits
- Centre for AgriBioscienceAgriculture VictoriaAgriBioBundooraVIC3083Australia
| | - Jane Rogers
- International Wheat Genome Sequencing ConsortiumEau ClaireWI54701USA
| | - Kellye Eversole
- International Wheat Genome Sequencing ConsortiumEau ClaireWI54701USA
| | - Rudi Appels
- Centre for AgriBioscienceAgriculture VictoriaAgriBioBundooraVIC3083Australia
- International Wheat Genome Sequencing ConsortiumEau ClaireWI54701USA
| | - Yong Q. Gu
- Crop Improvement and Genetics Research UnitUSDA‐ARSAlbanyCA94710USA
| | - Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)SeelandGermany
| | - Jan Dvorak
- Department of Plant SciencesUniversity of CaliforniaDavisCA95616USA
| | - Ming‐Cheng Luo
- Department of Plant SciencesUniversity of CaliforniaDavisCA95616USA
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13
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Hao C, Jiao C, Hou J, Li T, Liu H, Wang Y, Zheng J, Liu H, Bi Z, Xu F, Zhao J, Ma L, Wang Y, Majeed U, Liu X, Appels R, Maccaferri M, Tuberosa R, Lu H, Zhang X. Resequencing of 145 Landmark Cultivars Reveals Asymmetric Sub-genome Selection and Strong Founder Genotype Effects on Wheat Breeding in China. Mol Plant 2020; 13:1733-1751. [PMID: 32896642 DOI: 10.1016/j.molp.2020.09.001] [Citation(s) in RCA: 97] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 08/19/2020] [Accepted: 09/02/2020] [Indexed: 05/18/2023]
Abstract
Controlled pedigrees and the multi-decade timescale of national crop plant breeding programs offer a unique experimental context for examining how selection affects plant genomes. More than 3000 wheat cultivars have been registered, released, and documented since 1949 in China. In this study, a set of 145 elite cultivars selected from historical points of wheat breeding in China were re-sequenced. A total of 43.75 Tb of sequence data were generated with an average read depth of 17.94× for each cultivar, and more than 60.92 million SNPs and 2.54 million InDels were captured, based on the Chinese Spring RefSeq genome v1.0. Seventy years of breeder-driven selection led to dramatic changes in grain yield and related phenotypes, with distinct genomic regions and phenotypes targeted by different breeders across the decades. There are very clear instances illustrating how introduced Italian and other foreign germplasm was integrated into Chinese wheat programs and reshaped the genomic landscape of local modern cultivars. Importantly, the resequencing data also highlighted significant asymmetric breeding selection among the three sub-genomes: this was evident in both the collinear blocks for homeologous chromosomes and among sets of three homeologous genes. Accumulation of more newly assembled genes in newer cultivars implied the potential value of these genes in breeding. Conserved and extended sharing of linkage disequilibrium (LD) blocks was highlighted among pedigree-related cultivars, in which fewer haplotype differences were detected. Fixation or replacement of haplotypes from founder genotypes after generations of breeding was related to their breeding value. Based on the haplotype frequency changes in LD blocks of pedigree-related cultivars, we propose a strategy for evaluating the breeding value of any given line on the basis of the accumulation (pyramiding) of beneficial haplotypes. Collectively, our study demonstrates the influence of "founder genotypes" on the output of breeding efforts over many decades and also suggests that founder genotype perspectives are in fact more dynamic when applied in the context of modern genomics-informed breeding.
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Affiliation(s)
- Chenyang Hao
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs/The National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Chengzhi Jiao
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs/The National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; Novogene Bioinformatics Institute, Beijing 100083, China
| | - Jian Hou
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs/The National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Tian Li
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs/The National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Hongxia Liu
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs/The National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yuquan Wang
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs/The National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jun Zheng
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs/The National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Hong Liu
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs/The National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Zhihong Bi
- Novogene Bioinformatics Institute, Beijing 100083, China
| | - Fengfeng Xu
- Novogene Bioinformatics Institute, Beijing 100083, China
| | - Jing Zhao
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs/The National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Lin Ma
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs/The National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yamei Wang
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs/The National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Uzma Majeed
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs/The National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xu Liu
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs/The National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Rudi Appels
- AgriBio, Centre for AgriBioscience, Department of Economic Development, Jobs, Transport, and Resources, 5 Ring Road, La Trobe University, Bundoora, VIC 3083, Australia
| | - Marco Maccaferri
- Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy
| | - Roberto Tuberosa
- Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy
| | - Hongfeng Lu
- Novogene Bioinformatics Institute, Beijing 100083, China.
| | - Xueyong Zhang
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs/The National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
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14
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Iqbal MM, Hurgobin B, Holme AL, Appels R, Kaur P. Status and Potential of Single‐Cell Transcriptomics for Understanding Plant Development and Functional Biology. Cytometry A 2020; 97:997-1006. [DOI: 10.1002/cyto.a.24196] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 07/08/2020] [Accepted: 07/23/2020] [Indexed: 12/20/2022]
Affiliation(s)
- Muhammad Munir Iqbal
- UWA School of Agriculture and Environment, Faculty of Science The University of Western Australia 35 Stirling Hwy Perth WA 6009 Australia
- Genome Innovation Hub Telethon Kids Institute, Perth Children Hospital Nedlands WA 6009 Australia
| | - Bhavna Hurgobin
- School of Life Sciences, La Trobe University Bundoora Victoria 3086 Australia
| | - Andrea Lisa Holme
- Iain Fraser Cytometry Centre, IFCC Institute of Medical Sciences (IMS), School of Medicine, Medical Sciences and Nutrition University of Aberdeen Forester Hill Aberdeen AB25 2ZD UK
| | - Rudi Appels
- School of BioSciences, The University of Melbourne Victoria 3010 Australia
- School of Applied Biology, La Trobe University Bundoora Victoria 3086 Australia
| | - Parwinder Kaur
- UWA School of Agriculture and Environment, Faculty of Science The University of Western Australia 35 Stirling Hwy Perth WA 6009 Australia
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15
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Winters M, Arneborg N, Appels R, Howell K. Can community-based signalling behaviour in Saccharomyces cerevisiae be called quorum sensing? A critical review of the literature. FEMS Yeast Res 2020; 19:5528315. [PMID: 31271429 DOI: 10.1093/femsyr/foz046] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 07/02/2019] [Indexed: 12/15/2022] Open
Abstract
Quorum sensing is a well-described mechanism of intercellular signalling among bacteria, which involves cell-density-dependent chemical signal molecules. The concentration of these quorum-sensing molecules increases in proportion to cell density until a threshold value is exceeded, which triggers a community-wide response. In this review, we propose that intercellular signalling mechanisms can be associated with a corresponding ecological interaction type based on similarities between how the interaction affects the signal receiver and producer. Thus, we do not confine quorum sensing, a specific form of intercellular signalling, to only cooperative behaviours. Instead, we define it as cell-density-dependent responses that occur at a critical concentration of signal molecules and through a specific signalling pathway. For fungal species, the medically important yeast Candida albicans has a well-described quorum sensing system, while this system is not well described in Saccharomyces cerevisiae, which is involved in food and beverage fermentations. The more precise definition for quorum sensing proposed in this review is based on the studies suggesting that S. cerevisiae may undergo intercellular signalling through quorum sensing. Through this lens, we conclude that there is a lack of evidence to support a specific signalling mechanism and a critical signal concentration of these behaviours in S. cerevisiae, and, thus, these features require further investigation.
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Affiliation(s)
- Michela Winters
- School of Agriculture and Food, Faculty of Veterinary and Agricultural Science, University of Melbourne, Parkville 3010, Australia
| | - Nils Arneborg
- Department of Food Science, University of Copenhagen, Frederiksberg 1958, Denmark
| | - Rudi Appels
- School of Agriculture and Food, Faculty of Veterinary and Agricultural Science, University of Melbourne, Parkville 3010, Australia
| | - Kate Howell
- School of Agriculture and Food, Faculty of Veterinary and Agricultural Science, University of Melbourne, Parkville 3010, Australia
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16
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Guan J, Garcia DF, Zhou Y, Appels R, Li A, Mao L. The Battle to Sequence the Bread Wheat Genome: A Tale of the Three Kingdoms. Genomics Proteomics Bioinformatics 2020; 18:221-229. [PMID: 32561470 PMCID: PMC7801200 DOI: 10.1016/j.gpb.2019.09.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 08/15/2019] [Accepted: 10/23/2019] [Indexed: 02/06/2023]
Abstract
In the year 2018, the world witnessed the finale of the race to sequence the genome of the world's most widely grown crop, the common wheat. Wheat has been known to bear a notoriously large and complicated genome of a polyploidy nature. A decade competition to sequence the wheat genome initiated with a single consortium of multiple countries, taking a conventional strategy similar to that for sequencing Arabidopsis and rice, became ferocious over time as both sequencing technologies and genome assembling methodologies advanced. At different stages, multiple versions of genome sequences of the same variety (e.g., Chinese Spring) were produced by several groups with their special strategies. Finally, 16 years after the rice genome was finished and 9 years after that of maize, the wheat research community now possesses its own reference genome. Armed with these genomics tools, wheat will reestablish itself as a model for polyploid plants in studying the mechanisms of polyploidy evolution, domestication, genetic and epigenetic regulation of homoeolog expression, as well as defining its genetic diversity and breeding on the genome level. The enhanced resolution of the wheat genome should also help accelerate development of wheat cultivars that are more tolerant to biotic and/or abiotic stresses with better quality and higher yield.
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Affiliation(s)
- Jiantao Guan
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Diego F Garcia
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yun Zhou
- Collaborative Innovation Center of Crop Stress Biology & Institute of Plant Stress Biology, School of Life Science, Henan University, Kaifeng 475004, China
| | - Rudi Appels
- AgriBio, Centre for AgriBioscience, Department of Economic Development, Jobs, Transport, and Resources, La Trobe University, Melbourne, VIC 3083, Australia
| | - Aili Li
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Long Mao
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
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17
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Feng K, Cui L, Wang L, Shan D, Tong W, Deng P, Yan Z, Wang M, Zhan H, Wu X, He W, Zhou X, Ji J, Zhang G, Mao L, Karafiátová M, Šimková H, Doležel J, Du X, Zhao S, Luo M, Han D, Zhang C, Kang Z, Appels R, Edwards D, Nie X, Weining S. The improved assembly of 7DL chromosome provides insight into the structure and evolution of bread wheat. Plant Biotechnol J 2020; 18:732-742. [PMID: 31471988 PMCID: PMC7004910 DOI: 10.1111/pbi.13240] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Revised: 07/27/2019] [Accepted: 08/15/2019] [Indexed: 05/03/2023]
Abstract
Wheat is one of the most important staple crops worldwide and also an excellent model species for crop evolution and polyploidization studies. The breakthrough of sequencing the bread wheat genome and progenitor genomes lays the foundation to decipher the complexity of wheat origin and evolutionary process as well as the genetic consequences of polyploidization. In this study, we sequenced 3286 BACs from chromosome 7DL of bread wheat cv. Chinese Spring and integrated the unmapped contigs from IWGSC v1 and available PacBio sequences to close gaps present in the 7DL assembly. In total, 8043 out of 12 825 gaps, representing 3 491 264 bp, were closed. We then used the improved assembly of 7DL to perform comparative genomic analysis of bread wheat (Ta7DL) and its D donor, Aegilops tauschii (At7DL), to identify domestication signatures. Results showed a strong syntenic relationship between Ta7DL and At7DL, although some small rearrangements were detected at the distal regions. A total of 53 genes appear to be lost genes during wheat polyploidization, with 23% (12 genes) as RGA (disease resistance gene analogue). Furthermore, 86 positively selected genes (PSGs) were identified, considered to be domestication-related candidates. Finally, overlapping of QTLs obtained from GWAS analysis and PSGs indicated that TraesCS7D02G321000 may be one of the domestication genes involved in grain morphology. This study provides comparative information on the sequence, structure and organization between bread wheat and Ae. tauschii from the perspective of the 7DL chromosome, which contribute to better understanding of the evolution of wheat, and supports wheat crop improvement.
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Affiliation(s)
- Kewei Feng
- State Key Laboratory of Crop Stress Biology in Arid AreasCollege of Agronomy and Yangling Branch of China Wheat Improvement CenterNorthwest A&F UniversityYanglingShaanxiChina
| | - Licao Cui
- State Key Laboratory of Crop Stress Biology in Arid AreasCollege of Agronomy and Yangling Branch of China Wheat Improvement CenterNorthwest A&F UniversityYanglingShaanxiChina
- College of Bioscience and EngineeringJiangxi Agricultural UniversityNanchangJiangxiChina
| | - Le Wang
- Department of Plant SciencesUniversity of CaliforniaDavisCAUSA
| | - Dai Shan
- BGI GenomicsBGI‐ShenzhenShenzhenChina
| | - Wei Tong
- State Key Laboratory of Crop Stress Biology in Arid AreasCollege of Agronomy and Yangling Branch of China Wheat Improvement CenterNorthwest A&F UniversityYanglingShaanxiChina
| | - Pingchuan Deng
- State Key Laboratory of Crop Stress Biology in Arid AreasCollege of Agronomy and Yangling Branch of China Wheat Improvement CenterNorthwest A&F UniversityYanglingShaanxiChina
| | - Zhaogui Yan
- College of Horticulture and Forestry Sciences/Hubei Engineering Technology Research Center for Forestry InformationHuazhong Agricultural UniversityWuhanChina
| | - Mengxing Wang
- State Key Laboratory of Crop Stress Biology in Arid AreasCollege of Agronomy and Yangling Branch of China Wheat Improvement CenterNorthwest A&F UniversityYanglingShaanxiChina
| | - Haoshuang Zhan
- State Key Laboratory of Crop Stress Biology in Arid AreasCollege of Agronomy and Yangling Branch of China Wheat Improvement CenterNorthwest A&F UniversityYanglingShaanxiChina
| | - Xiaotong Wu
- State Key Laboratory of Crop Stress Biology in Arid AreasCollege of Agronomy and Yangling Branch of China Wheat Improvement CenterNorthwest A&F UniversityYanglingShaanxiChina
| | | | | | | | | | - Long Mao
- Key Laboratory of Crop Gene Resources and Germplasm EnhancementMinistry of AgricultureThe National Key Facility for Crop Gene Resources and Genetic ImprovementInstitute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Miroslava Karafiátová
- Centre of the Region Haná for Biotechnological and Agricultural ResearchInstitute of Experimental BotanyOlomoucCzech Republic
| | - Hana Šimková
- Centre of the Region Haná for Biotechnological and Agricultural ResearchInstitute of Experimental BotanyOlomoucCzech Republic
| | - Jaroslav Doležel
- Centre of the Region Haná for Biotechnological and Agricultural ResearchInstitute of Experimental BotanyOlomoucCzech Republic
| | - Xianghong Du
- State Key Laboratory of Crop Stress Biology in Arid AreasCollege of Agronomy and Yangling Branch of China Wheat Improvement CenterNorthwest A&F UniversityYanglingShaanxiChina
| | - Shancen Zhao
- BGI Institute of Applied AgricultureBGI‐ShenzhenShenzhenChina
| | - Ming‐Cheng Luo
- Department of Plant SciencesUniversity of CaliforniaDavisCAUSA
| | - Dejun Han
- State Key Laboratory of Crop Stress Biology in Arid AreasCollege of Agronomy and Yangling Branch of China Wheat Improvement CenterNorthwest A&F UniversityYanglingShaanxiChina
| | - Chi Zhang
- BGI GenomicsBGI‐ShenzhenShenzhenChina
| | - Zhensheng Kang
- State Key Laboratory of Crop Stress Biology for Arid AreasCollege of Plant ProtectionNorthwest A&F UniversityYanglingShaanxiChina
| | - Rudi Appels
- State Agriculture Biotechnology CentreSchool of Veterinary and Life SciencesAustralia Export Grains Innovation CentreMurdoch UniversityPerthWAAustralia
| | - David Edwards
- School of Biological Sciences and Institute of AgricultureThe University of Western AustraliaPerthWAAustralia
| | - Xiaojun Nie
- State Key Laboratory of Crop Stress Biology in Arid AreasCollege of Agronomy and Yangling Branch of China Wheat Improvement CenterNorthwest A&F UniversityYanglingShaanxiChina
| | - Song Weining
- State Key Laboratory of Crop Stress Biology in Arid AreasCollege of Agronomy and Yangling Branch of China Wheat Improvement CenterNorthwest A&F UniversityYanglingShaanxiChina
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18
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Wang X, Appels R, Zhang X, Bekes F, Diepeveen D, Ma W, Hu X, Islam S. Solubility variation of wheat dough proteins: A practical way to track protein behaviors in dough processing. Food Chem 2019; 312:126038. [PMID: 31896458 DOI: 10.1016/j.foodchem.2019.126038] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Revised: 11/05/2019] [Accepted: 12/06/2019] [Indexed: 01/22/2023]
Abstract
To understand wheat dough protein behavior under dual mixing and thermal treatment, solubility of Mixolab-dough proteins were investigated using nine extraction buffers of different dissociation capacities. Size exclusion high performance liquid chromatography (SE-HPLC) and two-dimensional gel electrophoresis (2-DGE) demonstrated that overall changes of protein fractions and dynamic responses of specific proteins during dough processing were well reflected by their solubility variations. After starch pasting, the abundance of 0.5 M NaCl extractable proteins were decreased except for six protein groups including α-amylase inhibitors and superoxide dismutase (SOD). The solubility loss of glutenin proteins at C3 (32 min; 80 ℃) was mainly ascribed to the un-extractable HMW-GSs, LMW-GSs, globulin and triticin, while the extract yield of α-, β-, γ-gliadins and avenin-like proteins (ALPs) increased after starch pasting. Differential responses of dough proteins to extraction systems provides the basis for further exploring wheat protein dynamics in processing.
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Affiliation(s)
- Xiaolong Wang
- College of Food Engineering and Nutritional Science, Shaanxi Normal University, Xi'an 710119, China; Australia China Centre for Wheat Improvement, College of Science Health Engineering and Education, Murdoch University, 90, South Street, Murdoch, WA 6150, Australia
| | - Rudi Appels
- School of Bio Sciences, University of Melbourne, Parkville, VIC 3010, Australia.
| | - Xiaoke Zhang
- College of Agronomy, Northwest A & F University, Yangling, Shaanxi 712100, China
| | | | - Dean Diepeveen
- Australia China Centre for Wheat Improvement, College of Science Health Engineering and Education, Murdoch University, 90, South Street, Murdoch, WA 6150, Australia; Department of Primary Industries and Regional Development, Western Australia, 3 Baron-Hay Court, South Perth, WA 6151, Australia
| | - Wujun Ma
- Australia China Centre for Wheat Improvement, College of Science Health Engineering and Education, Murdoch University, 90, South Street, Murdoch, WA 6150, Australia
| | - Xinzhong Hu
- College of Food Engineering and Nutritional Science, Shaanxi Normal University, Xi'an 710119, China
| | - Shahidul Islam
- Australia China Centre for Wheat Improvement, College of Science Health Engineering and Education, Murdoch University, 90, South Street, Murdoch, WA 6150, Australia.
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19
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Voss-Fels KP, Keeble-Gagnère G, Hickey LT, Tibbits J, Nagornyy S, Hayden MJ, Pasam RK, Kant S, Friedt W, Snowdon RJ, Appels R, Wittkop B. High-resolution mapping of rachis nodes per rachis, a critical determinant of grain yield components in wheat. Theor Appl Genet 2019; 132:2707-2719. [PMID: 31254025 DOI: 10.1007/s00122-019-03383-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Accepted: 06/16/2019] [Indexed: 05/23/2023]
Abstract
Exploring large genomic data sets based on the latest reference genome assembly identifies the rice ortholog APO1 as a key candidate gene for number of rachis nodes per spike in wheat. Increasing grain yield in wheat is a key breeding objective worldwide. Several component traits contribute to grain yield with spike attributes being among the most important. In this study, we performed a genome-wide association analysis for 12 grain yield and component traits measured in field trials with contrasting agrochemical input levels in a panel of 220 hexaploid winter wheats. A highly significant, environmentally consistent QTL was detected for number of rachis nodes per rachis (NRN) on chromosome 7AL. The five most significant SNPs formed a strong linkage disequilibrium (LD) block and tagged a 2.23 Mb region. Using pairwise LD for exome SNPs located across this interval in a large worldwide hexaploid wheat collection, we reduced the genomic region for NRN to a 258 Kb interval containing four of the original SNP and six high-confidence genes. The ortholog of one (TraesCS7A01G481600) of these genes in rice was ABBERANT PANICLE ORGANIZATION1 (APO1), which is known to have significant effects on panicle attributes. The APO1 ortholog was the best candidate for NRN and was associated with a 115 bp promoter deletion and two amino acid (C47F and D384 N) changes. Using a large worldwide collection of tetraploid and hexaploid wheat, we found 12 haplotypes for the NRN QTL and evidence for positive enrichment of two haplotypes in modern germplasm. Comparison of five QTL haplotypes in Australian yield trials revealed their relative, context-dependent contribution to grain yield. Our study provides diagnostic SNPs and value propositions to support deployment of the NRN trait in wheat breeding.
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Affiliation(s)
- Kai P Voss-Fels
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, 4072, Australia
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Heinrich-Buff-Ring 26-32, 35392, Giessen, Germany
| | - Gabriel Keeble-Gagnère
- Agriculture Victoria Research, Department of Job, Precincts and Regions (DJPR), AgriBio, Centre for AgriBioscience, Bundoora, VIC, 3083, Australia
| | - Lee T Hickey
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - Josquin Tibbits
- Agriculture Victoria Research, Department of Job, Precincts and Regions (DJPR), AgriBio, Centre for AgriBioscience, Bundoora, VIC, 3083, Australia
| | - Sergej Nagornyy
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Heinrich-Buff-Ring 26-32, 35392, Giessen, Germany
| | - Matthew J Hayden
- Agriculture Victoria Research, Department of Job, Precincts and Regions (DJPR), AgriBio, Centre for AgriBioscience, Bundoora, VIC, 3083, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, Australia
| | - Raj K Pasam
- Agriculture Victoria Research, Department of Job, Precincts and Regions (DJPR), AgriBio, Centre for AgriBioscience, Bundoora, VIC, 3083, Australia
| | - Surya Kant
- Agriculture Victoria Research, Department of Job, Precincts and Regions (DJPR), AgriBio, Centre for AgriBioscience, Bundoora, VIC, 3083, Australia
| | - Wolfgang Friedt
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Heinrich-Buff-Ring 26-32, 35392, Giessen, Germany
| | - Rod J Snowdon
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Heinrich-Buff-Ring 26-32, 35392, Giessen, Germany
| | - Rudi Appels
- Agriculture Victoria Research, Department of Job, Precincts and Regions (DJPR), AgriBio, Centre for AgriBioscience, Bundoora, VIC, 3083, Australia.
| | - Benjamin Wittkop
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Heinrich-Buff-Ring 26-32, 35392, Giessen, Germany.
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20
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Cheng H, Liu J, Wen J, Nie X, Xu L, Chen N, Li Z, Wang Q, Zheng Z, Li M, Cui L, Liu Z, Bian J, Wang Z, Xu S, Yang Q, Appels R, Han D, Song W, Sun Q, Jiang Y. Frequent intra- and inter-species introgression shapes the landscape of genetic variation in bread wheat. Genome Biol 2019; 20:136. [PMID: 31300020 PMCID: PMC6624984 DOI: 10.1186/s13059-019-1744-x] [Citation(s) in RCA: 100] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Accepted: 06/22/2019] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND Bread wheat is one of the most important and broadly studied crops. However, due to the complexity of its genome and incomplete genome collection of wild populations, the bread wheat genome landscape and domestication history remain elusive. RESULTS By investigating the whole-genome resequencing data of 93 accessions from worldwide populations of bread wheat and its diploid and tetraploid progenitors, together with 90 published exome-capture data, we find that the B subgenome has more variations than A and D subgenomes, including SNPs and deletions. Population genetics analyses support a monophyletic origin of domesticated wheat from wild emmer in northern Levant, with substantial introgressed genomic fragments from southern Levant. Southern Levant contributes more than 676 Mb in AB subgenomes and enriched in the pericentromeric regions. The AB subgenome introgression happens at the early stage of wheat speciation and partially contributes to their greater genetic diversity. Furthermore, we detect massive alien introgressions that originated from distant species through natural and artificial hybridizations, resulting in the reintroduction of ~ 709 Mb and ~ 1577 Mb sequences into bread wheat landraces and varieties, respectively. A large fraction of these intra- and inter-introgression fragments are associated with quantitative trait loci of important traits, and selection events are also identified. CONCLUSION We reveal the significance of multiple introgressions from distant wild populations and alien species in shaping the genetic components of bread wheat, and provide important resources and new perspectives for future wheat breeding.
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Affiliation(s)
- Hong Cheng
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100 China
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100 China
| | - Jing Liu
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100 China
- Department of Molecular Evolution and Development, University of Vienna, Vienna, Austria
| | - Jia Wen
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100 China
| | - Xiaojun Nie
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100 China
| | - Luohao Xu
- Department of Molecular Evolution and Development, University of Vienna, Vienna, Austria
| | - Ningbo Chen
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100 China
| | - Zhongxing Li
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, 712100 China
| | - Qilin Wang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100 China
| | - Zhuqing Zheng
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100 China
| | - Ming Li
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100 China
| | - Licao Cui
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100 China
| | - Zihua Liu
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100 China
| | - Jianxin Bian
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100 China
| | - Zhonghua Wang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100 China
| | - Shengbao Xu
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100 China
| | - Qin Yang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100 China
| | - Rudi Appels
- AgriBio, Centre for AgriBioscience, Department of Economic Development, Jobs, Transport, and Resources, La Trobe University, 5 Ring Road, Bundoora, VIC 3083 Australia
| | - Dejun Han
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100 China
| | - Weining Song
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100 China
| | - Qixin Sun
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100 China
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193 China
| | - Yu Jiang
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100 China
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21
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Ryan MH, Kaur P, Nazeri NK, Clode PL, Keeble-Gagnère G, Doolette AL, Smernik RJ, Van Aken O, Nicol D, Maruyama H, Ezawa T, Lambers H, Millar AH, Appels R. Globular structures in roots accumulate phosphorus to extremely high concentrations following phosphorus addition. Plant Cell Environ 2019; 42:1987-2002. [PMID: 30734927 DOI: 10.1111/pce.13531] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2018] [Revised: 02/04/2019] [Accepted: 02/05/2019] [Indexed: 06/09/2023]
Abstract
Crops with improved uptake of fertilizer phosphorus (P) would reduce P losses and confer environmental benefits. We examined how P-sufficient 6-week-old soil-grown Trifolium subterraneum plants, and 2-week-old seedlings in solution culture, accumulated P in roots after inorganic P (Pi) addition. In contrast to our expectation that vacuoles would accumulate excess P, after 7 days, X-ray microanalysis showed that vacuolar [P] remained low (<12 mmol kg-1 ). However, in the plants after P addition, some cortex cells contained globular structures extraordinarily rich in P (often >3,000 mmol kg-1 ), potassium, magnesium, and sodium. Similar structures were evident in seedlings, both before and after P addition, with their [P] increasing threefold after P addition. Nuclear magnetic resonance (NMR) spectroscopy showed seedling roots accumulated Pi following P addition, and transmission electron microscopy (TEM) revealed large plastids. For seedlings, we demonstrated that roots differentially expressed genes after P addition using RNAseq mapped to the T. subterraneum reference genome assembly and transcriptome profiles. Among the most up-regulated genes after 4 hr was TSub_g9430.t1, which is similar to plastid envelope Pi transporters (PHT4;1, PHT4;4): expression of vacuolar Pi-transporter homologs did not change. We suggest that subcellular P accumulation in globular structures, which may include plastids, aids cytosolic Pi homeostasis under high-P availability.
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Affiliation(s)
- Megan H Ryan
- UWA School of Agriculture and Environment and Institute of Agriculture, The University of Western Australia, Crawley, Australia
| | - Parwinder Kaur
- UWA School of Agriculture and Environment and Institute of Agriculture, The University of Western Australia, Crawley, Australia
- Centre for Plant Genetics and Breeding and Institute of Agriculture, The University of Western Australia, Crawley, Australia
| | - Nazanin K Nazeri
- UWA School of Agriculture and Environment and Institute of Agriculture, The University of Western Australia, Crawley, Australia
| | - Peta L Clode
- Centre for Microscopy, Characterisation and Analysis and UWA School of Biological Sciences, The University of Western Australia, Crawley, Australia
| | - Gabriel Keeble-Gagnère
- Agriculture Victoria Research, Department of Jobs, Precincts and Regions, AgriBio, Bundoora, Australia
| | - Ashlea L Doolette
- School of Agriculture, Food and Wine and Waite Research Institute, The University of Adelaide, Waite Campus, Urrbrae, Australia
| | - Ronald J Smernik
- School of Agriculture, Food and Wine and Waite Research Institute, The University of Adelaide, Waite Campus, Urrbrae, Australia
| | - Olivier Van Aken
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Crawley, Australia
- Department of Biology, Lund University, Lund, Sweden
| | - Dion Nicol
- UWA School of Agriculture and Environment and Institute of Agriculture, The University of Western Australia, Crawley, Australia
- Department of Primary Industries and Regional Development, Western Australia, Dryland Research Institute, Merredin, Australia
| | - Hayato Maruyama
- Graduate School of Agriculture, Hokkaido University, Sapporo, Japan
| | - Tatsuhiro Ezawa
- Graduate School of Agriculture, Hokkaido University, Sapporo, Japan
| | - Hans Lambers
- UWA School of Biological Sciences and Institute of Agriculture, The University of Western Australia, Crawley, Australia
| | - A Harvey Millar
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Crawley, Australia
| | - Rudi Appels
- Agriculture Victoria Research, Department of Jobs, Precincts and Regions, AgriBio, Bundoora, Australia
- University of Melbourne, Bioscience, Parkville, Australia
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22
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Gálvez S, Mérida-García R, Camino C, Borrill P, Abrouk M, Ramírez-González RH, Biyiklioglu S, Amil-Ruiz F, Dorado G, Budak H, Gonzalez-Dugo V, Zarco-Tejada PJ, Appels R, Uauy C, Hernandez P. Hotspots in the genomic architecture of field drought responses in wheat as breeding targets. Funct Integr Genomics 2018; 19:295-309. [PMID: 30446876 PMCID: PMC6394720 DOI: 10.1007/s10142-018-0639-3] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Accepted: 10/01/2018] [Indexed: 12/21/2022]
Abstract
Wheat can adapt to most agricultural conditions across temperate regions. This success is the result of phenotypic plasticity conferred by a large and complex genome composed of three homoeologous genomes (A, B, and D). Although drought is a major cause of yield and quality loss in wheat, the adaptive mechanisms and gene networks underlying drought responses in the field remain largely unknown. Here, we addressed this by utilizing an interdisciplinary approach involving field water status phenotyping, sampling, and gene expression analyses. Overall, changes at the transcriptional level were reflected in plant spectral traits amenable to field-level physiological measurements, although changes in photosynthesis-related pathways were found likely to be under more complex post-transcriptional control. Examining homoeologous genes with a 1:1:1 relationship across the A, B, and D genomes (triads), we revealed a complex genomic architecture for drought responses under field conditions, involving gene homoeolog specialization, multiple gene clusters, gene families, miRNAs, and transcription factors coordinating these responses. Our results provide a new focus for genomics-assisted breeding of drought-tolerant wheat cultivars.
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Affiliation(s)
- Sergio Gálvez
- Departamento de Lenguajes y Ciencias de la Computación, ETSI Informática, Campus de Teatinos, Universidad de Málaga, 29071, Málaga, Spain.
| | - Rosa Mérida-García
- Instituto de Agricultura Sostenible (IAS), Consejo Superior de Investigaciones Científicas (CSIC), Alameda del Obispo s/n, 14004, Córdoba, Spain
| | - Carlos Camino
- Instituto de Agricultura Sostenible (IAS), Consejo Superior de Investigaciones Científicas (CSIC), Alameda del Obispo s/n, 14004, Córdoba, Spain
| | | | - Michael Abrouk
- Institute of Experimental Botany, Centre of Plant Structural and Functional Genomics, CZ-78371, Olomouc, Czech Republic
- Biological and Environmental Science & Engineering Division, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | | | - Sezgi Biyiklioglu
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT, 59717-3150, USA
| | - Francisco Amil-Ruiz
- Bioinformatics Unit, SCAI, Campus Rabanales, University of Córdoba, 14014, Córdoba, Spain
| | - Gabriel Dorado
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario (ceiA3), Universidad de Córdoba, Campus Rabanales C6-1-E17, 14071, Córdoba, Spain
| | - Hikmet Budak
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT, 59717-3150, USA
| | - Victoria Gonzalez-Dugo
- Instituto de Agricultura Sostenible (IAS), Consejo Superior de Investigaciones Científicas (CSIC), Alameda del Obispo s/n, 14004, Córdoba, Spain
| | - Pablo J Zarco-Tejada
- Instituto de Agricultura Sostenible (IAS), Consejo Superior de Investigaciones Científicas (CSIC), Alameda del Obispo s/n, 14004, Córdoba, Spain.
| | - Rudi Appels
- Veterinary and Agricultural Sciences, University of Melbourne, Gratten St, Parkville, Victoria, 3010, Australia
- Department of Economic Development, AgriBio, Centre for AgriBioscience, Jobs, Transport and Resources, La Trobe University, 5 Ring Rd, Bundoora, Victoria, 3083, Australia
| | - Cristobal Uauy
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK.
| | - Pilar Hernandez
- Instituto de Agricultura Sostenible (IAS), Consejo Superior de Investigaciones Científicas (CSIC), Alameda del Obispo s/n, 14004, Córdoba, Spain.
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23
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Rey E, Abrouk M, Keeble‐Gagnère G, Karafiátová M, Vrána J, Balzergue S, Soubigou‐Taconnat L, Brunaud V, Martin‐Magniette M, Endo TR, Bartoš J, Appels R, Doležel J. Transcriptome reprogramming due to the introduction of a barley telosome into bread wheat affects more barley genes than wheat. Plant Biotechnol J 2018; 16:1767-1777. [PMID: 29510004 PMCID: PMC6131412 DOI: 10.1111/pbi.12913] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Revised: 02/17/2018] [Accepted: 02/24/2018] [Indexed: 05/03/2023]
Abstract
Despite a long history, the production of useful alien introgression lines in wheat remains difficult mainly due to linkage drag and incomplete genetic compensation. In addition, little is known about the molecular mechanisms underlying the impact of foreign chromatin on plant phenotype. Here, a comparison of the transcriptomes of barley, wheat and a wheat-barley 7HL addition line allowed the transcriptional impact both on 7HL genes of a non-native genetic background and on the wheat gene complement as a result of the presence of 7HL to be assessed. Some 42% (389/923) of the 7HL genes assayed were differentially transcribed, which was the case for only 3% (960/35 301) of the wheat gene complement. The absence of any transcript in the addition line of a suite of chromosome 7A genes implied the presence of a 36 Mbp deletion at the distal end of the 7AL arm; this deletion was found to be in common across the full set of Chinese Spring/Betzes barley addition lines. The remaining differentially transcribed wheat genes were distributed across the whole genome. The up-regulated barley genes were mostly located in the proximal part of the 7HL arm, while the down-regulated ones were concentrated in the distal part; as a result, genes encoding basal cellular functions tended to be transcribed, while those encoding specific functions were suppressed. An insight has been gained into gene transcription in an alien introgression line, thereby providing a basis for understanding the interactions between wheat and exotic genes in introgression materials.
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Affiliation(s)
- Elodie Rey
- Institute of Experimental BotanyCentre of the Region Haná for Biotechnological and Agricultural ResearchOlomoucCzech Republic
| | - Michael Abrouk
- Institute of Experimental BotanyCentre of the Region Haná for Biotechnological and Agricultural ResearchOlomoucCzech Republic
| | - Gabriel Keeble‐Gagnère
- Agriculture Research VictoriaDepartment of Economic DevelopmentJobsTransport and ResourcesAgriBioBundooraVIC 3083Australia
| | - Miroslava Karafiátová
- Institute of Experimental BotanyCentre of the Region Haná for Biotechnological and Agricultural ResearchOlomoucCzech Republic
| | - Jan Vrána
- Institute of Experimental BotanyCentre of the Region Haná for Biotechnological and Agricultural ResearchOlomoucCzech Republic
| | - Sandrine Balzergue
- Institute of Plant Sciences Paris Saclay IPS2CNRSINRAUniversité Paris‐SudUniversité EvryUniversité Paris‐SaclayOrsayFrance
- Institute of Plant Sciences Paris‐Saclay IPS2Paris DiderotSorbonne Paris‐CitéOrsayFrance
- IRHSUniversité d'AngersINRAAGROCAMPUS‐OuestSFR4207 QUASAVUniversité Bretagne LoireBeaucouzéFrance
| | - Ludivine Soubigou‐Taconnat
- Institute of Plant Sciences Paris Saclay IPS2CNRSINRAUniversité Paris‐SudUniversité EvryUniversité Paris‐SaclayOrsayFrance
- Institute of Plant Sciences Paris‐Saclay IPS2Paris DiderotSorbonne Paris‐CitéOrsayFrance
| | - Véronique Brunaud
- Institute of Plant Sciences Paris Saclay IPS2CNRSINRAUniversité Paris‐SudUniversité EvryUniversité Paris‐SaclayOrsayFrance
- Institute of Plant Sciences Paris‐Saclay IPS2Paris DiderotSorbonne Paris‐CitéOrsayFrance
| | - Marie‐Laure Martin‐Magniette
- Institute of Plant Sciences Paris Saclay IPS2CNRSINRAUniversité Paris‐SudUniversité EvryUniversité Paris‐SaclayOrsayFrance
- Institute of Plant Sciences Paris‐Saclay IPS2Paris DiderotSorbonne Paris‐CitéOrsayFrance
- UMR MIA‐ParisAgroParisTechINRAUniversité Paris‐SaclayParisFrance
| | - Takashi R. Endo
- Department of Plant Life ScienceFaculty of AgricultureRyukoku UniversityShigaJapan
| | - Jan Bartoš
- Institute of Experimental BotanyCentre of the Region Haná for Biotechnological and Agricultural ResearchOlomoucCzech Republic
| | | | | | - Jaroslav Doležel
- Institute of Experimental BotanyCentre of the Region Haná for Biotechnological and Agricultural ResearchOlomoucCzech Republic
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24
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Keeble-Gagnère G, Rigault P, Tibbits J, Pasam R, Hayden M, Forrest K, Frenkel Z, Korol A, Huang BE, Cavanagh C, Taylor J, Abrouk M, Sharpe A, Konkin D, Sourdille P, Darrier B, Choulet F, Bernard A, Rochfort S, Dimech A, Watson-Haigh N, Baumann U, Eckermann P, Fleury D, Juhasz A, Boisvert S, Nolin MA, Doležel J, Šimková H, Toegelová H, Šafář J, Luo MC, Câmara F, Pfeifer M, Isdale D, Nyström-Persson J, IWGSC, Koo DH, Tinning M, Cui D, Ru Z, Appels R. Optical and physical mapping with local finishing enables megabase-scale resolution of agronomically important regions in the wheat genome. Genome Biol 2018; 19:112. [PMID: 30115128 PMCID: PMC6097218 DOI: 10.1186/s13059-018-1475-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2018] [Accepted: 07/09/2018] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND Numerous scaffold-level sequences for wheat are now being released and, in this context, we report on a strategy for improving the overall assembly to a level comparable to that of the human genome. RESULTS Using chromosome 7A of wheat as a model, sequence-finished megabase-scale sections of this chromosome were established by combining a new independent assembly using a bacterial artificial chromosome (BAC)-based physical map, BAC pool paired-end sequencing, chromosome-arm-specific mate-pair sequencing and Bionano optical mapping with the International Wheat Genome Sequencing Consortium RefSeq v1.0 sequence and its underlying raw data. The combined assembly results in 18 super-scaffolds across the chromosome. The value of finished genome regions is demonstrated for two approximately 2.5 Mb regions associated with yield and the grain quality phenotype of fructan carbohydrate grain levels. In addition, the 50 Mb centromere region analysis incorporates cytological data highlighting the importance of non-sequence data in the assembly of this complex genome region. CONCLUSIONS Sufficient genome sequence information is shown to now be available for the wheat community to produce sequence-finished releases of each chromosome of the reference genome. The high-level completion identified that an array of seven fructosyl transferase genes underpins grain quality and that yield attributes are affected by five F-box-only-protein-ubiquitin ligase domain and four root-specific lipid transfer domain genes. The completed sequence also includes the centromere.
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Affiliation(s)
- Gabriel Keeble-Gagnère
- Agriculture Victoria Research, Department of Economic Development, Jobs, Transport and Resources, AgriBio, Bundoora, VIC 3083 Australia
| | - Philippe Rigault
- GYDLE, 1135 Grande Allée Ouest, Suite 220, Québec, QC G1S 1E7 Canada
- Center for Organismal Studies (COS), University of Heidelberg, Im Neuenheimer Feld 345, 69120 Heidelberg, Germany
| | - Josquin Tibbits
- Agriculture Victoria Research, Department of Economic Development, Jobs, Transport and Resources, AgriBio, Bundoora, VIC 3083 Australia
| | - Raj Pasam
- Agriculture Victoria Research, Department of Economic Development, Jobs, Transport and Resources, AgriBio, Bundoora, VIC 3083 Australia
| | - Matthew Hayden
- Agriculture Victoria Research, Department of Economic Development, Jobs, Transport and Resources, AgriBio, Bundoora, VIC 3083 Australia
| | - Kerrie Forrest
- Agriculture Victoria Research, Department of Economic Development, Jobs, Transport and Resources, AgriBio, Bundoora, VIC 3083 Australia
| | - Zeev Frenkel
- Institute of Evolution, University of Haifa, Haifa, Israel
| | - Abraham Korol
- Institute of Evolution, University of Haifa, Haifa, Israel
| | - B. Emma Huang
- CSIRO-Plant Industry, Black Mountain, Canberra, ACT 2601 Australia
| | - Colin Cavanagh
- CSIRO-Plant Industry, Black Mountain, Canberra, ACT 2601 Australia
| | - Jen Taylor
- CSIRO-Plant Industry, Black Mountain, Canberra, ACT 2601 Australia
| | - Michael Abrouk
- King Abdullah University of Science and Technology, Desert Agriculture Initiative, Thuwal, Saudi Arabia
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Slechtitelu 31, CZ-78371 Olomouc, Czech Republic
| | - Andrew Sharpe
- Global Institute of Food Security, University of Saskatchewan, 110 Gymnasium Place, Saskatoon, SK Canada
| | - David Konkin
- National Research Council of Canada, University of Saskatchewan, 110 Gymnasium Place, Saskatoon, SK Canada
| | - Pierre Sourdille
- INRA UMR1095 Genetics, Diversity and Ecophysiology of Cereals, 5 chemin de Beaulieu, 63039 Clermont-Ferrand, France
| | - Benoît Darrier
- INRA UMR1095 Genetics, Diversity and Ecophysiology of Cereals, 5 chemin de Beaulieu, 63039 Clermont-Ferrand, France
| | - Frédéric Choulet
- INRA UMR1095 Genetics, Diversity and Ecophysiology of Cereals, 5 chemin de Beaulieu, 63039 Clermont-Ferrand, France
| | - Aurélien Bernard
- INRA UMR1095 Genetics, Diversity and Ecophysiology of Cereals, 5 chemin de Beaulieu, 63039 Clermont-Ferrand, France
| | - Simone Rochfort
- Agriculture Victoria Research, Department of Economic Development, Jobs, Transport and Resources, AgriBio, Bundoora, VIC 3083 Australia
| | - Adam Dimech
- Agriculture Victoria Research, Department of Economic Development, Jobs, Transport and Resources, AgriBio, Bundoora, VIC 3083 Australia
| | - Nathan Watson-Haigh
- School of Agriculture, Food and Wine, University of Adelaide, Urrbrae, South Australia 5064 Australia
| | - Ute Baumann
- School of Agriculture, Food and Wine, University of Adelaide, Urrbrae, South Australia 5064 Australia
| | - Paul Eckermann
- School of Agriculture, Food and Wine, University of Adelaide, Urrbrae, South Australia 5064 Australia
| | - Delphine Fleury
- School of Agriculture, Food and Wine, University of Adelaide, Urrbrae, South Australia 5064 Australia
| | - Angela Juhasz
- Veterinary and Agriculture, Murdoch University, 90 South St, Murdoch, Western Australia 6150 Australia
| | | | | | - Jaroslav Doležel
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Slechtitelu 31, CZ-78371 Olomouc, Czech Republic
| | - Hana Šimková
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Slechtitelu 31, CZ-78371 Olomouc, Czech Republic
| | - Helena Toegelová
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Slechtitelu 31, CZ-78371 Olomouc, Czech Republic
| | - Jan Šafář
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Slechtitelu 31, CZ-78371 Olomouc, Czech Republic
| | - Ming-Cheng Luo
- UC Davis Plant Sciences, Plant Genetics and Bioinformatics, 258A Hunt Hall, Davis, CA 95616 USA
| | - Francisco Câmara
- Bioinformatics and Genomics Program, Centre for Genomic Regulation (CRG) and Universitat Pompeu Fabra (UPF), 88 Dr. Aiguader, 08003 Barcelona, Spain
| | - Matthias Pfeifer
- Plant Genome and Systems Biology, Helmholtz Center, Munich, 85764 Neuherberg, Germany
| | - Don Isdale
- Agriculture Victoria Research, Department of Economic Development, Jobs, Transport and Resources, AgriBio, Bundoora, VIC 3083 Australia
| | - Johan Nyström-Persson
- Level Five Co. Ltd. GYB Akihabara, Kanda-Sudacho 2-25, Chiyoda-ku, Tokyo, 101-0041 Japan
| | - IWGSC
- International Wheat Genome Sequencing Consortium, 2841 NE Marywood Ct, Lee’s Summit, MO 64086 USA
| | - Dal-Hoe Koo
- Wheat Genetics Resource Center and Department of Plant Pathology, Kansas State University, Manhattan, KS 66506 USA
| | - Matthew Tinning
- Australian Genome Research Facility, Suite 219, 55 Flemington Road, North Melbourne, VIC 3051 Australia
| | - Dangqun Cui
- Henan Agricultural University, Zhengzhou, China
| | - Zhengang Ru
- Henan Institute of Science and Technology, Zhengzhou, China
| | - Rudi Appels
- Agriculture Victoria Research, Department of Economic Development, Jobs, Transport and Resources, AgriBio, Bundoora, VIC 3083 Australia
- Veterinary and Agriculture, Murdoch University, 90 South St, Murdoch, Western Australia 6150 Australia
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25
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Ramírez-González RH, Borrill P, Lang D, Harrington SA, Brinton J, Venturini L, Davey M, Jacobs J, van Ex F, Pasha A, Khedikar Y, Robinson SJ, Cory AT, Florio T, Concia L, Juery C, Schoonbeek H, Steuernagel B, Xiang D, Ridout CJ, Chalhoub B, Mayer KFX, Benhamed M, Latrasse D, Bendahmane A, Wulff BBH, Appels R, Tiwari V, Datla R, Choulet F, Pozniak CJ, Provart NJ, Sharpe AG, Paux E, Spannagl M, Bräutigam A, Uauy C. The transcriptional landscape of polyploid wheat. Science 2018; 361:eaar6089. [PMID: 30115782 DOI: 10.1126/science.aar6089] [Citation(s) in RCA: 497] [Impact Index Per Article: 82.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Accepted: 07/11/2018] [Indexed: 12/14/2022]
Abstract
The coordinated expression of highly related homoeologous genes in polyploid species underlies the phenotypes of many of the world's major crops. Here we combine extensive gene expression datasets to produce a comprehensive, genome-wide analysis of homoeolog expression patterns in hexaploid bread wheat. Bias in homoeolog expression varies between tissues, with ~30% of wheat homoeologs showing nonbalanced expression. We found expression asymmetries along wheat chromosomes, with homoeologs showing the largest inter-tissue, inter-cultivar, and coding sequence variation, most often located in high-recombination distal ends of chromosomes. These transcriptionally dynamic genes potentially represent the first steps toward neo- or subfunctionalization of wheat homoeologs. Coexpression networks reveal extensive coordination of homoeologs throughout development and, alongside a detailed expression atlas, provide a framework to target candidate genes underpinning agronomic traits in wheat.
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26
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Appels R, Eversole K, Feuillet C, Keller B, Rogers J, Stein N, Pozniak CJ, Stein N, Choulet F, Distelfeld A, Eversole K, Poland J, Rogers J, Ronen G, Sharpe AG, Pozniak C, Ronen G, Stein N, Barad O, Baruch K, Choulet F, Keeble-Gagnère G, Mascher M, Sharpe AG, Ben-Zvi G, Josselin AA, Stein N, Mascher M, Himmelbach A, Choulet F, Keeble-Gagnère G, Mascher M, Rogers J, Balfourier F, Gutierrez-Gonzalez J, Hayden M, Josselin AA, Koh C, Muehlbauer G, Pasam RK, Paux E, Pozniak CJ, Rigault P, Sharpe AG, Tibbits J, Tiwari V, Choulet F, Keeble-Gagnère G, Mascher M, Josselin AA, Rogers J, Spannagl M, Choulet F, Lang D, Gundlach H, Haberer G, Keeble-Gagnère G, Mayer KFX, Ormanbekova D, Paux E, Prade V, Šimková H, Wicker T, Choulet F, Spannagl M, Swarbreck D, Rimbert H, Felder M, Guilhot N, Gundlach H, Haberer G, Kaithakottil G, Keilwagen J, Lang D, Leroy P, Lux T, Mayer KFX, Twardziok S, Venturini L, Appels R, Rimbert H, Choulet F, Juhász A, Keeble-Gagnère G, Choulet F, Spannagl M, Lang D, Abrouk M, Haberer G, Keeble-Gagnère G, Mayer KFX, Wicker T, Choulet F, Wicker T, Gundlach H, Lang D, Spannagl M, Lang D, Spannagl M, Appels R, Fischer I, Uauy C, Borrill P, Ramirez-Gonzalez RH, Appels R, Arnaud D, Chalabi S, Chalhoub B, Choulet F, Cory A, Datla R, Davey MW, Hayden M, Jacobs J, Lang D, Robinson SJ, Spannagl M, Steuernagel B, Tibbits J, Tiwari V, van Ex F, Wulff BBH, Pozniak CJ, Robinson SJ, Sharpe AG, Cory A, Benhamed M, Paux E, Bendahmane A, Concia L, Latrasse D, Rogers J, Jacobs J, Alaux M, Appels R, Bartoš J, Bellec A, Berges H, Doležel J, Feuillet C, Frenkel Z, Gill B, Korol A, Letellier T, Olsen OA, Šimková H, Singh K, Valárik M, van der Vossen E, Vautrin S, Weining S, Korol A, Frenkel Z, Fahima T, Glikson V, Raats D, Rogers J, Tiwari V, Gill B, Paux E, Poland J, Doležel J, Číhalíková J, Šimková H, Toegelová H, Vrána J, Sourdille P, Darrier B, Appels R, Spannagl M, Lang D, Fischer I, Ormanbekova D, Prade V, Barabaschi D, Cattivelli L, Hernandez P, Galvez S, Budak H, Steuernagel B, Jones JDG, Witek K, Wulff BBH, Yu G, Small I, Melonek J, Zhou R, Juhász A, Belova T, Appels R, Olsen OA, Kanyuka K, King R, Nilsen K, Walkowiak S, Pozniak CJ, Cuthbert R, Datla R, Knox R, Wiebe K, Xiang D, Rohde A, Golds T, Doležel J, Čížková J, Tibbits J, Budak H, Akpinar BA, Biyiklioglu S, Muehlbauer G, Poland J, Gao L, Gutierrez-Gonzalez J, N'Daiye A, Doležel J, Šimková H, Číhalíková J, Kubaláková M, Šafář J, Vrána J, Berges H, Bellec A, Vautrin S, Alaux M, Alfama F, Adam-Blondon AF, Flores R, Guerche C, Letellier T, Loaec M, Quesneville H, Pozniak CJ, Sharpe AG, Walkowiak S, Budak H, Condie J, Ens J, Koh C, Maclachlan R, Tan Y, Wicker T, Choulet F, Paux E, Alberti A, Aury JM, Balfourier F, Barbe V, Couloux A, Cruaud C, Labadie K, Mangenot S, Wincker P, Gill B, Kaur G, Luo M, Sehgal S, Singh K, Chhuneja P, Gupta OP, Jindal S, Kaur P, Malik P, Sharma P, Yadav B, Singh NK, Khurana J, Chaudhary C, Khurana P, Kumar V, Mahato A, Mathur S, Sevanthi A, Sharma N, Tomar RS, Rogers J, Jacobs J, Alaux M, Bellec A, Berges H, Doležel J, Feuillet C, Frenkel Z, Gill B, Korol A, van der Vossen E, Vautrin S, Gill B, Kaur G, Luo M, Sehgal S, Bartoš J, Holušová K, Plíhal O, Clark MD, Heavens D, Kettleborough G, Wright J, Valárik M, Abrouk M, Balcárková B, Holušová K, Hu Y, Luo M, Salina E, Ravin N, Skryabin K, Beletsky A, Kadnikov V, Mardanov A, Nesterov M, Rakitin A, Sergeeva E, Handa H, Kanamori H, Katagiri S, Kobayashi F, Nasuda S, Tanaka T, Wu J, Appels R, Hayden M, Keeble-Gagnère G, Rigault P, Tibbits J, Olsen OA, Belova T, Cattonaro F, Jiumeng M, Kugler K, Mayer KFX, Pfeifer M, Sandve S, Xun X, Zhan B, Šimková H, Abrouk M, Batley J, Bayer PE, Edwards D, Hayashi S, Toegelová H, Tulpová Z, Visendi P, Weining S, Cui L, Du X, Feng K, Nie X, Tong W, Wang L, Borrill P, Gundlach H, Galvez S, Kaithakottil G, Lang D, Lux T, Mascher M, Ormanbekova D, Prade V, Ramirez-Gonzalez RH, Spannagl M, Stein N, Uauy C, Venturini L, Stein N, Appels R, Eversole K, Rogers J, Borrill P, Cattivelli L, Choulet F, Hernandez P, Kanyuka K, Lang D, Mascher M, Nilsen K, Paux E, Pozniak CJ, Ramirez-Gonzalez RH, Šimková H, Small I, Spannagl M, Swarbreck D, Uauy C. Shifting the limits in wheat research and breeding using a fully annotated reference genome. Science 2018; 361:361/6403/eaar7191. [PMID: 30115783 DOI: 10.1126/science.aar7191] [Citation(s) in RCA: 1459] [Impact Index Per Article: 243.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Accepted: 07/11/2018] [Indexed: 12/14/2022]
Abstract
An annotated reference sequence representing the hexaploid bread wheat genome in 21 pseudomolecules has been analyzed to identify the distribution and genomic context of coding and noncoding elements across the A, B, and D subgenomes. With an estimated coverage of 94% of the genome and containing 107,891 high-confidence gene models, this assembly enabled the discovery of tissue- and developmental stage-related coexpression networks by providing a transcriptome atlas representing major stages of wheat development. Dynamics of complex gene families involved in environmental adaptation and end-use quality were revealed at subgenome resolution and contextualized to known agronomic single-gene or quantitative trait loci. This community resource establishes the foundation for accelerating wheat research and application through improved understanding of wheat biology and genomics-assisted breeding.
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Affiliation(s)
| | | | - Rudi Appels
- AgriBio, Centre for AgriBioscience, Department of Economic Development, Jobs, Transport, and Resources, 5 Ring Road, La Trobe University, Bundoora, VIC 3083, Australia. .,Murdoch University, Australia-China Centre for Wheat Improvement, School of Veterinary and Life Sciences, 90 South Street, Murdoch, WA 6150, Australia
| | - Kellye Eversole
- International Wheat Genome Sequencing Consortium (IWGSC), 5207 Wyoming Road, Bethesda, MD 20816, USA. .,Eversole Associates, 5207 Wyoming Road, Bethesda, MD 20816, USA
| | - Catherine Feuillet
- Bayer CropScience, Crop Science Division, Research and Development, Innovation Centre, 3500 Paramount Parkway, Morrisville, NC 27560, USA
| | - Beat Keller
- Department of Plant and Microbial Biology, University of Zurich, Zollikerstrasse 107, 8008 Zurich, Switzerland
| | - Jane Rogers
- International Wheat Genome Sequencing Consortium (IWGSC), 18 High Street, Little Eversden, Cambridge CB23 1HE, UK
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Genebank, Corrensstr. 3, 06466 Stadt Seeland, Germany. .,The University of Western Australia (UWA), School of Agriculture and Environment, 35 Stirling Highway, Crawley, WA 6009, Australia
| | | | - Curtis J Pozniak
- University of Saskatchewan, Crop Development Centre, Agriculture Building, 51 Campus Drive, Saskatoon, SK S7N 5A8, Canada
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Genebank, Corrensstr. 3, 06466 Stadt Seeland, Germany. .,The University of Western Australia (UWA), School of Agriculture and Environment, 35 Stirling Highway, Crawley, WA 6009, Australia
| | - Frédéric Choulet
- GDEC (Genetics, Diversity and Ecophysiology of Cereals), INRA, Université Clermont Auvergne (UCA), 5 chemin de Beaulieu, 63039 Clermont-Ferrand, France
| | - Assaf Distelfeld
- School of Plant Sciences and Food Security, Tel Aviv University, Ramat Aviv 69978, Israel
| | - Kellye Eversole
- International Wheat Genome Sequencing Consortium (IWGSC), 5207 Wyoming Road, Bethesda, MD 20816, USA. .,Eversole Associates, 5207 Wyoming Road, Bethesda, MD 20816, USA
| | - Jesse Poland
- Plant Pathology, Throckmorton Hall, Kansas State University, Manhattan, KS 66506, USA
| | - Jane Rogers
- International Wheat Genome Sequencing Consortium (IWGSC), 18 High Street, Little Eversden, Cambridge CB23 1HE, UK
| | - Gil Ronen
- NRGene Ltd., 5 Golda Meir Street, Ness Ziona 7403648, Israel
| | - Andrew G Sharpe
- University of Saskatchewan, Global Institute for Food Security, 110 Gymnasium Place, Saskatoon, SK S7N 4J8, Canada
| | | | - Curtis Pozniak
- University of Saskatchewan, Crop Development Centre, Agriculture Building, 51 Campus Drive, Saskatoon, SK S7N 5A8, Canada
| | - Gil Ronen
- NRGene Ltd., 5 Golda Meir Street, Ness Ziona 7403648, Israel
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Genebank, Corrensstr. 3, 06466 Stadt Seeland, Germany. .,The University of Western Australia (UWA), School of Agriculture and Environment, 35 Stirling Highway, Crawley, WA 6009, Australia
| | - Omer Barad
- NRGene Ltd., 5 Golda Meir Street, Ness Ziona 7403648, Israel
| | - Kobi Baruch
- NRGene Ltd., 5 Golda Meir Street, Ness Ziona 7403648, Israel
| | - Frédéric Choulet
- GDEC (Genetics, Diversity and Ecophysiology of Cereals), INRA, Université Clermont Auvergne (UCA), 5 chemin de Beaulieu, 63039 Clermont-Ferrand, France
| | - Gabriel Keeble-Gagnère
- AgriBio, Centre for AgriBioscience, Department of Economic Development, Jobs, Transport, and Resources, 5 Ring Road, La Trobe University, Bundoora, VIC 3083, Australia
| | - Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Genebank, Corrensstr. 3, 06466 Stadt Seeland, Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103 Leipzig, Germany
| | - Andrew G Sharpe
- University of Saskatchewan, Global Institute for Food Security, 110 Gymnasium Place, Saskatoon, SK S7N 4J8, Canada
| | - Gil Ben-Zvi
- NRGene Ltd., 5 Golda Meir Street, Ness Ziona 7403648, Israel
| | - Ambre-Aurore Josselin
- GDEC (Genetics, Diversity and Ecophysiology of Cereals), INRA, Université Clermont Auvergne (UCA), 5 chemin de Beaulieu, 63039 Clermont-Ferrand, France
| | | | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Genebank, Corrensstr. 3, 06466 Stadt Seeland, Germany. .,The University of Western Australia (UWA), School of Agriculture and Environment, 35 Stirling Highway, Crawley, WA 6009, Australia
| | - Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Genebank, Corrensstr. 3, 06466 Stadt Seeland, Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103 Leipzig, Germany
| | - Axel Himmelbach
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Genebank, Corrensstr. 3, 06466 Stadt Seeland, Germany
| | | | - Frédéric Choulet
- GDEC (Genetics, Diversity and Ecophysiology of Cereals), INRA, Université Clermont Auvergne (UCA), 5 chemin de Beaulieu, 63039 Clermont-Ferrand, France
| | - Gabriel Keeble-Gagnère
- AgriBio, Centre for AgriBioscience, Department of Economic Development, Jobs, Transport, and Resources, 5 Ring Road, La Trobe University, Bundoora, VIC 3083, Australia
| | - Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Genebank, Corrensstr. 3, 06466 Stadt Seeland, Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103 Leipzig, Germany
| | - Jane Rogers
- International Wheat Genome Sequencing Consortium (IWGSC), 18 High Street, Little Eversden, Cambridge CB23 1HE, UK
| | - François Balfourier
- GDEC (Genetics, Diversity and Ecophysiology of Cereals), INRA, Université Clermont Auvergne (UCA), 5 chemin de Beaulieu, 63039 Clermont-Ferrand, France
| | - Juan Gutierrez-Gonzalez
- Department of Agronomy and Plant Genetics, University of Minnesota, 411 Borlaug Hall, St. Paul, MN 55108, USA
| | - Matthew Hayden
- AgriBio, Centre for AgriBioscience, Department of Economic Development, Jobs, Transport, and Resources, 5 Ring Road, La Trobe University, Bundoora, VIC 3083, Australia
| | - Ambre-Aurore Josselin
- GDEC (Genetics, Diversity and Ecophysiology of Cereals), INRA, Université Clermont Auvergne (UCA), 5 chemin de Beaulieu, 63039 Clermont-Ferrand, France
| | - ChuShin Koh
- University of Saskatchewan, Global Institute for Food Security, 110 Gymnasium Place, Saskatoon, SK S7N 4J8, Canada
| | - Gary Muehlbauer
- Department of Agronomy and Plant Genetics, University of Minnesota, 411 Borlaug Hall, St. Paul, MN 55108, USA
| | - Raj K Pasam
- AgriBio, Centre for AgriBioscience, Department of Economic Development, Jobs, Transport, and Resources, 5 Ring Road, La Trobe University, Bundoora, VIC 3083, Australia
| | - Etienne Paux
- GDEC (Genetics, Diversity and Ecophysiology of Cereals), INRA, Université Clermont Auvergne (UCA), 5 chemin de Beaulieu, 63039 Clermont-Ferrand, France
| | - Curtis J Pozniak
- University of Saskatchewan, Crop Development Centre, Agriculture Building, 51 Campus Drive, Saskatoon, SK S7N 5A8, Canada
| | - Philippe Rigault
- GYDLE, Suite 220, 1135 Grande Allée, Ouest, Québec, QC G1S 1E7, Canada
| | - Andrew G Sharpe
- University of Saskatchewan, Global Institute for Food Security, 110 Gymnasium Place, Saskatoon, SK S7N 4J8, Canada
| | - Josquin Tibbits
- AgriBio, Centre for AgriBioscience, Department of Economic Development, Jobs, Transport, and Resources, 5 Ring Road, La Trobe University, Bundoora, VIC 3083, Australia
| | - Vijay Tiwari
- Plant Science and Landscape Architecture, University of Maryland, 4291 Fieldhouse Road, 2102 Plant Sciences Building, College Park, MD 20742, USA
| | | | - Frédéric Choulet
- GDEC (Genetics, Diversity and Ecophysiology of Cereals), INRA, Université Clermont Auvergne (UCA), 5 chemin de Beaulieu, 63039 Clermont-Ferrand, France
| | - Gabriel Keeble-Gagnère
- AgriBio, Centre for AgriBioscience, Department of Economic Development, Jobs, Transport, and Resources, 5 Ring Road, La Trobe University, Bundoora, VIC 3083, Australia
| | - Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Genebank, Corrensstr. 3, 06466 Stadt Seeland, Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103 Leipzig, Germany
| | - Ambre-Aurore Josselin
- GDEC (Genetics, Diversity and Ecophysiology of Cereals), INRA, Université Clermont Auvergne (UCA), 5 chemin de Beaulieu, 63039 Clermont-Ferrand, France
| | - Jane Rogers
- International Wheat Genome Sequencing Consortium (IWGSC), 18 High Street, Little Eversden, Cambridge CB23 1HE, UK
| | | | - Manuel Spannagl
- Helmholtz Center Munich, Plant Genome and Systems Biology (PGSB), Ingolstaedter Landstr. 1, 85764 Neuherberg, Germany
| | - Frédéric Choulet
- GDEC (Genetics, Diversity and Ecophysiology of Cereals), INRA, Université Clermont Auvergne (UCA), 5 chemin de Beaulieu, 63039 Clermont-Ferrand, France
| | - Daniel Lang
- Helmholtz Center Munich, Plant Genome and Systems Biology (PGSB), Ingolstaedter Landstr. 1, 85764 Neuherberg, Germany
| | - Heidrun Gundlach
- Helmholtz Center Munich, Plant Genome and Systems Biology (PGSB), Ingolstaedter Landstr. 1, 85764 Neuherberg, Germany
| | - Georg Haberer
- Helmholtz Center Munich, Plant Genome and Systems Biology (PGSB), Ingolstaedter Landstr. 1, 85764 Neuherberg, Germany
| | - Gabriel Keeble-Gagnère
- AgriBio, Centre for AgriBioscience, Department of Economic Development, Jobs, Transport, and Resources, 5 Ring Road, La Trobe University, Bundoora, VIC 3083, Australia
| | - Klaus F X Mayer
- Helmholtz Center Munich, Plant Genome and Systems Biology (PGSB), Ingolstaedter Landstr. 1, 85764 Neuherberg, Germany.,School of Life Sciences Weihenstephan, Technical University of Munich, 85354 Freising, Germany
| | - Danara Ormanbekova
- Helmholtz Center Munich, Plant Genome and Systems Biology (PGSB), Ingolstaedter Landstr. 1, 85764 Neuherberg, Germany.,Department of Agricultural Sciences, University of Bologna, Viale Fanin, 44 40127 Bologna, Italy
| | - Etienne Paux
- GDEC (Genetics, Diversity and Ecophysiology of Cereals), INRA, Université Clermont Auvergne (UCA), 5 chemin de Beaulieu, 63039 Clermont-Ferrand, France
| | - Verena Prade
- Helmholtz Center Munich, Plant Genome and Systems Biology (PGSB), Ingolstaedter Landstr. 1, 85764 Neuherberg, Germany
| | - Hana Šimková
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-78371 Olomouc, Czech Republic
| | - Thomas Wicker
- Department of Plant and Microbial Biology, University of Zurich, Zollikerstrasse 107, 8008 Zurich, Switzerland
| | | | - Frédéric Choulet
- GDEC (Genetics, Diversity and Ecophysiology of Cereals), INRA, Université Clermont Auvergne (UCA), 5 chemin de Beaulieu, 63039 Clermont-Ferrand, France
| | - Manuel Spannagl
- Helmholtz Center Munich, Plant Genome and Systems Biology (PGSB), Ingolstaedter Landstr. 1, 85764 Neuherberg, Germany
| | | | - Hélène Rimbert
- GDEC (Genetics, Diversity and Ecophysiology of Cereals), INRA, Université Clermont Auvergne (UCA), 5 chemin de Beaulieu, 63039 Clermont-Ferrand, France
| | - Marius Felder
- Helmholtz Center Munich, Plant Genome and Systems Biology (PGSB), Ingolstaedter Landstr. 1, 85764 Neuherberg, Germany
| | - Nicolas Guilhot
- GDEC (Genetics, Diversity and Ecophysiology of Cereals), INRA, Université Clermont Auvergne (UCA), 5 chemin de Beaulieu, 63039 Clermont-Ferrand, France
| | - Heidrun Gundlach
- Helmholtz Center Munich, Plant Genome and Systems Biology (PGSB), Ingolstaedter Landstr. 1, 85764 Neuherberg, Germany
| | - Georg Haberer
- Helmholtz Center Munich, Plant Genome and Systems Biology (PGSB), Ingolstaedter Landstr. 1, 85764 Neuherberg, Germany
| | | | - Jens Keilwagen
- Julius Kühn-Institut, Institute for Biosafety in Plant Biotechnology, Erwin-Baur-Str. 27, 06484 Quedlinburg, Germany
| | - Daniel Lang
- Helmholtz Center Munich, Plant Genome and Systems Biology (PGSB), Ingolstaedter Landstr. 1, 85764 Neuherberg, Germany
| | - Philippe Leroy
- GDEC (Genetics, Diversity and Ecophysiology of Cereals), INRA, Université Clermont Auvergne (UCA), 5 chemin de Beaulieu, 63039 Clermont-Ferrand, France
| | - Thomas Lux
- Helmholtz Center Munich, Plant Genome and Systems Biology (PGSB), Ingolstaedter Landstr. 1, 85764 Neuherberg, Germany
| | - Klaus F X Mayer
- Helmholtz Center Munich, Plant Genome and Systems Biology (PGSB), Ingolstaedter Landstr. 1, 85764 Neuherberg, Germany.,School of Life Sciences Weihenstephan, Technical University of Munich, 85354 Freising, Germany
| | - Sven Twardziok
- Helmholtz Center Munich, Plant Genome and Systems Biology (PGSB), Ingolstaedter Landstr. 1, 85764 Neuherberg, Germany
| | - Luca Venturini
- Earlham Institute, Core Bioinformatics, Norwich NR4 7UZ, UK
| | | | - Rudi Appels
- AgriBio, Centre for AgriBioscience, Department of Economic Development, Jobs, Transport, and Resources, 5 Ring Road, La Trobe University, Bundoora, VIC 3083, Australia. .,Murdoch University, Australia-China Centre for Wheat Improvement, School of Veterinary and Life Sciences, 90 South Street, Murdoch, WA 6150, Australia
| | - Hélène Rimbert
- GDEC (Genetics, Diversity and Ecophysiology of Cereals), INRA, Université Clermont Auvergne (UCA), 5 chemin de Beaulieu, 63039 Clermont-Ferrand, France
| | - Frédéric Choulet
- GDEC (Genetics, Diversity and Ecophysiology of Cereals), INRA, Université Clermont Auvergne (UCA), 5 chemin de Beaulieu, 63039 Clermont-Ferrand, France
| | - Angéla Juhász
- Murdoch University, Australia-China Centre for Wheat Improvement, School of Veterinary and Life Sciences, 90 South Street, Murdoch, WA 6150, Australia.,Agricultural Institute, MTA Centre for Agricultural Research, Applied Genomics Department, 2 Brunszvik Street, Martonvásár H 2462, Hungary
| | - Gabriel Keeble-Gagnère
- AgriBio, Centre for AgriBioscience, Department of Economic Development, Jobs, Transport, and Resources, 5 Ring Road, La Trobe University, Bundoora, VIC 3083, Australia
| | | | - Frédéric Choulet
- GDEC (Genetics, Diversity and Ecophysiology of Cereals), INRA, Université Clermont Auvergne (UCA), 5 chemin de Beaulieu, 63039 Clermont-Ferrand, France
| | - Manuel Spannagl
- Helmholtz Center Munich, Plant Genome and Systems Biology (PGSB), Ingolstaedter Landstr. 1, 85764 Neuherberg, Germany
| | - Daniel Lang
- Helmholtz Center Munich, Plant Genome and Systems Biology (PGSB), Ingolstaedter Landstr. 1, 85764 Neuherberg, Germany
| | - Michael Abrouk
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-78371 Olomouc, Czech Republic.,Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - Georg Haberer
- Helmholtz Center Munich, Plant Genome and Systems Biology (PGSB), Ingolstaedter Landstr. 1, 85764 Neuherberg, Germany
| | - Gabriel Keeble-Gagnère
- AgriBio, Centre for AgriBioscience, Department of Economic Development, Jobs, Transport, and Resources, 5 Ring Road, La Trobe University, Bundoora, VIC 3083, Australia
| | - Klaus F X Mayer
- Helmholtz Center Munich, Plant Genome and Systems Biology (PGSB), Ingolstaedter Landstr. 1, 85764 Neuherberg, Germany.,School of Life Sciences Weihenstephan, Technical University of Munich, 85354 Freising, Germany
| | - Thomas Wicker
- Department of Plant and Microbial Biology, University of Zurich, Zollikerstrasse 107, 8008 Zurich, Switzerland
| | | | - Frédéric Choulet
- GDEC (Genetics, Diversity and Ecophysiology of Cereals), INRA, Université Clermont Auvergne (UCA), 5 chemin de Beaulieu, 63039 Clermont-Ferrand, France
| | - Thomas Wicker
- Department of Plant and Microbial Biology, University of Zurich, Zollikerstrasse 107, 8008 Zurich, Switzerland
| | - Heidrun Gundlach
- Helmholtz Center Munich, Plant Genome and Systems Biology (PGSB), Ingolstaedter Landstr. 1, 85764 Neuherberg, Germany
| | - Daniel Lang
- Helmholtz Center Munich, Plant Genome and Systems Biology (PGSB), Ingolstaedter Landstr. 1, 85764 Neuherberg, Germany
| | - Manuel Spannagl
- Helmholtz Center Munich, Plant Genome and Systems Biology (PGSB), Ingolstaedter Landstr. 1, 85764 Neuherberg, Germany
| | | | - Daniel Lang
- Helmholtz Center Munich, Plant Genome and Systems Biology (PGSB), Ingolstaedter Landstr. 1, 85764 Neuherberg, Germany
| | - Manuel Spannagl
- Helmholtz Center Munich, Plant Genome and Systems Biology (PGSB), Ingolstaedter Landstr. 1, 85764 Neuherberg, Germany
| | - Rudi Appels
- AgriBio, Centre for AgriBioscience, Department of Economic Development, Jobs, Transport, and Resources, 5 Ring Road, La Trobe University, Bundoora, VIC 3083, Australia. .,Murdoch University, Australia-China Centre for Wheat Improvement, School of Veterinary and Life Sciences, 90 South Street, Murdoch, WA 6150, Australia
| | - Iris Fischer
- Helmholtz Center Munich, Plant Genome and Systems Biology (PGSB), Ingolstaedter Landstr. 1, 85764 Neuherberg, Germany
| | | | - Cristobal Uauy
- John Innes Centre, Crop Genetics, Norwich Research Park, Norwich NR4 7UH, UK
| | - Philippa Borrill
- John Innes Centre, Crop Genetics, Norwich Research Park, Norwich NR4 7UH, UK
| | | | - Rudi Appels
- AgriBio, Centre for AgriBioscience, Department of Economic Development, Jobs, Transport, and Resources, 5 Ring Road, La Trobe University, Bundoora, VIC 3083, Australia. .,Murdoch University, Australia-China Centre for Wheat Improvement, School of Veterinary and Life Sciences, 90 South Street, Murdoch, WA 6150, Australia
| | - Dominique Arnaud
- Institut National de la Recherche Agronomique (INRA), 2 rue Gaston Crémieux, 91057 Evry Cedex, France
| | - Smahane Chalabi
- Institut National de la Recherche Agronomique (INRA), 2 rue Gaston Crémieux, 91057 Evry Cedex, France
| | - Boulos Chalhoub
- Monsanto SAS, 28000 Boissay, France.,Institut National de la Recherche Agronomique (INRA), 2 rue Gaston Crémieux, 91057 Evry Cedex, France
| | - Frédéric Choulet
- GDEC (Genetics, Diversity and Ecophysiology of Cereals), INRA, Université Clermont Auvergne (UCA), 5 chemin de Beaulieu, 63039 Clermont-Ferrand, France
| | - Aron Cory
- University of Saskatchewan, Crop Development Centre, Agriculture Building, 51 Campus Drive, Saskatoon, SK S7N 5A8, Canada
| | - Raju Datla
- National Research Council Canada, Aquatic and Crop Resource Development, 110 Gymnasium Place, Saskatoon, SK S7N 0W9, Canada
| | - Mark W Davey
- Bayer CropScience, Trait Research, Innovation Center, Technologiepark 38, 9052 Gent, Belgium
| | - Matthew Hayden
- AgriBio, Centre for AgriBioscience, Department of Economic Development, Jobs, Transport, and Resources, 5 Ring Road, La Trobe University, Bundoora, VIC 3083, Australia
| | - John Jacobs
- Bayer CropScience, Trait Research, Innovation Center, Technologiepark 38, 9052 Gent, Belgium
| | - Daniel Lang
- Helmholtz Center Munich, Plant Genome and Systems Biology (PGSB), Ingolstaedter Landstr. 1, 85764 Neuherberg, Germany
| | - Stephen J Robinson
- Agriculture and Agri-Food Canada, Saskatoon Research and Development Centre, 107 Science Place, Saskatoon, SK S7N 0X2, Canada
| | - Manuel Spannagl
- Helmholtz Center Munich, Plant Genome and Systems Biology (PGSB), Ingolstaedter Landstr. 1, 85764 Neuherberg, Germany
| | | | - Josquin Tibbits
- AgriBio, Centre for AgriBioscience, Department of Economic Development, Jobs, Transport, and Resources, 5 Ring Road, La Trobe University, Bundoora, VIC 3083, Australia
| | - Vijay Tiwari
- Plant Science and Landscape Architecture, University of Maryland, 4291 Fieldhouse Road, 2102 Plant Sciences Building, College Park, MD 20742, USA
| | - Fred van Ex
- Bayer CropScience, Trait Research, Innovation Center, Technologiepark 38, 9052 Gent, Belgium
| | - Brande B H Wulff
- John Innes Centre, Crop Genetics, Norwich Research Park, Norwich NR4 7UH, UK
| | | | - Curtis J Pozniak
- University of Saskatchewan, Crop Development Centre, Agriculture Building, 51 Campus Drive, Saskatoon, SK S7N 5A8, Canada
| | - Stephen J Robinson
- Agriculture and Agri-Food Canada, Saskatoon Research and Development Centre, 107 Science Place, Saskatoon, SK S7N 0X2, Canada
| | - Andrew G Sharpe
- University of Saskatchewan, Global Institute for Food Security, 110 Gymnasium Place, Saskatoon, SK S7N 4J8, Canada
| | - Aron Cory
- University of Saskatchewan, Crop Development Centre, Agriculture Building, 51 Campus Drive, Saskatoon, SK S7N 5A8, Canada
| | | | - Moussa Benhamed
- Biology Department, Institute of Plant Sciences-Paris-Saclay, Bâtiment 630, rue de Noetzlin, Plateau du Moulon, CS80004, 91192 Gif-sur-Yvette Cedex, France
| | - Etienne Paux
- GDEC (Genetics, Diversity and Ecophysiology of Cereals), INRA, Université Clermont Auvergne (UCA), 5 chemin de Beaulieu, 63039 Clermont-Ferrand, France
| | - Abdelhafid Bendahmane
- Biology Department, Institute of Plant Sciences-Paris-Saclay, Bâtiment 630, rue de Noetzlin, Plateau du Moulon, CS80004, 91192 Gif-sur-Yvette Cedex, France
| | - Lorenzo Concia
- Biology Department, Institute of Plant Sciences-Paris-Saclay, Bâtiment 630, rue de Noetzlin, Plateau du Moulon, CS80004, 91192 Gif-sur-Yvette Cedex, France
| | - David Latrasse
- Biology Department, Institute of Plant Sciences-Paris-Saclay, Bâtiment 630, rue de Noetzlin, Plateau du Moulon, CS80004, 91192 Gif-sur-Yvette Cedex, France
| | | | - Jane Rogers
- International Wheat Genome Sequencing Consortium (IWGSC), 18 High Street, Little Eversden, Cambridge CB23 1HE, UK
| | - John Jacobs
- Bayer CropScience, Trait Research, Innovation Center, Technologiepark 38, 9052 Gent, Belgium
| | - Michael Alaux
- URGI, INRA, Université Paris-Saclay, 78026 Versailles, France
| | - Rudi Appels
- AgriBio, Centre for AgriBioscience, Department of Economic Development, Jobs, Transport, and Resources, 5 Ring Road, La Trobe University, Bundoora, VIC 3083, Australia. .,Murdoch University, Australia-China Centre for Wheat Improvement, School of Veterinary and Life Sciences, 90 South Street, Murdoch, WA 6150, Australia
| | - Jan Bartoš
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-78371 Olomouc, Czech Republic
| | - Arnaud Bellec
- INRA, CNRGV, chemin de Borde Rouge, CS 52627, 31326 Castanet-Tolosan Cedex, France
| | - Hélène Berges
- INRA, CNRGV, chemin de Borde Rouge, CS 52627, 31326 Castanet-Tolosan Cedex, France
| | - Jaroslav Doležel
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-78371 Olomouc, Czech Republic
| | - Catherine Feuillet
- Bayer CropScience, Crop Science Division, Research and Development, Innovation Centre, 3500 Paramount Parkway, Morrisville, NC 27560, USA
| | - Zeev Frenkel
- University of Haifa, Institute of Evolution and the Department of Evolutionary and Environmental Biology, 199 Abba-Hushi Avenue, Mount Carmel, Haifa 3498838, Israel
| | - Bikram Gill
- Plant Pathology, Throckmorton Hall, Kansas State University, Manhattan, KS 66506, USA
| | - Abraham Korol
- University of Haifa, Institute of Evolution and the Department of Evolutionary and Environmental Biology, 199 Abba-Hushi Avenue, Mount Carmel, Haifa 3498838, Israel
| | | | - Odd-Arne Olsen
- Faculty of Bioscience, Department of Plant Science, Norwegian University of Life Sciences, Arboretveien 6, 1433 Ås, Norway
| | - Hana Šimková
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-78371 Olomouc, Czech Republic
| | - Kuldeep Singh
- Punjab Agricultural University, Ludhiana, School of Agricultural Biotechnology, ICAR-National Bureau of Plant Genetic Resources, Dev Prakash Shastri Marg, New Delhi 110012, India
| | - Miroslav Valárik
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-78371 Olomouc, Czech Republic
| | | | - Sonia Vautrin
- INRA, CNRGV, chemin de Borde Rouge, CS 52627, 31326 Castanet-Tolosan Cedex, France
| | - Song Weining
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712101, China
| | | | - Abraham Korol
- University of Haifa, Institute of Evolution and the Department of Evolutionary and Environmental Biology, 199 Abba-Hushi Avenue, Mount Carmel, Haifa 3498838, Israel
| | - Zeev Frenkel
- University of Haifa, Institute of Evolution and the Department of Evolutionary and Environmental Biology, 199 Abba-Hushi Avenue, Mount Carmel, Haifa 3498838, Israel
| | - Tzion Fahima
- University of Haifa, Institute of Evolution and the Department of Evolutionary and Environmental Biology, 199 Abba-Hushi Avenue, Mount Carmel, Haifa 3498838, Israel
| | | | - Dina Raats
- Earlham Institute, Core Bioinformatics, Norwich NR4 7UZ, UK
| | - Jane Rogers
- International Wheat Genome Sequencing Consortium (IWGSC), 18 High Street, Little Eversden, Cambridge CB23 1HE, UK
| | | | - Vijay Tiwari
- Plant Science and Landscape Architecture, University of Maryland, 4291 Fieldhouse Road, 2102 Plant Sciences Building, College Park, MD 20742, USA
| | - Bikram Gill
- Plant Pathology, Throckmorton Hall, Kansas State University, Manhattan, KS 66506, USA
| | - Etienne Paux
- GDEC (Genetics, Diversity and Ecophysiology of Cereals), INRA, Université Clermont Auvergne (UCA), 5 chemin de Beaulieu, 63039 Clermont-Ferrand, France
| | - Jesse Poland
- Plant Pathology, Throckmorton Hall, Kansas State University, Manhattan, KS 66506, USA
| | | | - Jaroslav Doležel
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-78371 Olomouc, Czech Republic
| | - Jarmila Číhalíková
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-78371 Olomouc, Czech Republic
| | - Hana Šimková
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-78371 Olomouc, Czech Republic
| | - Helena Toegelová
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-78371 Olomouc, Czech Republic
| | - Jan Vrána
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-78371 Olomouc, Czech Republic
| | | | | | - Benoit Darrier
- GDEC (Genetics, Diversity and Ecophysiology of Cereals), INRA, Université Clermont Auvergne (UCA), 5 chemin de Beaulieu, 63039 Clermont-Ferrand, France
| | | | - Rudi Appels
- AgriBio, Centre for AgriBioscience, Department of Economic Development, Jobs, Transport, and Resources, 5 Ring Road, La Trobe University, Bundoora, VIC 3083, Australia. .,Murdoch University, Australia-China Centre for Wheat Improvement, School of Veterinary and Life Sciences, 90 South Street, Murdoch, WA 6150, Australia
| | - Manuel Spannagl
- Helmholtz Center Munich, Plant Genome and Systems Biology (PGSB), Ingolstaedter Landstr. 1, 85764 Neuherberg, Germany
| | - Daniel Lang
- Helmholtz Center Munich, Plant Genome and Systems Biology (PGSB), Ingolstaedter Landstr. 1, 85764 Neuherberg, Germany
| | - Iris Fischer
- Helmholtz Center Munich, Plant Genome and Systems Biology (PGSB), Ingolstaedter Landstr. 1, 85764 Neuherberg, Germany
| | - Danara Ormanbekova
- Helmholtz Center Munich, Plant Genome and Systems Biology (PGSB), Ingolstaedter Landstr. 1, 85764 Neuherberg, Germany.,Department of Agricultural Sciences, University of Bologna, Viale Fanin, 44 40127 Bologna, Italy
| | - Verena Prade
- Helmholtz Center Munich, Plant Genome and Systems Biology (PGSB), Ingolstaedter Landstr. 1, 85764 Neuherberg, Germany
| | | | - Delfina Barabaschi
- Council for Agricultural Research and Economics (CREA), Research Centre for Genomics and Bioinformatics, via S. Protaso, 302, I -29017 Fiorenzuola d'Arda, Italy
| | - Luigi Cattivelli
- Council for Agricultural Research and Economics (CREA), Research Centre for Genomics and Bioinformatics, via S. Protaso, 302, I -29017 Fiorenzuola d'Arda, Italy
| | | | - Pilar Hernandez
- Instituto de Agricultura Sostenible (IAS-CSIC), Consejo Superior de Investigaciones Científicas, Alameda del Obispo s/n, 14004 Córdoba, Spain
| | - Sergio Galvez
- Universidad de Málaga, Lenguajes y Ciencias de la Computación, Campus de Teatinos, 29071 Málaga, Spain
| | - Hikmet Budak
- Plant Sciences and Plant Pathology, Cereal Genomics Lab, Montana State University, 412 Leon Johnson Hall, Bozeman, MT 59717, USA
| | | | | | | | - Kamil Witek
- The Sainsbury Laboratory, Norwich Research Park, Norwich NR4 7UH, UK
| | - Brande B H Wulff
- John Innes Centre, Crop Genetics, Norwich Research Park, Norwich NR4 7UH, UK
| | - Guotai Yu
- John Innes Centre, Crop Genetics, Norwich Research Park, Norwich NR4 7UH, UK
| | | | - Ian Small
- School of Molecular Sciences, ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia
| | - Joanna Melonek
- School of Molecular Sciences, ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia
| | - Ruonan Zhou
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Genebank, Corrensstr. 3, 06466 Stadt Seeland, Germany
| | | | - Angéla Juhász
- Murdoch University, Australia-China Centre for Wheat Improvement, School of Veterinary and Life Sciences, 90 South Street, Murdoch, WA 6150, Australia.,Agricultural Institute, MTA Centre for Agricultural Research, Applied Genomics Department, 2 Brunszvik Street, Martonvásár H 2462, Hungary
| | - Tatiana Belova
- Faculty of Bioscience, Department of Plant Science, Norwegian University of Life Sciences, Arboretveien 6, 1433 Ås, Norway
| | - Rudi Appels
- AgriBio, Centre for AgriBioscience, Department of Economic Development, Jobs, Transport, and Resources, 5 Ring Road, La Trobe University, Bundoora, VIC 3083, Australia. .,Murdoch University, Australia-China Centre for Wheat Improvement, School of Veterinary and Life Sciences, 90 South Street, Murdoch, WA 6150, Australia
| | - Odd-Arne Olsen
- Faculty of Bioscience, Department of Plant Science, Norwegian University of Life Sciences, Arboretveien 6, 1433 Ås, Norway
| | | | - Kostya Kanyuka
- Rothamsted Research, Biointeractions and Crop Protection, West Common, Harpenden AL5 2JQ, UK
| | - Robert King
- Rothamsted Research, Computational and Analytical Sciences, West Common, Harpenden AL5 2JQ, UK
| | | | - Kirby Nilsen
- University of Saskatchewan, Crop Development Centre, Agriculture Building, 51 Campus Drive, Saskatoon, SK S7N 5A8, Canada
| | - Sean Walkowiak
- University of Saskatchewan, Crop Development Centre, Agriculture Building, 51 Campus Drive, Saskatoon, SK S7N 5A8, Canada
| | - Curtis J Pozniak
- University of Saskatchewan, Crop Development Centre, Agriculture Building, 51 Campus Drive, Saskatoon, SK S7N 5A8, Canada
| | - Richard Cuthbert
- Agriculture and Agri-Food Canada, Swift Current Research and Development Centre, Box 1030, Swift Current, SK S9H 3X2, Canada
| | - Raju Datla
- National Research Council Canada, Aquatic and Crop Resource Development, 110 Gymnasium Place, Saskatoon, SK S7N 0W9, Canada
| | - Ron Knox
- Agriculture and Agri-Food Canada, Swift Current Research and Development Centre, Box 1030, Swift Current, SK S9H 3X2, Canada
| | - Krysta Wiebe
- University of Saskatchewan, Crop Development Centre, Agriculture Building, 51 Campus Drive, Saskatoon, SK S7N 5A8, Canada
| | - Daoquan Xiang
- National Research Council Canada, Aquatic and Crop Resource Development, 110 Gymnasium Place, Saskatoon, SK S7N 0W9, Canada
| | | | - Antje Rohde
- Bayer CropScience, Breeding and Trait Development, Technologiepark 38, 9052 Gent, Belgium
| | - Timothy Golds
- Bayer CropScience, Trait Research, Innovation Center, Technologiepark 38, 9052 Gent, Belgium
| | | | - Jaroslav Doležel
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-78371 Olomouc, Czech Republic
| | - Jana Čížková
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-78371 Olomouc, Czech Republic
| | - Josquin Tibbits
- AgriBio, Centre for AgriBioscience, Department of Economic Development, Jobs, Transport, and Resources, 5 Ring Road, La Trobe University, Bundoora, VIC 3083, Australia
| | | | - Hikmet Budak
- Plant Sciences and Plant Pathology, Cereal Genomics Lab, Montana State University, 412 Leon Johnson Hall, Bozeman, MT 59717, USA
| | - Bala Ani Akpinar
- Plant Sciences and Plant Pathology, Cereal Genomics Lab, Montana State University, 412 Leon Johnson Hall, Bozeman, MT 59717, USA
| | - Sezgi Biyiklioglu
- Plant Sciences and Plant Pathology, Cereal Genomics Lab, Montana State University, 412 Leon Johnson Hall, Bozeman, MT 59717, USA
| | | | - Gary Muehlbauer
- Department of Agronomy and Plant Genetics, University of Minnesota, 411 Borlaug Hall, St. Paul, MN 55108, USA
| | - Jesse Poland
- Plant Pathology, Throckmorton Hall, Kansas State University, Manhattan, KS 66506, USA
| | - Liangliang Gao
- Plant Pathology, Throckmorton Hall, Kansas State University, Manhattan, KS 66506, USA
| | - Juan Gutierrez-Gonzalez
- Department of Agronomy and Plant Genetics, University of Minnesota, 411 Borlaug Hall, St. Paul, MN 55108, USA
| | - Amidou N'Daiye
- University of Saskatchewan, Crop Development Centre, Agriculture Building, 51 Campus Drive, Saskatoon, SK S7N 5A8, Canada
| | | | - Jaroslav Doležel
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-78371 Olomouc, Czech Republic
| | - Hana Šimková
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-78371 Olomouc, Czech Republic
| | - Jarmila Číhalíková
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-78371 Olomouc, Czech Republic
| | - Marie Kubaláková
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-78371 Olomouc, Czech Republic
| | - Jan Šafář
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-78371 Olomouc, Czech Republic
| | - Jan Vrána
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-78371 Olomouc, Czech Republic
| | | | - Hélène Berges
- INRA, CNRGV, chemin de Borde Rouge, CS 52627, 31326 Castanet-Tolosan Cedex, France
| | - Arnaud Bellec
- INRA, CNRGV, chemin de Borde Rouge, CS 52627, 31326 Castanet-Tolosan Cedex, France
| | - Sonia Vautrin
- INRA, CNRGV, chemin de Borde Rouge, CS 52627, 31326 Castanet-Tolosan Cedex, France
| | | | - Michael Alaux
- URGI, INRA, Université Paris-Saclay, 78026 Versailles, France
| | | | | | - Raphael Flores
- URGI, INRA, Université Paris-Saclay, 78026 Versailles, France
| | - Claire Guerche
- URGI, INRA, Université Paris-Saclay, 78026 Versailles, France
| | | | - Mikaël Loaec
- URGI, INRA, Université Paris-Saclay, 78026 Versailles, France
| | | | | | | | - Curtis J Pozniak
- University of Saskatchewan, Crop Development Centre, Agriculture Building, 51 Campus Drive, Saskatoon, SK S7N 5A8, Canada
| | - Andrew G Sharpe
- National Research Council Canada, Aquatic and Crop Resource Development, 110 Gymnasium Place, Saskatoon, SK S7N 0W9, Canada.,University of Saskatchewan, Global Institute for Food Security, 110 Gymnasium Place, Saskatoon, SK S7N 4J8, Canada
| | | | - Hikmet Budak
- Plant Sciences and Plant Pathology, Cereal Genomics Lab, Montana State University, 412 Leon Johnson Hall, Bozeman, MT 59717, USA
| | - Janet Condie
- National Research Council Canada, Aquatic and Crop Resource Development, 110 Gymnasium Place, Saskatoon, SK S7N 0W9, Canada
| | - Jennifer Ens
- University of Saskatchewan, Crop Development Centre, Agriculture Building, 51 Campus Drive, Saskatoon, SK S7N 5A8, Canada
| | - ChuShin Koh
- University of Saskatchewan, Global Institute for Food Security, 110 Gymnasium Place, Saskatoon, SK S7N 4J8, Canada
| | - Ron Maclachlan
- University of Saskatchewan, Crop Development Centre, Agriculture Building, 51 Campus Drive, Saskatoon, SK S7N 5A8, Canada
| | - Yifang Tan
- National Research Council Canada, Aquatic and Crop Resource Development, 110 Gymnasium Place, Saskatoon, SK S7N 0W9, Canada
| | - Thomas Wicker
- Department of Plant and Microbial Biology, University of Zurich, Zollikerstrasse 107, 8008 Zurich, Switzerland
| | | | - Frédéric Choulet
- GDEC (Genetics, Diversity and Ecophysiology of Cereals), INRA, Université Clermont Auvergne (UCA), 5 chemin de Beaulieu, 63039 Clermont-Ferrand, France
| | - Etienne Paux
- GDEC (Genetics, Diversity and Ecophysiology of Cereals), INRA, Université Clermont Auvergne (UCA), 5 chemin de Beaulieu, 63039 Clermont-Ferrand, France
| | - Adriana Alberti
- CEA-Institut de Biologie François-Jacob, Genoscope, 2 rue Gaston Crémieux, 91057 Evry Cedex, France
| | - Jean-Marc Aury
- CEA-Institut de Biologie François-Jacob, Genoscope, 2 rue Gaston Crémieux, 91057 Evry Cedex, France
| | - François Balfourier
- GDEC (Genetics, Diversity and Ecophysiology of Cereals), INRA, Université Clermont Auvergne (UCA), 5 chemin de Beaulieu, 63039 Clermont-Ferrand, France
| | - Valérie Barbe
- CEA-Institut de Biologie François-Jacob, Genoscope, 2 rue Gaston Crémieux, 91057 Evry Cedex, France
| | - Arnaud Couloux
- CEA-Institut de Biologie François-Jacob, Genoscope, 2 rue Gaston Crémieux, 91057 Evry Cedex, France
| | - Corinne Cruaud
- CEA-Institut de Biologie François-Jacob, Genoscope, 2 rue Gaston Crémieux, 91057 Evry Cedex, France
| | - Karine Labadie
- CEA-Institut de Biologie François-Jacob, Genoscope, 2 rue Gaston Crémieux, 91057 Evry Cedex, France
| | - Sophie Mangenot
- CEA-Institut de Biologie François-Jacob, Genoscope, 2 rue Gaston Crémieux, 91057 Evry Cedex, France
| | - Patrick Wincker
- CEA-Institut de Biologie François-Jacob, Genoscope, 2 rue Gaston Crémieux, 91057 Evry Cedex, France.,CNRS, UMR 8030, CP5706, 91057 Evry, France.,Université d'Evry, UMR 8030, CP5706, 91057 Evry, France
| | | | - Bikram Gill
- Plant Pathology, Throckmorton Hall, Kansas State University, Manhattan, KS 66506, USA
| | - Gaganpreet Kaur
- Plant Pathology, Throckmorton Hall, Kansas State University, Manhattan, KS 66506, USA
| | - Mingcheng Luo
- Department of Plant Sciences, University of California, Davis, One Shield Avenue, Davis, CA 95617, USA
| | - Sunish Sehgal
- Agronomy Horticulture and Plant Science, South Dakota State University, 2108 Jackrabbit Drive, Brookings, SD 57006, USA
| | | | - Kuldeep Singh
- Punjab Agricultural University, Ludhiana, School of Agricultural Biotechnology, ICAR-National Bureau of Plant Genetic Resources, Dev Prakash Shastri Marg, New Delhi 110012, India
| | - Parveen Chhuneja
- Punjab Agricultural University, Ludhiana, School of Agricultural Biotechnology, ICAR-National Bureau of Plant Genetic Resources, Dev Prakash Shastri Marg, New Delhi 110012, India
| | - Om Prakash Gupta
- Punjab Agricultural University, Ludhiana, School of Agricultural Biotechnology, ICAR-National Bureau of Plant Genetic Resources, Dev Prakash Shastri Marg, New Delhi 110012, India
| | - Suruchi Jindal
- Punjab Agricultural University, Ludhiana, School of Agricultural Biotechnology, ICAR-National Bureau of Plant Genetic Resources, Dev Prakash Shastri Marg, New Delhi 110012, India
| | - Parampreet Kaur
- Punjab Agricultural University, Ludhiana, School of Agricultural Biotechnology, ICAR-National Bureau of Plant Genetic Resources, Dev Prakash Shastri Marg, New Delhi 110012, India
| | - Palvi Malik
- Punjab Agricultural University, Ludhiana, School of Agricultural Biotechnology, ICAR-National Bureau of Plant Genetic Resources, Dev Prakash Shastri Marg, New Delhi 110012, India
| | - Priti Sharma
- Punjab Agricultural University, Ludhiana, School of Agricultural Biotechnology, ICAR-National Bureau of Plant Genetic Resources, Dev Prakash Shastri Marg, New Delhi 110012, India
| | - Bharat Yadav
- Punjab Agricultural University, Ludhiana, School of Agricultural Biotechnology, ICAR-National Bureau of Plant Genetic Resources, Dev Prakash Shastri Marg, New Delhi 110012, India
| | | | - Nagendra K Singh
- ICAR-National Research Centre on Plant Biotechnology, LBS Building, Pusa Campus, New Delhi 110012, India
| | - JitendraP Khurana
- University of Delhi South Campus, Interdisciplinary Center for Plant Genomics and Department of Plant Molecular Biology, Benito Juarez Road, New Delhi 110021, India
| | - Chanderkant Chaudhary
- University of Delhi South Campus, Interdisciplinary Center for Plant Genomics and Department of Plant Molecular Biology, Benito Juarez Road, New Delhi 110021, India
| | - Paramjit Khurana
- University of Delhi South Campus, Interdisciplinary Center for Plant Genomics and Department of Plant Molecular Biology, Benito Juarez Road, New Delhi 110021, India
| | - Vinod Kumar
- ICAR-National Research Centre on Plant Biotechnology, LBS Building, Pusa Campus, New Delhi 110012, India
| | - Ajay Mahato
- ICAR-National Research Centre on Plant Biotechnology, LBS Building, Pusa Campus, New Delhi 110012, India
| | - Saloni Mathur
- University of Delhi South Campus, Interdisciplinary Center for Plant Genomics and Department of Plant Molecular Biology, Benito Juarez Road, New Delhi 110021, India
| | - Amitha Sevanthi
- ICAR-National Research Centre on Plant Biotechnology, LBS Building, Pusa Campus, New Delhi 110012, India
| | - Naveen Sharma
- University of Delhi South Campus, Interdisciplinary Center for Plant Genomics and Department of Plant Molecular Biology, Benito Juarez Road, New Delhi 110021, India
| | - Ram Sewak Tomar
- ICAR-National Research Centre on Plant Biotechnology, LBS Building, Pusa Campus, New Delhi 110012, India
| | | | - Jane Rogers
- International Wheat Genome Sequencing Consortium (IWGSC), 18 High Street, Little Eversden, Cambridge CB23 1HE, UK
| | - John Jacobs
- Bayer CropScience, Trait Research, Innovation Center, Technologiepark 38, 9052 Gent, Belgium
| | - Michael Alaux
- URGI, INRA, Université Paris-Saclay, 78026 Versailles, France
| | - Arnaud Bellec
- INRA, CNRGV, chemin de Borde Rouge, CS 52627, 31326 Castanet-Tolosan Cedex, France
| | - Hélène Berges
- INRA, CNRGV, chemin de Borde Rouge, CS 52627, 31326 Castanet-Tolosan Cedex, France
| | - Jaroslav Doležel
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-78371 Olomouc, Czech Republic
| | - Catherine Feuillet
- Bayer CropScience, Crop Science Division, Research and Development, Innovation Centre, 3500 Paramount Parkway, Morrisville, NC 27560, USA
| | - Zeev Frenkel
- University of Haifa, Institute of Evolution and the Department of Evolutionary and Environmental Biology, 199 Abba-Hushi Avenue, Mount Carmel, Haifa 3498838, Israel
| | - Bikram Gill
- Plant Pathology, Throckmorton Hall, Kansas State University, Manhattan, KS 66506, USA
| | - Abraham Korol
- University of Haifa, Institute of Evolution and the Department of Evolutionary and Environmental Biology, 199 Abba-Hushi Avenue, Mount Carmel, Haifa 3498838, Israel
| | | | - Sonia Vautrin
- INRA, CNRGV, chemin de Borde Rouge, CS 52627, 31326 Castanet-Tolosan Cedex, France
| | | | - Bikram Gill
- Plant Pathology, Throckmorton Hall, Kansas State University, Manhattan, KS 66506, USA
| | - Gaganpreet Kaur
- Plant Pathology, Throckmorton Hall, Kansas State University, Manhattan, KS 66506, USA
| | - Mingcheng Luo
- Department of Plant Sciences, University of California, Davis, One Shield Avenue, Davis, CA 95617, USA
| | - Sunish Sehgal
- Agronomy Horticulture and Plant Science, South Dakota State University, 2108 Jackrabbit Drive, Brookings, SD 57006, USA
| | | | - Jan Bartoš
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-78371 Olomouc, Czech Republic
| | - Kateřina Holušová
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-78371 Olomouc, Czech Republic
| | - Ondřej Plíhal
- Department of Molecular Biology, Centre of the Region Haná for Biotechnological and Agricultural Research, Palacký University, Šlechtitelů 27, CZ-78371 Olomouc, Czech Republic
| | | | - Matthew D Clark
- Earlham Institute, Core Bioinformatics, Norwich NR4 7UZ, UK.,Department of Lifesciences, Natural History Museum, Cromwell Road, London SW7 5BD, UK
| | - Darren Heavens
- Earlham Institute, Core Bioinformatics, Norwich NR4 7UZ, UK
| | | | - Jon Wright
- Earlham Institute, Core Bioinformatics, Norwich NR4 7UZ, UK
| | | | - Miroslav Valárik
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-78371 Olomouc, Czech Republic
| | - Michael Abrouk
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-78371 Olomouc, Czech Republic.,Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - Barbora Balcárková
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-78371 Olomouc, Czech Republic
| | - Kateřina Holušová
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-78371 Olomouc, Czech Republic
| | - Yuqin Hu
- Department of Plant Sciences, University of California, Davis, One Shield Avenue, Davis, CA 95617, USA
| | - Mingcheng Luo
- Department of Plant Sciences, University of California, Davis, One Shield Avenue, Davis, CA 95617, USA
| | | | - Elena Salina
- The Federal Research Center Institute of Cytology and Genetics, SB RAS, pr. Lavrentyeva 10, Novosibirsk 630090, Russia
| | - Nikolai Ravin
- Research Center of Biotechnology of the Russian Academy of Sciences, Institute of Bioengineering, Leninsky Avenue 33, Building 2, Moscow 119071, Russia.,Faculty of Biology, Moscow State University, Leninskie Gory, 1, Moscow 119991, Russia
| | - Konstantin Skryabin
- Research Center of Biotechnology of the Russian Academy of Sciences, Institute of Bioengineering, Leninsky Avenue 33, Building 2, Moscow 119071, Russia.,Faculty of Biology, Moscow State University, Leninskie Gory, 1, Moscow 119991, Russia
| | - Alexey Beletsky
- Research Center of Biotechnology of the Russian Academy of Sciences, Institute of Bioengineering, Leninsky Avenue 33, Building 2, Moscow 119071, Russia
| | - Vitaly Kadnikov
- Research Center of Biotechnology of the Russian Academy of Sciences, Institute of Bioengineering, Leninsky Avenue 33, Building 2, Moscow 119071, Russia
| | - Andrey Mardanov
- Research Center of Biotechnology of the Russian Academy of Sciences, Institute of Bioengineering, Leninsky Avenue 33, Building 2, Moscow 119071, Russia
| | - Michail Nesterov
- The Federal Research Center Institute of Cytology and Genetics, SB RAS, pr. Lavrentyeva 10, Novosibirsk 630090, Russia
| | - Andrey Rakitin
- Research Center of Biotechnology of the Russian Academy of Sciences, Institute of Bioengineering, Leninsky Avenue 33, Building 2, Moscow 119071, Russia
| | - Ekaterina Sergeeva
- The Federal Research Center Institute of Cytology and Genetics, SB RAS, pr. Lavrentyeva 10, Novosibirsk 630090, Russia
| | | | - Hirokazu Handa
- Institute of Crop Science, NARO, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Hiroyuki Kanamori
- Institute of Crop Science, NARO, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Satoshi Katagiri
- Institute of Crop Science, NARO, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Fuminori Kobayashi
- Institute of Crop Science, NARO, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Shuhei Nasuda
- Graduate School of Agriculture, Kyoto University, Kitashirakawaoiwake-cho, Sakyo-ku, Kyoto 606-8502, Japan
| | - Tsuyoshi Tanaka
- Institute of Crop Science, NARO, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Jianzhong Wu
- Institute of Crop Science, NARO, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | | | - Rudi Appels
- AgriBio, Centre for AgriBioscience, Department of Economic Development, Jobs, Transport, and Resources, 5 Ring Road, La Trobe University, Bundoora, VIC 3083, Australia. .,Murdoch University, Australia-China Centre for Wheat Improvement, School of Veterinary and Life Sciences, 90 South Street, Murdoch, WA 6150, Australia
| | - Matthew Hayden
- AgriBio, Centre for AgriBioscience, Department of Economic Development, Jobs, Transport, and Resources, 5 Ring Road, La Trobe University, Bundoora, VIC 3083, Australia
| | - Gabriel Keeble-Gagnère
- AgriBio, Centre for AgriBioscience, Department of Economic Development, Jobs, Transport, and Resources, 5 Ring Road, La Trobe University, Bundoora, VIC 3083, Australia
| | - Philippe Rigault
- GYDLE, Suite 220, 1135 Grande Allée, Ouest, Québec, QC G1S 1E7, Canada
| | - Josquin Tibbits
- AgriBio, Centre for AgriBioscience, Department of Economic Development, Jobs, Transport, and Resources, 5 Ring Road, La Trobe University, Bundoora, VIC 3083, Australia
| | | | - Odd-Arne Olsen
- Faculty of Bioscience, Department of Plant Science, Norwegian University of Life Sciences, Arboretveien 6, 1433 Ås, Norway
| | - Tatiana Belova
- Faculty of Bioscience, Department of Plant Science, Norwegian University of Life Sciences, Arboretveien 6, 1433 Ås, Norway
| | | | - Min Jiumeng
- BGI-Shenzhen, BGI Genomics, Building No. 7, BGI Park, No. 21 Hongan 3rd Street, Yantian District, Shenzhen 518083, China
| | - Karl Kugler
- Helmholtz Center Munich, Plant Genome and Systems Biology (PGSB), Ingolstaedter Landstr. 1, 85764 Neuherberg, Germany
| | - Klaus F X Mayer
- Helmholtz Center Munich, Plant Genome and Systems Biology (PGSB), Ingolstaedter Landstr. 1, 85764 Neuherberg, Germany.,School of Life Sciences Weihenstephan, Technical University of Munich, 85354 Freising, Germany
| | - Matthias Pfeifer
- Helmholtz Center Munich, Plant Genome and Systems Biology (PGSB), Ingolstaedter Landstr. 1, 85764 Neuherberg, Germany
| | - Simen Sandve
- Faculty of Bioscience, Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences, Arboretveien 6, 1433 Ås, Norway
| | - Xu Xun
- BGI-Shenzhen, BGI Genomics, Yantian District, Shenzhen 518083, Guangdong, China
| | - Bujie Zhan
- Faculty of Bioscience, Department of Plant Science, Norwegian University of Life Sciences, Arboretveien 6, 1433 Ås, Norway
| | | | - Hana Šimková
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-78371 Olomouc, Czech Republic
| | - Michael Abrouk
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-78371 Olomouc, Czech Republic.,Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - Jacqueline Batley
- School of Biological Sciences and Institute of Agriculture, University of Western Australia, Perth, WA 6009, Australia
| | - Philipp E Bayer
- School of Biological Sciences and Institute of Agriculture, University of Western Australia, Perth, WA 6009, Australia
| | - David Edwards
- School of Biological Sciences and Institute of Agriculture, University of Western Australia, Perth, WA 6009, Australia
| | - Satomi Hayashi
- Queensland University of Technology, Earth, Environmental and Biological Sciences, Brisbane, QLD 4001, Australia
| | - Helena Toegelová
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-78371 Olomouc, Czech Republic
| | - Zuzana Tulpová
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-78371 Olomouc, Czech Republic
| | - Paul Visendi
- University of Greenwich, Natural Resources Institute, Central Avenue, Chatham, Kent ME4 4TB, UK
| | | | - Song Weining
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712101, China
| | - Licao Cui
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712101, China
| | - Xianghong Du
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712101, China
| | - Kewei Feng
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712101, China
| | - Xiaojun Nie
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712101, China
| | - Wei Tong
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712101, China
| | - Le Wang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712101, China
| | | | - Philippa Borrill
- John Innes Centre, Crop Genetics, Norwich Research Park, Norwich NR4 7UH, UK
| | - Heidrun Gundlach
- Helmholtz Center Munich, Plant Genome and Systems Biology (PGSB), Ingolstaedter Landstr. 1, 85764 Neuherberg, Germany
| | - Sergio Galvez
- Universidad de Málaga, Lenguajes y Ciencias de la Computación, Campus de Teatinos, 29071 Málaga, Spain
| | | | - Daniel Lang
- Helmholtz Center Munich, Plant Genome and Systems Biology (PGSB), Ingolstaedter Landstr. 1, 85764 Neuherberg, Germany
| | - Thomas Lux
- Helmholtz Center Munich, Plant Genome and Systems Biology (PGSB), Ingolstaedter Landstr. 1, 85764 Neuherberg, Germany
| | - Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Genebank, Corrensstr. 3, 06466 Stadt Seeland, Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103 Leipzig, Germany
| | - Danara Ormanbekova
- Helmholtz Center Munich, Plant Genome and Systems Biology (PGSB), Ingolstaedter Landstr. 1, 85764 Neuherberg, Germany.,Department of Agricultural Sciences, University of Bologna, Viale Fanin, 44 40127 Bologna, Italy
| | - Verena Prade
- Helmholtz Center Munich, Plant Genome and Systems Biology (PGSB), Ingolstaedter Landstr. 1, 85764 Neuherberg, Germany
| | | | - Manuel Spannagl
- Helmholtz Center Munich, Plant Genome and Systems Biology (PGSB), Ingolstaedter Landstr. 1, 85764 Neuherberg, Germany
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Genebank, Corrensstr. 3, 06466 Stadt Seeland, Germany. .,The University of Western Australia (UWA), School of Agriculture and Environment, 35 Stirling Highway, Crawley, WA 6009, Australia
| | - Cristobal Uauy
- John Innes Centre, Crop Genetics, Norwich Research Park, Norwich NR4 7UH, UK
| | - Luca Venturini
- Earlham Institute, Core Bioinformatics, Norwich NR4 7UZ, UK
| | | | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Genebank, Corrensstr. 3, 06466 Stadt Seeland, Germany. .,The University of Western Australia (UWA), School of Agriculture and Environment, 35 Stirling Highway, Crawley, WA 6009, Australia
| | - Rudi Appels
- AgriBio, Centre for AgriBioscience, Department of Economic Development, Jobs, Transport, and Resources, 5 Ring Road, La Trobe University, Bundoora, VIC 3083, Australia. .,Murdoch University, Australia-China Centre for Wheat Improvement, School of Veterinary and Life Sciences, 90 South Street, Murdoch, WA 6150, Australia
| | - Kellye Eversole
- International Wheat Genome Sequencing Consortium (IWGSC), 5207 Wyoming Road, Bethesda, MD 20816, USA. .,Eversole Associates, 5207 Wyoming Road, Bethesda, MD 20816, USA
| | - Jane Rogers
- International Wheat Genome Sequencing Consortium (IWGSC), 18 High Street, Little Eversden, Cambridge CB23 1HE, UK
| | - Philippa Borrill
- John Innes Centre, Crop Genetics, Norwich Research Park, Norwich NR4 7UH, UK
| | - Luigi Cattivelli
- Council for Agricultural Research and Economics (CREA), Research Centre for Genomics and Bioinformatics, via S. Protaso, 302, I -29017 Fiorenzuola d'Arda, Italy
| | - Frédéric Choulet
- GDEC (Genetics, Diversity and Ecophysiology of Cereals), INRA, Université Clermont Auvergne (UCA), 5 chemin de Beaulieu, 63039 Clermont-Ferrand, France
| | - Pilar Hernandez
- Instituto de Agricultura Sostenible (IAS-CSIC), Consejo Superior de Investigaciones Científicas, Alameda del Obispo s/n, 14004 Córdoba, Spain
| | - Kostya Kanyuka
- Rothamsted Research, Biointeractions and Crop Protection, West Common, Harpenden AL5 2JQ, UK
| | - Daniel Lang
- Helmholtz Center Munich, Plant Genome and Systems Biology (PGSB), Ingolstaedter Landstr. 1, 85764 Neuherberg, Germany
| | - Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Genebank, Corrensstr. 3, 06466 Stadt Seeland, Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103 Leipzig, Germany
| | - Kirby Nilsen
- University of Saskatchewan, Crop Development Centre, Agriculture Building, 51 Campus Drive, Saskatoon, SK S7N 5A8, Canada
| | - Etienne Paux
- GDEC (Genetics, Diversity and Ecophysiology of Cereals), INRA, Université Clermont Auvergne (UCA), 5 chemin de Beaulieu, 63039 Clermont-Ferrand, France
| | - Curtis J Pozniak
- University of Saskatchewan, Crop Development Centre, Agriculture Building, 51 Campus Drive, Saskatoon, SK S7N 5A8, Canada
| | | | - Hana Šimková
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-78371 Olomouc, Czech Republic
| | - Ian Small
- School of Molecular Sciences, ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia
| | - Manuel Spannagl
- Helmholtz Center Munich, Plant Genome and Systems Biology (PGSB), Ingolstaedter Landstr. 1, 85764 Neuherberg, Germany
| | | | - Cristobal Uauy
- John Innes Centre, Crop Genetics, Norwich Research Park, Norwich NR4 7UH, UK
| |
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27
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Juhász A, Belova T, Florides CG, Maulis C, Fischer I, Gell G, Birinyi Z, Ong J, Keeble-Gagnère G, Maharajan A, Ma W, Gibson P, Jia J, Lang D, Mayer KFX, Spannagl M, Tye-Din JA, Appels R, Olsen OA. Genome mapping of seed-borne allergens and immunoresponsive proteins in wheat. Sci Adv 2018; 4:eaar8602. [PMID: 30128352 PMCID: PMC6097586 DOI: 10.1126/sciadv.aar8602] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/25/2017] [Accepted: 07/11/2018] [Indexed: 05/24/2023]
Abstract
Wheat is an important staple grain for humankind globally because of its end-use quality and nutritional properties and its adaptability to diverse climates. For a small proportion of the population, specific wheat proteins can trigger adverse immune responses and clinical manifestations such as celiac disease, wheat allergy, baker's asthma, and wheat-dependent exercise-induced anaphylaxis (WDEIA). Establishing the content and distribution of the immunostimulatory regions in wheat has been hampered by the complexity of the wheat genome and the lack of complete genome sequence information. We provide novel insights into the wheat grain proteins based on a comprehensive analysis and annotation of the wheat prolamin Pfam clan grain proteins and other non-prolamin allergens implicated in these disorders using the new International Wheat Genome Sequencing Consortium bread wheat reference genome sequence, RefSeq v1.0. Celiac disease and WDEIA genes are primarily expressed in the starchy endosperm and show wide variation in protein- and transcript-level expression in response to temperature stress. Nonspecific lipid transfer proteins and α-amylase trypsin inhibitor gene families, implicated in baker's asthma, are primarily expressed in the aleurone layer and transfer cells of grains and are more sensitive to cold temperature. The study establishes a new reference map for immunostimulatory wheat proteins and provides a fresh basis for selecting wheat lines and developing diagnostics for products with more favorable consumer attributes.
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Affiliation(s)
- Angéla Juhász
- State Agricultural Biotechnology Centre, School of Veterinary and Life Sciences, Murdoch University, Murdoch, Western Australia, Australia
- Applied Genomics Department, Agricultural Institute, Centre for Agricultural Research, Hungarian Academy of Sciences, Martonvásár, Hungary
| | | | - Chris G. Florides
- State Agricultural Biotechnology Centre, School of Veterinary and Life Sciences, Murdoch University, Murdoch, Western Australia, Australia
| | - Csaba Maulis
- State Agricultural Biotechnology Centre, School of Veterinary and Life Sciences, Murdoch University, Murdoch, Western Australia, Australia
| | - Iris Fischer
- Helmholtz Zentrum München, Plant Genome and Systems Biology, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany
| | - Gyöngyvér Gell
- Applied Genomics Department, Agricultural Institute, Centre for Agricultural Research, Hungarian Academy of Sciences, Martonvásár, Hungary
| | - Zsófia Birinyi
- Applied Genomics Department, Agricultural Institute, Centre for Agricultural Research, Hungarian Academy of Sciences, Martonvásár, Hungary
| | - Jamie Ong
- State Agricultural Biotechnology Centre, School of Veterinary and Life Sciences, Murdoch University, Murdoch, Western Australia, Australia
| | - Gabriel Keeble-Gagnère
- Agriculture Victoria Research, Department of Economic Development, Jobs, Transport and Resources, AgriBio, Bundoora, VIC 3083, Australia
| | | | - Wujun Ma
- State Agricultural Biotechnology Centre, School of Veterinary and Life Sciences, Murdoch University, Murdoch, Western Australia, Australia
| | - Peter Gibson
- Department of Medicine Nursing and Health Sciences, Monash University, Melbourne, Victoria, Australia
| | - Jizeng Jia
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture, National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Daniel Lang
- Helmholtz Zentrum München, Plant Genome and Systems Biology, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany
| | - Klaus F. X. Mayer
- Helmholtz Zentrum München, Plant Genome and Systems Biology, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany
- Technical University of Munich, School of Life Sciences, Campus Weihenstephan, Freising, Germany
| | - Manuel Spannagl
- Helmholtz Zentrum München, Plant Genome and Systems Biology, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany
| | | | - Jason A. Tye-Din
- Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
| | - Rudi Appels
- State Agricultural Biotechnology Centre, School of Veterinary and Life Sciences, Murdoch University, Murdoch, Western Australia, Australia
- Agriculture Victoria Research, Department of Economic Development, Jobs, Transport and Resources, AgriBio, Bundoora, VIC 3083, Australia
- School of BioSciences, Faculty of Science, University of Melbourne, Parkville, Victoria, Australia
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28
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Affiliation(s)
- Awais Rasheed
- Institute of Crop Science, CAAS, Beijing, China
- CIMMYT, CAAS, Beijing, China
| | - Francis C Ogbonnaya
- Grains Research & Development Corporation, Kingston, Australian Capital Territory, Australia
| | - Evans Lagudah
- CSIRO, Agriculture and Food, Canberra, ACT, Australia
| | - Rudi Appels
- Murdoch University, Perth, Western Australia, Australia
| | - Zhonghu He
- Institute of Crop Science, CAAS, Beijing, China.
- CIMMYT, CAAS, Beijing, China.
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29
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Kaur P, Bayer PE, Milec Z, Vrána J, Yuan Y, Appels R, Edwards D, Batley J, Nichols P, Erskine W, Doležel J. An advanced reference genome of Trifolium subterraneum L. reveals genes related to agronomic performance. Plant Biotechnol J 2017; 15:1034-1046. [PMID: 28111887 PMCID: PMC5506647 DOI: 10.1111/pbi.12697] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Revised: 01/05/2017] [Accepted: 01/11/2017] [Indexed: 05/08/2023]
Abstract
Subterranean clover is an important annual forage legume, whose diploidy and inbreeding nature make it an ideal model for genomic analysis in Trifolium. We reported a draft genome assembly of the subterranean clover TSUd_r1.1. Here we evaluate genome mapping on nanochannel arrays and generation of a transcriptome atlas across tissues to advance the assembly and gene annotation. Using a BioNano-based assembly spanning 512 Mb (93% genome coverage), we validated the draft assembly, anchored unplaced contigs and resolved misassemblies. Multiple contigs (264) from the draft assembly coalesced into 97 super-scaffolds (43% of genome). Sequences longer than >1 Mb increased from 40 to 189 Mb giving 1.4-fold increase in N50 with total genome in pseudomolecules improved from 73 to 80%. The advanced assembly was re-annotated using transcriptome atlas data to contain 31 272 protein-coding genes capturing >96% of the gene content. Functional characterization and GO enrichment confirmed gene expression for response to water deprivation, flavonoid biosynthesis and embryo development ending in seed dormancy, reflecting adaptation to the harsh Mediterranean environment. Comparative analyses across Papilionoideae identified 24 893 Trifolium-specific and 6325 subterranean-clover-specific genes that could be mined further for traits such as geocarpy and grazing tolerance. Eight key traits, including persistence, improved livestock health by isoflavonoid production in addition to important agro-morphological traits, were fine-mapped on the high-density SNP linkage map anchored to the assembly. This new genomic information is crucial to identify loci governing traits allowing marker-assisted breeding, comparative mapping and identification of tissue-specific gene promoters for biotechnological improvement of forage legumes.
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Affiliation(s)
- Parwinder Kaur
- Centre for Plant Genetics and Breeding and Institute of AgricultureThe University of Western AustraliaCrawleyWAAustralia
| | - Philipp E. Bayer
- School of Plant Biology and Institute of AgricultureThe University of Western AustraliaCrawleyWAAustralia
| | - Zbyněk Milec
- Institute of Experimental BotanyCentre of the Region Haná for Biotechnological and Agricultural ResearchOlomoucCzech Republic
| | - Jan Vrána
- Institute of Experimental BotanyCentre of the Region Haná for Biotechnological and Agricultural ResearchOlomoucCzech Republic
| | - Yuxuan Yuan
- School of Plant Biology and Institute of AgricultureThe University of Western AustraliaCrawleyWAAustralia
| | | | - David Edwards
- School of Plant Biology and Institute of AgricultureThe University of Western AustraliaCrawleyWAAustralia
| | - Jacqueline Batley
- School of Plant Biology and Institute of AgricultureThe University of Western AustraliaCrawleyWAAustralia
| | - Phillip Nichols
- School of Plant Biology and Institute of AgricultureThe University of Western AustraliaCrawleyWAAustralia
- Department of Agriculture and Food Western AustraliaSouth PerthWAAustralia
| | - William Erskine
- Centre for Plant Genetics and Breeding and Institute of AgricultureThe University of Western AustraliaCrawleyWAAustralia
| | - Jaroslav Doležel
- Institute of Experimental BotanyCentre of the Region Haná for Biotechnological and Agricultural ResearchOlomoucCzech Republic
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Voss-Fels KP, Qian L, Parra-Londono S, Uptmoor R, Frisch M, Keeble-Gagnère G, Appels R, Snowdon RJ. Linkage drag constrains the roots of modern wheat. Plant Cell Environ 2017; 40:717-725. [PMID: 28036107 DOI: 10.1111/pce.12888] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Revised: 12/20/2016] [Accepted: 12/21/2016] [Indexed: 05/19/2023]
Abstract
Roots, the hidden half of crop plants, are essential for resource acquisition. However, knowledge about the genetic control of below-ground plant development in wheat, one of the most important small-grain crops in the world, is very limited. The molecular interactions connecting root and shoot development and growth, and thus modulating the plant's demand for water and nutrients along with its ability to access them, are largely unexplored. Here, we demonstrate that linkage drag in European bread wheat, driven by strong selection for a haplotype variant controlling heading date, has eliminated a specific combination of two flanking, highly conserved haplotype variants whose interaction confers increased root biomass. Reversing this inadvertent consequence of selection could recover root diversity that may prove essential for future food production in fluctuating environments. Highly conserved synteny to rice across this chromosome segment suggests that adaptive selection has shaped the diversity landscape of this locus across different, globally important cereal crops. By mining wheat gene expression data, we identified root-expressed genes within the region of interest that could help breeders to select positive variants adapted to specific target soil environments.
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Affiliation(s)
- Kai P Voss-Fels
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Heinrich-Buff-Ring 26-32, 35392, Giessen, Germany
| | - Lunwen Qian
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Heinrich-Buff-Ring 26-32, 35392, Giessen, Germany
| | - Sebastian Parra-Londono
- Department of Agronomy, University of Rostock, Justus-von-Liebig-Weg 6, 18059, Rostock, Germany
| | - Ralf Uptmoor
- Department of Agronomy, University of Rostock, Justus-von-Liebig-Weg 6, 18059, Rostock, Germany
| | - Matthias Frisch
- Department of Biometry and Population Genetics, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Heinrich-Buff-Ring 26-32, 35392, Giessen, Germany
| | - Gabriel Keeble-Gagnère
- AgriBio, Centre for AgriBioscience, Department of Economic Development, Jobs, Transport and Resources (DEDJTR), Bundoora, Victoria, 3083, Australia
| | - Rudi Appels
- State Agriculture Biotechnology Centre, School of Veterinary and Life Sciences, Murdoch University, Australia Export Grains Innovation Centre (AEGIC), Perth, WA, 6150, Australia
| | - Rod J Snowdon
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Heinrich-Buff-Ring 26-32, 35392, Giessen, Germany
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31
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Wang X, Appels R, Zhang X, Bekes F, Torok K, Tomoskozi S, Diepeveen D, Ma W, Islam S. Protein-transitions in and out of the dough matrix in wheat flour mixing. Food Chem 2017; 217:542-551. [DOI: 10.1016/j.foodchem.2016.08.060] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Revised: 07/20/2016] [Accepted: 08/22/2016] [Indexed: 11/30/2022]
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Kaur P, Appels R, Bayer PE, Keeble-Gagnere G, Wang J, Hirakawa H, Shirasawa K, Vercoe P, Stefanova K, Durmic Z, Nichols P, Revell C, Isobe SN, Edwards D, Erskine W. Climate Clever Clovers: New Paradigm to Reduce the Environmental Footprint of Ruminants by Breeding Low Methanogenic Forages Utilizing Haplotype Variation. Front Plant Sci 2017; 8:1463. [PMID: 28928752 PMCID: PMC5591941 DOI: 10.3389/fpls.2017.01463] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Accepted: 08/07/2017] [Indexed: 05/15/2023]
Abstract
Mitigating methane production by ruminants is a significant challenge to global livestock production. This research offers a new paradigm to reduce methane emissions from ruminants by breeding climate-clever clovers. We demonstrate wide genetic diversity for the trait methanogenic potential in Australia's key pasture legume, subterranean clover (Trifolium subterraneum L.). In a bi-parental population the broadsense heritability in methanogenic potential was moderate (H2 = 0.4) and allelic variation in a region of Chr 8 accounted for 7.8% of phenotypic variation. In a genome-wide association study we identified four loci controlling methanogenic potential assessed by an in vitro fermentation system. Significantly, the discovery of a single nucleotide polymorphism (SNP) on Chr 5 in a defined haplotype block with an upstream putative candidate gene from a plant peroxidase-like superfamily (TSub_g18548) and a downstream lectin receptor protein kinase (TSub_g18549) provides valuable candidates for an assay for this complex trait. In this way haplotype variation can be tracked to breed pastures with reduced methanogenic potential. Of the quantitative trait loci candidates, the DNA-damage-repair/toleration DRT100-like protein (TSub_g26967), linked to avoid the severity of DNA damage induced by secondary metabolites, is considered central to enteric methane production, as are disease resistance (TSub_g26971, TSub_g26972, and TSub_g18549) and ribonuclease proteins (TSub_g26974, TSub_g26975). These proteins are good pointers to elucidate the genetic basis of in vitro microbial fermentability and enteric methanogenic potential in subterranean clover. The genes identified allow the design of a suite of markers for marker-assisted selection to reduce rumen methane emission in selected pasture legumes. We demonstrate the feasibility of a plant breeding approach without compromising animal productivity to mitigate enteric methane emissions, which is one of the most significant challenges to global livestock production.
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Affiliation(s)
- Parwinder Kaur
- Centre for Plant Genetics and Breeding, The University of Western Australia, CrawleyWA, Australia
- School of Agriculture and Environment, The University of Western Australia, CrawleyWA, Australia
- Institute of Agriculture, The University of Western Australia, CrawleyWA, Australia
- Centre for Personalised Medicine for Children, Telethon Kids Institute, SubiacoWA, Australia
- *Correspondence: Parwinder Kaur,
| | | | - Philipp E. Bayer
- School of Biological Sciences, The University of Western Australia, CrawleyWA, Australia
| | | | - Jiankang Wang
- Institute of Crop Science, The National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural SciencesBeijing, China
| | | | | | - Philip Vercoe
- School of Agriculture and Environment, The University of Western Australia, CrawleyWA, Australia
- Institute of Agriculture, The University of Western Australia, CrawleyWA, Australia
| | - Katia Stefanova
- Institute of Agriculture, The University of Western Australia, CrawleyWA, Australia
- Department of Agriculture and Food Western Australia, South PerthWA, Australia
| | - Zoey Durmic
- School of Agriculture and Environment, The University of Western Australia, CrawleyWA, Australia
- Institute of Agriculture, The University of Western Australia, CrawleyWA, Australia
| | - Phillip Nichols
- Centre for Plant Genetics and Breeding, The University of Western Australia, CrawleyWA, Australia
- Department of Agriculture and Food Western Australia, South PerthWA, Australia
| | - Clinton Revell
- Centre for Plant Genetics and Breeding, The University of Western Australia, CrawleyWA, Australia
- Department of Agriculture and Food Western Australia, South PerthWA, Australia
| | | | - David Edwards
- Institute of Agriculture, The University of Western Australia, CrawleyWA, Australia
- School of Biological Sciences, The University of Western Australia, CrawleyWA, Australia
| | - William Erskine
- Centre for Plant Genetics and Breeding, The University of Western Australia, CrawleyWA, Australia
- School of Agriculture and Environment, The University of Western Australia, CrawleyWA, Australia
- Institute of Agriculture, The University of Western Australia, CrawleyWA, Australia
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Hirakawa H, Kaur P, Shirasawa K, Nichols P, Nagano S, Appels R, Erskine W, Isobe SN. Draft genome sequence of subterranean clover, a reference for genus Trifolium. Sci Rep 2016; 6:30358. [PMID: 27545089 PMCID: PMC4992838 DOI: 10.1038/srep30358] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Accepted: 07/04/2016] [Indexed: 11/26/2022] Open
Abstract
Clovers (genus Trifolium) are widely cultivated across the world as forage legumes and make a large contribution to livestock feed production and soil improvement. Subterranean clover (T. subterraneum L.) is well suited for genomic and genetic studies as a reference species in the Trifolium genus, because it is an annual with a simple genome structure (autogamous and diploid), unlike the other economically important perennial forage clovers, red clover (T. pratense) and white clover (T. repens). This report represents the first draft genome sequence of subterranean clover. The 471.8 Mb assembled sequence covers 85.4% of the subterranean clover genome and contains 42,706 genes. Eight pseudomolecules of 401.1 Mb in length were constructed, based on a linkage map consisting of 35,341 SNPs. The comparative genomic analysis revealed that different clover chromosomes showed different degrees of conservation with other Papilionoideae species. These results provide a reference for genetic and genomic analyses in the genus Trifolium and new insights into evolutionary divergence in Papilionoideae species.
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Affiliation(s)
- Hideki Hirakawa
- Kazusa DNA Research Institute, Kazusa-Kamatari 2-6-7, Kisarazu, Chiba 292-0818, Japan
| | - Parwinder Kaur
- Centre for Plant Genetics and Breeding, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia
| | - Kenta Shirasawa
- Kazusa DNA Research Institute, Kazusa-Kamatari 2-6-7, Kisarazu, Chiba 292-0818, Japan
| | - Phillip Nichols
- Department of Agriculture and Food Western Australia, 3 Baron-Hay Court, South Perth, WA 6151, Australia.,School of Plant Biology, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia
| | - Soichiro Nagano
- Kazusa DNA Research Institute, Kazusa-Kamatari 2-6-7, Kisarazu, Chiba 292-0818, Japan
| | - Rudi Appels
- Murdoch University, 90 South Street, Murdoch, WA 6150, Australia
| | - William Erskine
- Centre for Plant Genetics and Breeding, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia
| | - Sachiko N Isobe
- Kazusa DNA Research Institute, Kazusa-Kamatari 2-6-7, Kisarazu, Chiba 292-0818, Japan
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Chen XY, Cao XY, Zhang YJ, Islam S, Zhang JJ, Yang RC, Liu JJ, Li GY, Appels R, Keeble-Gagnere G, Ji WQ, He ZH, Ma WJ. Genetic characterization of cysteine-rich type-b avenin-like protein coding genes in common wheat. Sci Rep 2016; 6:30692. [PMID: 27503660 PMCID: PMC4977551 DOI: 10.1038/srep30692] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Accepted: 07/04/2016] [Indexed: 11/09/2022] Open
Abstract
The wheat avenin-like proteins (ALP) are considered atypical gluten constituents and have shown positive effects on dough properties revealed using a transgenic approach. However, to date the genetic architecture of ALP genes is unclear, making it impossible to be utilized in wheat breeding. In the current study, three genes of type-b ALPs were identified and mapped to chromosomes 7AS, 4AL and 7DS. The coding gene sequence of both TaALP-7A and TaALP-7D was 855 bp long, encoding two identical homologous 284 amino acid long proteins. TaALP-4A was 858 bp long, encoding a 285 amino acid protein variant. Three alleles were identified for TaALP-7A and four for TaALP-4A. TaALP-7A alleles were of two types: type-1, which includes TaALP-7A1 andTaALP-7A2, encodes mature proteins, while type-2, represented byTaALP-7A3, contains a stop codon in the coding region and thus does not encode a mature protein. Dough quality testing of 102 wheat cultivars established a highly significant association of the type-1 TaALP-7A allele with better wheat processing quality. This allelic effects were confirmed among a range of commercial wheat cultivars. Our research makes the ALP be the first of such genetic variation source that can be readily utilized in wheat breeding.
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Affiliation(s)
- X. Y. Chen
- College of Agronomy, Northwest A & F University, Yangling 712100, Shaanxi, China
- Australia-China Joint Centre for Wheat Improvement, School of Veterinary & Life Sciences, Murdoch University, Perth WA 6150, Australia
- Crop Research Institute, Shandong Academy of Agricultural Sciences/National Engineering Laboratory for Wheat and Maize/Key Laboratory of Wheat Biology and Genetic Improvement in North Yellow and Huai River Valley, Ministry of Agriculture, 250100, Jinan China
| | - X. Y. Cao
- Crop Research Institute, Shandong Academy of Agricultural Sciences/National Engineering Laboratory for Wheat and Maize/Key Laboratory of Wheat Biology and Genetic Improvement in North Yellow and Huai River Valley, Ministry of Agriculture, 250100, Jinan China
| | - Y. J. Zhang
- Australia-China Joint Centre for Wheat Improvement, School of Veterinary & Life Sciences, Murdoch University, Perth WA 6150, Australia
| | - S. Islam
- Australia-China Joint Centre for Wheat Improvement, School of Veterinary & Life Sciences, Murdoch University, Perth WA 6150, Australia
| | - J. J. Zhang
- Australia-China Joint Centre for Wheat Improvement, School of Veterinary & Life Sciences, Murdoch University, Perth WA 6150, Australia
| | - R. C. Yang
- Australia-China Joint Centre for Wheat Improvement, School of Veterinary & Life Sciences, Murdoch University, Perth WA 6150, Australia
| | - J. J. Liu
- Crop Research Institute, Shandong Academy of Agricultural Sciences/National Engineering Laboratory for Wheat and Maize/Key Laboratory of Wheat Biology and Genetic Improvement in North Yellow and Huai River Valley, Ministry of Agriculture, 250100, Jinan China
| | - G. Y. Li
- Crop Research Institute, Shandong Academy of Agricultural Sciences/National Engineering Laboratory for Wheat and Maize/Key Laboratory of Wheat Biology and Genetic Improvement in North Yellow and Huai River Valley, Ministry of Agriculture, 250100, Jinan China
| | - R. Appels
- Australia-China Joint Centre for Wheat Improvement, School of Veterinary & Life Sciences, Murdoch University, Perth WA 6150, Australia
| | - G. Keeble-Gagnere
- Australia-China Joint Centre for Wheat Improvement, School of Veterinary & Life Sciences, Murdoch University, Perth WA 6150, Australia
| | - W. Q. Ji
- College of Agronomy, Northwest A & F University, Yangling 712100, Shaanxi, China
| | - Z. H. He
- National Wheat Improvement Centre, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, 12 Zhongguancun South St, Haidian District, Beijing, China 100081
| | - W. J. Ma
- Australia-China Joint Centre for Wheat Improvement, School of Veterinary & Life Sciences, Murdoch University, Perth WA 6150, Australia
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Wang A, Liu L, Peng Y, Islam S, Applebee M, Appels R, Yan Y, Ma W. Identification of Low Molecular Weight Glutenin Alleles by Matrix-Assisted Laser Desorption/Ionization Time-Of-Flight Mass Spectrometry (MALDI-TOF-MS) in Common Wheat (Triticum aestivum L.). PLoS One 2015; 10:e0138981. [PMID: 26407296 PMCID: PMC4583301 DOI: 10.1371/journal.pone.0138981] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Accepted: 09/08/2015] [Indexed: 11/18/2022] Open
Abstract
Low molecular weight glutenin subunits (LMW-GS) play an important role in determining dough properties and breadmaking quality. However, resolution of the currently used methodologies for analyzing LMW-GS is rather low which prevents an efficient use of genetic variations associated with these alleles in wheat breeding. The aim of the current study is to evaluate and develop a rapid, simple, and accurate method to differentiate LMW-GS alleles using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. A set of standard single LMW-GS allele lines as well as a suite of well documented wheat cultivars were collected from France, CIMMYT, and Canada. Method development and optimization were focused on protein extraction procedures and MALDI-TOF instrument settings to generate reproducible diagnostic spectrum peak profiles for each of the known wheat LMW-GS allele. Results revealed a total of 48 unique allele combinations among the studied genotypes. Characteristic MALDI-TOF peak patterns were obtained for 17 common LMW-GS alleles, including 5 (b, a or c, d, e, f), 7 (a, b, c, d or i, f, g, h) and 5 (a, b, c, d, f) patterns or alleles for the Glu-A3, Glu-B3, and Glu-D3 loci, respectively. In addition, some reproducible MALDI-TOF peak patterns were also obtained that did not match with any known alleles. The results demonstrated a high resolution and throughput nature of MALDI-TOF technology in analyzing LMW-GS alleles, which is suitable for application in wheat breeding programs in processing a large number of wheat lines with high accuracy in limited time. It also suggested that the variation of LMW-GS alleles is more abundant than what has been defined by the current nomenclature system that is mainly based on SDS-PAGE system. The MALDI-TOF technology is useful to differentiate these variations. An international joint effort may be needed to assign allele symbols to these newly identified alleles and determine their effects on end-product quality attributes.
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Affiliation(s)
- Aili Wang
- State Agriculture Biotechnology Centre, School of Veterinary & Life Sciences, Murdoch University, Australia Export Grains Innovation Centre (AEGIC), Perth, WA, 6150, Australia
- Key Laboratory of Genetics and Biotechnology, College of Life Science, Capital Normal University, Beijing, 100037, China
| | - Li Liu
- State Agriculture Biotechnology Centre, School of Veterinary & Life Sciences, Murdoch University, Australia Export Grains Innovation Centre (AEGIC), Perth, WA, 6150, Australia
- National Wheat Improvement Centre, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), No. 12 Zhongguancun South Street, Beijing, 100081, China
| | - Yanchun Peng
- State Agriculture Biotechnology Centre, School of Veterinary & Life Sciences, Murdoch University, Australia Export Grains Innovation Centre (AEGIC), Perth, WA, 6150, Australia
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Shahidul Islam
- State Agriculture Biotechnology Centre, School of Veterinary & Life Sciences, Murdoch University, Australia Export Grains Innovation Centre (AEGIC), Perth, WA, 6150, Australia
| | - Marie Applebee
- South Australian Research & Development Institute, Waite Campus, 2b Hartley Grove, Urrbrae, SA, 5064, Australia
| | - Rudi Appels
- State Agriculture Biotechnology Centre, School of Veterinary & Life Sciences, Murdoch University, Australia Export Grains Innovation Centre (AEGIC), Perth, WA, 6150, Australia
| | - Yueming Yan
- Key Laboratory of Genetics and Biotechnology, College of Life Science, Capital Normal University, Beijing, 100037, China
| | - Wujun Ma
- State Agriculture Biotechnology Centre, School of Veterinary & Life Sciences, Murdoch University, Australia Export Grains Innovation Centre (AEGIC), Perth, WA, 6150, Australia
- * E-mail:
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Ma M, Wang Q, Li Z, Cheng H, Li Z, Liu X, Song W, Appels R, Zhao H. Expression of TaCYP78A3, a gene encoding cytochrome P450 CYP78A3 protein in wheat (Triticum aestivum L.), affects seed size. Plant J 2015; 83:312-25. [PMID: 26043144 DOI: 10.1111/tpj.12896] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Revised: 05/15/2015] [Accepted: 05/19/2015] [Indexed: 05/20/2023]
Abstract
Several studies have described quantitative trait loci (QTL) for seed size in wheat, but the relevant genes and molecular mechanisms remain largely unknown. Here we report the functional characterization of the wheat TaCYP78A3 gene and its effect on seed size. TaCYP78A3 encoded wheat cytochrome P450 CYP78A3, and was specifically expressed in wheat reproductive organs. TaCYP78A3 activity was positively correlated with the final seed size. Its silencing caused a reduction of cell number in the seed coat, resulting in an 11% decrease in wheat seed size, whereas TaCYP78A3 over-expression induced production of more cells in the seed coat, leading to an 11-48% increase in Arabidopsis seed size. In addition, the cell number in the final seed coat was determined by the TaCYP78A3 expression level, which affected the extent of integument cell proliferation in the developing ovule and seed. Unfortunately, TaCYP78A3 over-expression in Arabidopsis caused a reduced seed set due to an ovule developmental defect. Moreover, TaCYP78A3 over-expression affected embryo development by promoting embryo integument cell proliferation during seed development, which also ultimately affected the final seed size in Arabidopsis. In summary, our results indicated that TaCYP78A3 plays critical roles in influencing seed size by affecting the extent of integument cell proliferation. The present study provides direct evidence that TaCYP78A3 affects seed size in wheat, and contributes to an understanding of the cellular basis of the gene influencing seed development.
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Affiliation(s)
- Meng Ma
- College of Life Sciences, Northwest A & F University, Yangling, Shaanxi, 712100, China
| | - Qian Wang
- College of Life Sciences, Northwest A & F University, Yangling, Shaanxi, 712100, China
| | - Zhanjie Li
- College of Life Sciences, Northwest A & F University, Yangling, Shaanxi, 712100, China
| | - Huihui Cheng
- College of Life Sciences, Northwest A & F University, Yangling, Shaanxi, 712100, China
| | - Zhaojie Li
- College of Life Sciences, Northwest A & F University, Yangling, Shaanxi, 712100, China
| | - Xiangli Liu
- College of Life Sciences, Northwest A & F University, Yangling, Shaanxi, 712100, China
| | - Weining Song
- State Key Laboratory of Crop Stress Biology in Arid Areas, Northwest A & F University, Yangling, Shaanxi, 712100, China
- College of Agronomy, Northwest A & F University, Yangling, Shaanxi, 712100, China
| | - Rudi Appels
- School of Veterinary and Life Sciences, Murdoch University, South Street, Murdoch, WA, 6150, Australia
| | - Huixian Zhao
- College of Life Sciences, Northwest A & F University, Yangling, Shaanxi, 712100, China
- State Key Laboratory of Crop Stress Biology in Arid Areas, Northwest A & F University, Yangling, Shaanxi, 712100, China
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37
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Wang K, Islam S, Ma J, Anwar M, Chen J, Yan Y, Appels R, Ma W. An improved MALDI-TOF mass spectrometry procedure and a novel DNA marker for identifying over-expressed Bx7 glutenin protein subunit in wheat. Hereditas 2015; 151:196-200. [PMID: 25588305 DOI: 10.1111/hrd2.00069] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2014] [Accepted: 11/11/2014] [Indexed: 11/29/2022] Open
Abstract
Wheat bread-making quality is mainly determined by glutenin proteins in the grain, which exist in a wide range of variable alleles with differential influence on processing attributes. A recently identified allele, Bx7 over-expression (Bx7(oe) ), has been showing highly significant positive effects on wheat dough strength over the normally expressed Bx7 allele. SDS-PAGE and normal RP-HPLC procedures failed to separate the two alleles. In the current study, an extensively optimised MALDI-TOF based procedure and a refined DNA based marker for efficiently differentiating Bx7(oe) from normal Bx7 allele were established. Results indicated that the MALDI-TOF procedure is cost effective, high throughput, and proven reliable, while the refined PCR marker only amplifies Bx7(oe) allele, a clear advantage over the previously developed codominant marker.
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Affiliation(s)
- Ke Wang
- Australia-China Centre for Wheat Improvement, School of Veterinary and Life Sciences, Murdoch University, Perth, WA, Australia; Key Laboratory of Genetics and Biotechnology, College of Life Science, Capital Normal University, Beijing, China
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Appels R, Nystrom J, Webster H, Keeble-Gagnere G. Discoveries and advances in plant and animal genomics. Funct Integr Genomics 2015; 15:121-9. [PMID: 25763751 PMCID: PMC4361718 DOI: 10.1007/s10142-015-0434-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Revised: 02/17/2015] [Accepted: 02/19/2015] [Indexed: 12/04/2022]
Abstract
Plant and animal genomics is a broad area of research with respect to the biological issues covered because it continues to deal with the structure and function of genetic material underpinning all organisms. This mini-review utilizes the plenary lectures from the Plant and Animal Genome Conference as a basis for summarizing the trends in the genome-level studies of organisms.
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Affiliation(s)
- Rudi Appels
- School of Veterinary and Life Sciences, Murdoch University, 90 South Street, Murdoch, Perth, Australia, 6150,
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Zhang J, Xu Y, Chen W, Dell B, Vergauwen R, Biddulph B, Khan N, Luo H, Appels R, Van den Ende W. A wheat 1-FEH w3 variant underlies enzyme activity for stem WSC remobilization to grain under drought. New Phytol 2015; 205:293-305. [PMID: 25250511 DOI: 10.1111/nph.13030] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2014] [Accepted: 07/27/2014] [Indexed: 05/18/2023]
Abstract
In wheat stems, the levels of fructan-dominated water-soluble carbohydrates (WSC) do not always correlate well with grain yield. Field drought experiments were carried out to further explain this lack of correlation. Wheat (Triticum aestivum) varieties, Westonia, Kauz and c. 20 genetically diverse double haploid (DH) lines derived from them were investigated. Substantial genotypic differences in fructan remobilization were found and the 1-FEH w3 gene was shown to be the major contributor in the stem fructan remobilization process based on enzyme activity and gene expression results. A single nucleotide polymorphism (SNP) was detected in an auxin response element in the 1-FEH w3 promoter region, therefore we speculated that the mutated Westonia allele might affect gene expression and enzyme activity levels. A cleaved amplified polymorphic (CAP) marker was generated from the SNP. The harvested results showed that the mutated Westonia 1-FEH w3 allele was associated with a higher thousand grain weight (TGW) under drought conditions in 2011 and 2012. These results indicated that higher gene expression of 1-FEH w3 and 1-FEH w3 mediated enzyme activities that favoured stem WSC remobilization to the grains. The CAP marker residing in the 1-FEH w3 promoter region may facilitate wheat breeding by selecting lines with high stem fructan remobilization capacity under terminal drought.
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Affiliation(s)
- Jingjuan Zhang
- School of Veterinary and Life Sciences, Murdoch University, South Street, Murdoch, WA, 6150, Australia
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Mago R, Tabe L, Vautrin S, Šimková H, Kubaláková M, Upadhyaya N, Berges H, Kong X, Breen J, Doležel J, Appels R, Ellis JG, Spielmeyer W. Major haplotype divergence including multiple germin-like protein genes, at the wheat Sr2 adult plant stem rust resistance locus. BMC Plant Biol 2014; 14:379. [PMID: 25547135 PMCID: PMC4305260 DOI: 10.1186/s12870-014-0379-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2014] [Accepted: 12/11/2014] [Indexed: 05/20/2023]
Abstract
BACKGROUND The adult plant stem rust resistance gene Sr2 was introgressed into hexaploid wheat cultivar (cv) Marquis from tetraploid emmer wheat cv Yaroslav, to generate stem rust resistant cv Hope in the 1920s. Subsequently, Sr2 has been widely deployed and has provided durable partial resistance to all known races of Puccinia graminis f. sp. tritici. This report describes the physical map of the Sr2-carrying region on the short arm of chromosome 3B of cv Hope and compares the Hope haplotype with non-Sr2 wheat cv Chinese Spring. RESULTS Sr2 was located to a region of 867 kb on chromosome 3B in Hope, which corresponded to a region of 567 kb in Chinese Spring. The Hope Sr2 region carried 34 putative genes but only 17 were annotated in the comparable region of Chinese Spring. The two haplotypes differed by extensive DNA sequence polymorphisms between flanking markers as well as by a major insertion/deletion event including ten Germin-Like Protein (GLP) genes in Hope that were absent in Chinese Spring. Haplotype analysis of a limited number of wheat genotypes of interest showed that all wheat genotypes carrying Sr2 possessed the GLP cluster; while, of those lacking Sr2, some, including Marquis, possessed the cluster, while some lacked it. Thus, this region represents a common presence-absence polymorphism in wheat, with presence of the cluster not correlated with presence of Sr2. Comparison of Hope and Marquis GLP genes on 3BS found no polymorphisms in the coding regions of the ten genes but several SNPs in the shared promoter of one divergently transcribed GLP gene pair and a single SNP downstream of the transcribed region of a second GLP. CONCLUSION Physical mapping and sequence comparison showed major haplotype divergence at the Sr2 locus between Hope and Chinese Spring. Candidate genes within the Sr2 region of Hope are being evaluated for the ability to confer stem rust resistance. Based on the detailed mapping and sequencing of the locus, we predict that Sr2 does not belong to the NB-LRR gene family and is not related to previously cloned, race non-specific rust resistance genes Lr34 and Yr36.
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Affiliation(s)
- Rohit Mago
- />CSIRO Agriculture Flagship, Canberra, ACT 2601 Australia
| | - Linda Tabe
- />CSIRO Agriculture Flagship, Canberra, ACT 2601 Australia
| | - Sonia Vautrin
- />INRA – CNRGV, 24 Chemin de Borde Rouge, Auzeville, CS 52627, 31326 Castanet Tolosan Cedex, France
| | - Hana Šimková
- />Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-78371 Olomouc, Czech Republic
| | - Marie Kubaláková
- />Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-78371 Olomouc, Czech Republic
| | | | - Hélène Berges
- />INRA – CNRGV, 24 Chemin de Borde Rouge, Auzeville, CS 52627, 31326 Castanet Tolosan Cedex, France
| | - Xiuying Kong
- />Key Laboratory of Crop Germplasm Resources and Utilization, MOA/Institute of Crop Sciences, CAAS/The Key Facility for Crop Gene Resources and Genetic Improvement, Beijing, 100081 PR China
| | - James Breen
- />Centre for Comparative Genomics, Murdoch University, Murdoch, 6150 WA Australia
- />Current address: Australian Centre for Ancient DNA (ACAD), University of Adelaide, Adelaide, SA 5005 Australia
| | - Jaroslav Doležel
- />Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-78371 Olomouc, Czech Republic
| | - Rudi Appels
- />Centre for Comparative Genomics, Murdoch University, Murdoch, 6150 WA Australia
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Wang S, Wong D, Forrest K, Allen A, Chao S, Huang BE, Maccaferri M, Salvi S, Milner SG, Cattivelli L, Mastrangelo AM, Whan A, Stephen S, Barker G, Wieseke R, Plieske J, Lillemo M, Mather D, Appels R, Dolferus R, Brown-Guedira G, Korol A, Akhunova AR, Feuillet C, Salse J, Morgante M, Pozniak C, Luo MC, Dvorak J, Morell M, Dubcovsky J, Ganal M, Tuberosa R, Lawley C, Mikoulitch I, Cavanagh C, Edwards KJ, Hayden M, Akhunov E. Characterization of polyploid wheat genomic diversity using a high-density 90,000 single nucleotide polymorphism array. Plant Biotechnol J 2014; 12:787-796. [PMID: 24646323 DOI: 10.1111/pbi.12183/pdf] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Received: 10/29/2013] [Revised: 01/29/2014] [Accepted: 02/05/2014] [Indexed: 05/29/2023]
Abstract
High-density single nucleotide polymorphism (SNP) genotyping arrays are a powerful tool for studying genomic patterns of diversity, inferring ancestral relationships between individuals in populations and studying marker-trait associations in mapping experiments. We developed a genotyping array including about 90,000 gene-associated SNPs and used it to characterize genetic variation in allohexaploid and allotetraploid wheat populations. The array includes a significant fraction of common genome-wide distributed SNPs that are represented in populations of diverse geographical origin. We used density-based spatial clustering algorithms to enable high-throughput genotype calling in complex data sets obtained for polyploid wheat. We show that these model-free clustering algorithms provide accurate genotype calling in the presence of multiple clusters including clusters with low signal intensity resulting from significant sequence divergence at the target SNP site or gene deletions. Assays that detect low-intensity clusters can provide insight into the distribution of presence-absence variation (PAV) in wheat populations. A total of 46 977 SNPs from the wheat 90K array were genetically mapped using a combination of eight mapping populations. The developed array and cluster identification algorithms provide an opportunity to infer detailed haplotype structure in polyploid wheat and will serve as an invaluable resource for diversity studies and investigating the genetic basis of trait variation in wheat.
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Affiliation(s)
- Shichen Wang
- Department of Plant Pathology, Kansas State University, Manhattan, KS, USA
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Wang S, Wong D, Forrest K, Allen A, Chao S, Huang BE, Maccaferri M, Salvi S, Milner SG, Cattivelli L, Mastrangelo AM, Whan A, Stephen S, Barker G, Wieseke R, Plieske J, Lillemo M, Mather D, Appels R, Dolferus R, Brown‐Guedira G, Korol A, Akhunova AR, Feuillet C, Salse J, Morgante M, Pozniak C, Luo M, Dvorak J, Morell M, Dubcovsky J, Ganal M, Tuberosa R, Lawley C, Mikoulitch I, Cavanagh C, Edwards KJ, Hayden M, Akhunov E. Characterization of polyploid wheat genomic diversity using a high‐density 90 000 single nucleotide polymorphism array. Plant Biotechnol J 2014; 12:787-96. [PMID: 24646323 PMCID: PMC4265271 DOI: 10.1111/pbi.12183] [Citation(s) in RCA: 1067] [Impact Index Per Article: 106.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2013] [Revised: 01/29/2014] [Accepted: 02/05/2014] [Indexed: 05/18/2023]
Affiliation(s)
- Shichen Wang
- Department of Plant Pathology Kansas State University Manhattan KS USA
| | - Debbie Wong
- Department of Environment and Primary Industry AgriBioSciences La Trobe R&D Park Bundoora Vic. Australia
| | - Kerrie Forrest
- Department of Environment and Primary Industry AgriBioSciences La Trobe R&D Park Bundoora Vic. Australia
| | - Alexandra Allen
- School of Biological Sciences University of Bristol Bristol UK
| | - Shiaoman Chao
- US Department of Agriculture–Agricultural Research Service Biosciences Research Laboratory Fargo ND USA
| | - Bevan E. Huang
- Commonwealth Scientific and Industrial Research Organization Computational Informatics and Food Futures National Research Flagship Dutton Park Qld Australia
| | - Marco Maccaferri
- Department of Agricultural Sciences University of Bologna Bologna Italy
| | - Silvio Salvi
- Department of Agricultural Sciences University of Bologna Bologna Italy
| | - Sara G. Milner
- Department of Agricultural Sciences University of Bologna Bologna Italy
| | - Luigi Cattivelli
- Consiglio per la Ricerca e la sperimentazione in Agricoltura Genomics Research Centre Fiorenzuola d'arda Italy
| | - Anna M. Mastrangelo
- Consiglio per la Ricerca e la sperimentazione in Agricoltura Cereal Research Centre Foggia Italy
| | - Alex Whan
- Commonwealth Scientific and Industrial Research Organization Plant Industry and Food Futures National Research Flagship Canberra ACT Australia
| | - Stuart Stephen
- Commonwealth Scientific and Industrial Research Organization Plant Industry and Food Futures National Research Flagship Canberra ACT Australia
| | - Gary Barker
- School of Biological Sciences University of Bristol Bristol UK
| | | | | | - Morten Lillemo
- Department of Plant Sciences Norwegian University of Life Sciences Ås Norway
| | - Diane Mather
- Waite Research Institute School of Agriculture, Food and Wine University of Adelaide Urrbrae SA Australia
| | | | - Rudy Dolferus
- Commonwealth Scientific and Industrial Research Organization Plant Industry and Food Futures National Research Flagship Canberra ACT Australia
| | - Gina Brown‐Guedira
- US Department of Agriculture–Agricultural Research Service Eastern Regional Small Grains Genotyping Laboratory Raleigh NC USA
| | - Abraham Korol
- Department of Evolutionary and Environmental Biology and Institute of Evolution University of Haifa Mount Carmel Haifa Israel
| | - Alina R. Akhunova
- K‐State Integrated Genomics Facility Kansas State University Manhattan KS USA
| | - Catherine Feuillet
- INRA – Université Blaise Pascal, UMR 1095 Genetics Diversity and Ecophysiology of Cereals Clermont‐Ferrand France
| | - Jerome Salse
- INRA – Université Blaise Pascal, UMR 1095 Genetics Diversity and Ecophysiology of Cereals Clermont‐Ferrand France
| | - Michele Morgante
- Department of Crop and Environmental Sciences University of Udine Via delle Scienze Udine Italy
| | - Curtis Pozniak
- Crop Development Centre and Department of Plant Sciences University of Saskatchewan Saskatoon SK Canada
| | - Ming‐Cheng Luo
- Department of Plant Sciences University of California Davis CA USA
| | - Jan Dvorak
- Department of Plant Sciences University of California Davis CA USA
| | - Matthew Morell
- Commonwealth Scientific and Industrial Research Organization Plant Industry and Food Futures National Research Flagship Canberra ACT Australia
| | - Jorge Dubcovsky
- Department of Plant Sciences University of California Davis CA USA
- Howard Hughes Medical Institute Chevy Chase MD USA
| | | | - Roberto Tuberosa
- Department of Agricultural Sciences University of Bologna Bologna Italy
| | | | | | - Colin Cavanagh
- Commonwealth Scientific and Industrial Research Organization Plant Industry and Food Futures National Research Flagship Canberra ACT Australia
| | | | - Matthew Hayden
- Department of Environment and Primary Industry AgriBioSciences La Trobe R&D Park Bundoora Vic. Australia
| | - Eduard Akhunov
- Department of Plant Pathology Kansas State University Manhattan KS USA
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Rasheed A, Xia X, Yan Y, Appels R, Mahmood T, He Z. Wheat seed storage proteins: Advances in molecular genetics, diversity and breeding applications. J Cereal Sci 2014. [DOI: 10.1016/j.jcs.2014.01.020] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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Ouyang S, Zhang D, Han J, Zhao X, Cui Y, Song W, Huo N, Liang Y, Xie J, Wang Z, Wu Q, Chen YX, Lu P, Zhang DY, Wang L, Sun H, Yang T, Keeble-Gagnere G, Appels R, Doležel J, Ling HQ, Luo M, Gu Y, Sun Q, Liu Z. Fine physical and genetic mapping of powdery mildew resistance gene MlIW172 originating from wild emmer (Triticum dicoccoides). PLoS One 2014; 9:e100160. [PMID: 24955773 PMCID: PMC4067302 DOI: 10.1371/journal.pone.0100160] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2014] [Accepted: 05/22/2014] [Indexed: 11/18/2022] Open
Abstract
Powdery mildew, caused by Blumeria graminis f. sp. tritici, is one of the most important wheat diseases in the world. In this study, a single dominant powdery mildew resistance gene MlIW172 was identified in the IW172 wild emmer accession and mapped to the distal region of chromosome arm 7AL (bin7AL-16-0.86-0.90) via molecular marker analysis. MlIW172 was closely linked with the RFLP probe Xpsr680-derived STS marker Xmag2185 and the EST markers BE405531 and BE637476. This suggested that MlIW172 might be allelic to the Pm1 locus or a new locus closely linked to Pm1. By screening genomic BAC library of durum wheat cv. Langdon and 7AL-specific BAC library of hexaploid wheat cv. Chinese Spring, and after analyzing genome scaffolds of Triticum urartu containing the marker sequences, additional markers were developed to construct a fine genetic linkage map on the MlIW172 locus region and to delineate the resistance gene within a 0.48 cM interval. Comparative genetics analyses using ESTs and RFLP probe sequences flanking the MlIW172 region against other grass species revealed a general co-linearity in this region with the orthologous genomic regions of rice chromosome 6, Brachypodium chromosome 1, and sorghum chromosome 10. However, orthologous resistance gene-like RGA sequences were only present in wheat and Brachypodium. The BAC contigs and sequence scaffolds that we have developed provide a framework for the physical mapping and map-based cloning of MlIW172.
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Affiliation(s)
- Shuhong Ouyang
- State Key Laboratory for Agrobiotechnology/Beijing Key Laboratory of Crop Genetic Improvement/Key Laboratory of Crop Heterosis Research & Utilization, Ministry of Education, China Agricultural University, Beijing, China
| | - Dong Zhang
- State Key Laboratory for Agrobiotechnology/Beijing Key Laboratory of Crop Genetic Improvement/Key Laboratory of Crop Heterosis Research & Utilization, Ministry of Education, China Agricultural University, Beijing, China
| | - Jun Han
- State Key Laboratory for Agrobiotechnology/Beijing Key Laboratory of Crop Genetic Improvement/Key Laboratory of Crop Heterosis Research & Utilization, Ministry of Education, China Agricultural University, Beijing, China
- Agriculture University of Beijing, Beijing, China
| | - Xiaojie Zhao
- State Key Laboratory for Agrobiotechnology/Beijing Key Laboratory of Crop Genetic Improvement/Key Laboratory of Crop Heterosis Research & Utilization, Ministry of Education, China Agricultural University, Beijing, China
| | - Yu Cui
- State Key Laboratory for Agrobiotechnology/Beijing Key Laboratory of Crop Genetic Improvement/Key Laboratory of Crop Heterosis Research & Utilization, Ministry of Education, China Agricultural University, Beijing, China
| | - Wei Song
- State Key Laboratory for Agrobiotechnology/Beijing Key Laboratory of Crop Genetic Improvement/Key Laboratory of Crop Heterosis Research & Utilization, Ministry of Education, China Agricultural University, Beijing, China
- Maize Research Center, Beijing Academy of Agricultural and Forestry Sciences, Beijing, China
| | - Naxin Huo
- USDA-ARS West Regional Research Center, Albany, California, United States of America
| | - Yong Liang
- State Key Laboratory for Agrobiotechnology/Beijing Key Laboratory of Crop Genetic Improvement/Key Laboratory of Crop Heterosis Research & Utilization, Ministry of Education, China Agricultural University, Beijing, China
| | - Jingzhong Xie
- State Key Laboratory for Agrobiotechnology/Beijing Key Laboratory of Crop Genetic Improvement/Key Laboratory of Crop Heterosis Research & Utilization, Ministry of Education, China Agricultural University, Beijing, China
| | - Zhenzhong Wang
- State Key Laboratory for Agrobiotechnology/Beijing Key Laboratory of Crop Genetic Improvement/Key Laboratory of Crop Heterosis Research & Utilization, Ministry of Education, China Agricultural University, Beijing, China
| | - Qiuhong Wu
- State Key Laboratory for Agrobiotechnology/Beijing Key Laboratory of Crop Genetic Improvement/Key Laboratory of Crop Heterosis Research & Utilization, Ministry of Education, China Agricultural University, Beijing, China
| | - Yong-Xing Chen
- State Key Laboratory for Agrobiotechnology/Beijing Key Laboratory of Crop Genetic Improvement/Key Laboratory of Crop Heterosis Research & Utilization, Ministry of Education, China Agricultural University, Beijing, China
| | - Ping Lu
- State Key Laboratory for Agrobiotechnology/Beijing Key Laboratory of Crop Genetic Improvement/Key Laboratory of Crop Heterosis Research & Utilization, Ministry of Education, China Agricultural University, Beijing, China
| | - De-Yun Zhang
- State Key Laboratory for Agrobiotechnology/Beijing Key Laboratory of Crop Genetic Improvement/Key Laboratory of Crop Heterosis Research & Utilization, Ministry of Education, China Agricultural University, Beijing, China
| | - Lili Wang
- State Key Laboratory for Agrobiotechnology/Beijing Key Laboratory of Crop Genetic Improvement/Key Laboratory of Crop Heterosis Research & Utilization, Ministry of Education, China Agricultural University, Beijing, China
| | - Hua Sun
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institutes of Genetics & Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Tsomin Yang
- State Key Laboratory for Agrobiotechnology/Beijing Key Laboratory of Crop Genetic Improvement/Key Laboratory of Crop Heterosis Research & Utilization, Ministry of Education, China Agricultural University, Beijing, China
| | | | - Rudi Appels
- Murdoch University, Perth, Western Australia, Australia
| | - Jaroslav Doležel
- Institute of Experimental Botany, Centre of Plant Structural and Functional Genomics, Olomouc, Czech Republic
| | - Hong-Qing Ling
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institutes of Genetics & Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Mingcheng Luo
- Department of Plant Sciences, University of California, Davis, Davis, California, United States of America
| | - Yongqiang Gu
- USDA-ARS West Regional Research Center, Albany, California, United States of America
| | - Qixin Sun
- State Key Laboratory for Agrobiotechnology/Beijing Key Laboratory of Crop Genetic Improvement/Key Laboratory of Crop Heterosis Research & Utilization, Ministry of Education, China Agricultural University, Beijing, China
| | - Zhiyong Liu
- State Key Laboratory for Agrobiotechnology/Beijing Key Laboratory of Crop Genetic Improvement/Key Laboratory of Crop Heterosis Research & Utilization, Ministry of Education, China Agricultural University, Beijing, China
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Abstract
The area of plant and animal genomics covers the entire suite of issues in biology because it aims to determine the structure and function of genetic material. Although specific issues define research advances at an organism level, it is evident that many of the fundamental features of genome structure and the translation of encoded information to function share common ground. The Plant and Animal Genome (PAG) conference held in San Diego (California), in January each year provides an overview across all organisms at the genome level, and often it is evident that investments in the human area provide leadership, applications, and discoveries for researchers studying other organisms. This mini-review utilizes the plenary lectures as a basis for summarizing the trends in the genome-level studies of organisms, and the lectures include presentations by Ewan Birney (EBI, UK), Eric Green (NIH, USA), John Butler (NIST, USA), Elaine Mardis (Washington, USA), Caroline Dean (John Innes Centre, UK), Trudy Mackay (NC State University, USA), Sue Wessler (UC Riverside, USA), and Patrick Wincker (Genoscope, France). The work reviewed is based on published papers. Where unpublished information is cited, permission to include the information in this manuscript was obtained from the presenters.
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Affiliation(s)
- R Appels
- Veterinary and Life Sciences, Murdoch University, 90 South Street, Murdoch, Perth, WA, 6150, Australia,
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46
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Lv DW, Subburaj S, Cao M, Yan X, Li X, Appels R, Sun DF, Ma W, Yan YM. Proteome and phosphoproteome characterization reveals new response and defense mechanisms of Brachypodium distachyon leaves under salt stress. Mol Cell Proteomics 2014; 13:632-52. [PMID: 24335353 PMCID: PMC3916659 DOI: 10.1074/mcp.m113.030171] [Citation(s) in RCA: 107] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2013] [Revised: 11/22/2013] [Indexed: 11/27/2022] Open
Abstract
Salinity is a major abiotic stress affecting plant growth and development. Understanding the molecular mechanisms of salt response and defense in plants will help in efforts to improve the salt tolerance of crops. Brachypodium distachyon is a new model plant for wheat, barley, and several potential biofuel grasses. In the current study, proteome and phosphoproteome changes induced by salt stress were the focus. The Bd21 leaves were initially treated with salt in concentrations ranging from 80 to 320 mm and then underwent a recovery process prior to proteome analysis. A total of 80 differentially expressed protein spots corresponding to 60 unique proteins were identified. The sample treated with a median salt level of 240 mm and the control were selected for phosphopeptide purification using TiO2 microcolumns and LC-MS/MS for phosphoproteome analysis to identify the phosphorylation sites and phosphoproteins. A total of 1509 phosphoproteins and 2839 phosphorylation sites were identified. Among them, 468 phosphoproteins containing 496 phosphorylation sites demonstrated significant changes at the phosphorylation level. Nine phosphorylation motifs were extracted from the 496 phosphorylation sites. Of the 60 unique differentially expressed proteins, 14 were also identified as phosphoproteins. Many proteins and phosphoproteins, as well as potential signal pathways associated with salt response and defense, were found, including three 14-3-3s (GF14A, GF14B, and 14-3-3A) for signal transduction and several ABA signal-associated proteins such as ABF2, TRAB1, and SAPK8. Finally, a schematic salt response and defense mechanism in B. distachyon was proposed.
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Affiliation(s)
- Dong-Wen Lv
- From the ‡College of Life Science, Capital Normal University, 100048 Beijing, China
| | - Saminathan Subburaj
- From the ‡College of Life Science, Capital Normal University, 100048 Beijing, China
| | - Min Cao
- From the ‡College of Life Science, Capital Normal University, 100048 Beijing, China
| | - Xing Yan
- From the ‡College of Life Science, Capital Normal University, 100048 Beijing, China
| | - Xiaohui Li
- From the ‡College of Life Science, Capital Normal University, 100048 Beijing, China
| | - Rudi Appels
- §State Agriculture Biotechnology Centre, Murdoch University and Western Australian Department of Agriculture and Food, Perth, WA 6150, Australia
| | - Dong-Fa Sun
- ¶College of Plant Science and Technology, Huazhong Agricultural University, 430070 Wuhan, China
| | - Wujun Ma
- §State Agriculture Biotechnology Centre, Murdoch University and Western Australian Department of Agriculture and Food, Perth, WA 6150, Australia
| | - Yue-Ming Yan
- From the ‡College of Life Science, Capital Normal University, 100048 Beijing, China
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Oszvald M, Balázs G, Pólya S, Tömösközi S, Appels R, Békés F, Tamás L. Wheat storage proteins in transgenic rice endosperm. J Agric Food Chem 2013; 61:7606-7614. [PMID: 23802557 DOI: 10.1021/jf402035n] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Transgenic rice seed expressing wheat HMW glutenin subunit was characterized to study the effects of the wheat prolamin on the protein expression pattern and protein size distribution in the endosperm and the functional and rheological properties of the rice flour and dough. Significant differences were found in the protein expression pattern between the transgenic and wild type samples. Comparing the protein expression profiles of transgenic and nontransgenic plants, combined with proteomic-based studies, indicated increased protein disulfide isomerase (PDI) levels in the transgenic rice lines. The accurate molecular size of HMW-GS in rice endosperm was identified by MALDI-TOF-MS analysis. The expressed wheat HMW (subunit 1Dx5) GS showed a positive effect on the functional properties of rice dough by significantly increasing the size distribution of the polymeric protein fraction and modifying the dough mixing parameters.
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Affiliation(s)
- Mária Oszvald
- Department of Plant Physiology and Molecular Plant Biology, Eötvös Loránd University , Budapest, Hungary
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Appels R, Barrero R, Bellgard M. Advances in biotechnology and informatics to link variation in the genome to phenotypes in plants and animals. Funct Integr Genomics 2013; 13:1-9. [PMID: 23494190 PMCID: PMC3605488 DOI: 10.1007/s10142-013-0319-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2013] [Revised: 03/02/2013] [Accepted: 03/03/2013] [Indexed: 11/27/2022]
Abstract
Advances in our understanding of genome structure provide consistent evidence for the existence of a core genome representing species classically defined by phenotype, as well as conditionally dispensable components of the genome that shows extensive variation between individuals of a given species. Generally, conservation of phenotypic features between species reflects conserved features of the genome; however, this is evidently not necessarily always the case as demonstrated by the analysis of the tunicate chordate Oikopleura dioica. In both plants and animals, the methylation activity of DNA and histones continues to present new variables for modifying (eventually) the phenotype of an organism and provides for structural variation that builds on the point mutations, rearrangements, indels, and amplification of retrotransposable elements traditionally considered. The translation of the advances in the structure/function analysis of the genome to industry is facilitated through the capture of research outputs in "toolboxes" that remain accessible in the public domain.
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Affiliation(s)
- R. Appels
- Centre for Comparative Genomics, Murdoch University, Perth, WA 6150 Australia
| | - R. Barrero
- Centre for Comparative Genomics, Murdoch University, Perth, WA 6150 Australia
| | - M. Bellgard
- Centre for Comparative Genomics, Murdoch University, Perth, WA 6150 Australia
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Wang S, Wang K, Chen G, Lv D, Han X, Yu Z, Li X, Ye X, Hsam SLK, Ma W, Appels R, Yan Y. Molecular characterization of LMW-GS genes in Brachypodium distachyon L. reveals highly conserved Glu-3 loci in Triticum and related species. BMC Plant Biol 2012; 12:221. [PMID: 23171363 PMCID: PMC3547698 DOI: 10.1186/1471-2229-12-221] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2012] [Accepted: 10/30/2012] [Indexed: 05/08/2023]
Abstract
BACKGROUND Brachypodium distachyon L. is a newly emerging model plant system for temperate cereal crop species. However, its grain protein compositions are still not clear. In the current study, we carried out a detailed proteomics and molecular genetics study on grain glutenin proteins in B. distachyon. RESULTS SDS-PAGE and RP-HPLC analysis of grain proteins showed that Brachypodium has few gliadins and high molecular weight glutenin subunits. In contrast the electrophoretic patterns for the albumin, globulin and low molecular weight glutenin subunit (LMW-GS) fractions of the grain protein were similar to those in wheat. In particular, the LMW-C type subunits in Brachypodium were more abundant than the equivalent proteins in common wheat. Southern blotting analysis confirmed that Brachypodium has 4-5 copies of LMW-GS genes. A total of 18 LMW-GS genes were cloned from Brachypodium by allele specific PCR. LMW-GS and 4 deduced amino acid sequences were further confirmed by using Western-blotting and MALDI-TOF-MS. Phylogenetic analysis indicated that Brachypodium was closer to Ae. markgrafii and Ae. umbellulata than to T. aestivum. CONCLUSIONS Brachypodium possessed a highly conserved Glu-3 locus that is closely related to Triticum and related species. The presence of LMW-GS in B. distachyon grains indicates that B. distachyon may be used as a model system for studying wheat quality attributes.
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Affiliation(s)
- Shunli Wang
- Key Laboratory of Genetics and Biotechnology, College of Life Science, Capital Normal University, 100048, Beijing, China
| | - Ke Wang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, 100081, Beijing, China
| | - Guanxing Chen
- Key Laboratory of Genetics and Biotechnology, College of Life Science, Capital Normal University, 100048, Beijing, China
| | - Dongwen Lv
- Key Laboratory of Genetics and Biotechnology, College of Life Science, Capital Normal University, 100048, Beijing, China
| | - Xiaofeng Han
- Key Laboratory of Genetics and Biotechnology, College of Life Science, Capital Normal University, 100048, Beijing, China
| | - Zitong Yu
- Key Laboratory of Genetics and Biotechnology, College of Life Science, Capital Normal University, 100048, Beijing, China
| | - Xiaohui Li
- Key Laboratory of Genetics and Biotechnology, College of Life Science, Capital Normal University, 100048, Beijing, China
| | - Xingguo Ye
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, 100081, Beijing, China
| | - SLK Hsam
- Division of Plant Breeding and Applied Genetics, Technical University of Munich, D-85350, Freising-Weihenstephan, Germany
| | - Wujun Ma
- State Agriculture Biotechnology Centre, Murdoch University; Western Australian Department of Agriculture and Food, Perth, WA, 6150, Australia
| | - Rudi Appels
- State Agriculture Biotechnology Centre, Murdoch University; Western Australian Department of Agriculture and Food, Perth, WA, 6150, Australia
| | - Yueming Yan
- Key Laboratory of Genetics and Biotechnology, College of Life Science, Capital Normal University, 100048, Beijing, China
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Feuillet C, Stein N, Rossini L, Praud S, Mayer K, Schulman A, Eversole K, Appels R. Integrating cereal genomics to support innovation in the Triticeae. Funct Integr Genomics 2012. [PMID: 23161406 DOI: 10.1007/s10142‐012‐0300‐5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The genomic resources of small grain cereals that include some of the most important crop species such as wheat, barley, and rye are attaining a level of completion that now is contributing to new structural and functional studies as well as refining molecular marker development and mapping strategies for increasing the efficiency of breeding processes. The integration of new efforts to obtain reference sequences in bread wheat and barley, in particular, is accelerating the acquisition and interpretation of genome-level analyses in both of these major crops.
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Affiliation(s)
- C Feuillet
- INRA-UBP UMR 1095 Genetics and Diversity of Cereals, Clermont-Ferrand, France.
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