1501
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Rawat N, Schoen A, Singh L, Mahlandt A, Wilson DL, Liu S, Lin G, Gill BS, Tiwari VK. TILL-D: An Aegilops tauschii TILLING Resource for Wheat Improvement. FRONTIERS IN PLANT SCIENCE 2018; 9:1665. [PMID: 30487809 PMCID: PMC6246738 DOI: 10.3389/fpls.2018.01665] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Accepted: 10/26/2018] [Indexed: 05/28/2023]
Abstract
Aegilops tauschii (2n = 2x = 14, genome DD), also known as Tausch's goatgrass, is the D genome donor of bread or hexaploid wheat Triticum aestivum (2n = 2x = 42, AABBDD genome). It is a rich reservoir of useful genes for biotic and abiotic stress tolerance for wheat improvement. We developed a TILLING (Targeting Induced Local Lesions In Genomes) resource for Ae. tauschii for discovery and validation of useful genes in the D genome of wheat. The population, referred to as TILL-D, was developed with ethyl methanesulfonate (EMS) mutagen. The survival rate in M1 generation was 73%, out of which 22% plants were sterile. In the M2 generation 25% of the planted seeds showed phenotypic mutations such as albinos, chlorinas, no germination, variegated, sterile and partially fertile events, and 2,656 produced fertile M2 plants. The waxy gene was used to calculate the mutation frequency (1/70 kb) of the developed population, which was found to be higher than known mutation frequencies for diploid plants (1/89-1/1000 kb), but lower than that for a polyploid species (1/24-1/51 kb). The TILL-D resource, together with the newly published Ae. tauschii reference genome sequence, will facilitate gene discoveries and validations of agronomically important traits and their eventual fine transfer in bread wheat.
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Affiliation(s)
- Nidhi Rawat
- Plant Science and Landscape Architecture Department, University of Maryland, College Park, College Park, MD, United States
| | - Adam Schoen
- Plant Science and Landscape Architecture Department, University of Maryland, College Park, College Park, MD, United States
| | - Lovepreet Singh
- Plant Science and Landscape Architecture Department, University of Maryland, College Park, College Park, MD, United States
| | - Alexander Mahlandt
- Plant Science and Landscape Architecture Department, University of Maryland, College Park, College Park, MD, United States
| | - Duane L. Wilson
- Plant Pathology Department, Kansas State University, Manhattan, KS, United States
| | - Sanzhen Liu
- Plant Pathology Department, Kansas State University, Manhattan, KS, United States
| | - Guifang Lin
- Plant Pathology Department, Kansas State University, Manhattan, KS, United States
| | - Bikram S. Gill
- Plant Pathology Department, Kansas State University, Manhattan, KS, United States
| | - Vijay K. Tiwari
- Plant Pathology Department, Kansas State University, Manhattan, KS, United States
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1502
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Doležel J, Čížková J, Šimková H, Bartoš J. One Major Challenge of Sequencing Large Plant Genomes Is to Know How Big They Really Are. Int J Mol Sci 2018; 19:ijms19113554. [PMID: 30423889 PMCID: PMC6274785 DOI: 10.3390/ijms19113554] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Revised: 11/03/2018] [Accepted: 11/06/2018] [Indexed: 11/16/2022] Open
Abstract
Any project seeking to deliver a plant or animal reference genome sequence must address the question as to the completeness of the assembly. Given the complexity introduced particularly by the presence of sequence redundancy, a problem which is especially acute in polyploid genomes, this question is not an easy one to answer. One approach is to use the sequence data, along with the appropriate computational tools, the other is to compare the estimate of genome size with an experimentally measured mass of nuclear DNA. The latter requires a reference standard in order to provide a robust relationship between the two independent measurements of genome size. Here, the proposal is to choose the human male leucocyte genome for this standard: its 1C DNA amount (the amount of DNA contained within unreplicated haploid chromosome set) of 3.50 pg is equivalent to a genome length of 3.423 Gbp, a size which is just 5% longer than predicted by the most current human genome assembly. Adopting this standard, this paper assesses the completeness of the reference genome assemblies of the leading cereal crops species wheat, barley and rye.
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Affiliation(s)
- 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.
| | - Hana Šimková
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-78371 Olomouc, Czech Republic.
| | - Jan Bartoš
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-78371 Olomouc, Czech Republic.
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1503
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N’Diaye A, Haile JK, Nilsen KT, Walkowiak S, Ruan Y, Singh AK, Clarke FR, Clarke JM, Pozniak CJ. Haplotype Loci Under Selection in Canadian Durum Wheat Germplasm Over 60 Years of Breeding: Association With Grain Yield, Quality Traits, Protein Loss, and Plant Height. FRONTIERS IN PLANT SCIENCE 2018; 9:1589. [PMID: 30455711 PMCID: PMC6230583 DOI: 10.3389/fpls.2018.01589] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Accepted: 10/15/2018] [Indexed: 05/21/2023]
Abstract
Durum wheat was introduced in the southern prairies of western Canada in the late nineteenth century. Breeding efforts have mainly focused on improving quality traits to meet the pasta industry demands. For this study, 192 durum wheat lines were genotyped using the Illumina 90K Infinium iSelect assay, and resulted in a total of 14,324 polymorphic SNPs. Genetic diversity changed over time, declining during the first 20 years of breeding in Canada, then increased in the late 1980s and early 1990s. We scanned the genome for signatures of selection, using the total variance Fst-based outlier detection method (Lositan), the hierarchical island model (Arlequin) and the Bayesian genome scan method (BayeScan). A total of 407 outliers were identified and clustered into 84 LD-based haplotype loci, spanning all 14 chromosomes of the durum wheat genome. The association analysis detected 54 haplotype loci, of which 39% contained markers with a complete reversal of allelic state. This tendency to fixation of favorable alleles corroborates the success of the Canadian durum wheat breeding programs over time. Twenty-one haplotype loci were associated with multiple traits. In particular, hap_4B_1 explained 20.6, 17.9 and 16.6% of the phenotypic variance of pigment loss, pasta b∗ and dough extensibility, respectively. The locus hap_2B_9 explained 15.9 and 17.8% of the variation of protein content and protein loss, respectively. All these pleiotropic haplotype loci offer breeders the unique opportunity for further improving multiple traits, facilitating marker-assisted selection in durum wheat, and could help in identifying genes as functional annotations of the wheat genome become available.
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Affiliation(s)
- Amidou N’Diaye
- Department of Plant Sciences, Crop Development Centre, University of Saskatchewan, Saskatoon, SK, Canada
| | - Jemanesh K. Haile
- Department of Plant Sciences, Crop Development Centre, University of Saskatchewan, Saskatoon, SK, Canada
| | - Kirby T. Nilsen
- Department of Plant Sciences, Crop Development Centre, University of Saskatchewan, Saskatoon, SK, Canada
| | - Sean Walkowiak
- Department of Plant Sciences, Crop Development Centre, University of Saskatchewan, Saskatoon, SK, Canada
| | - Yuefeng Ruan
- Agriculture and Agri-Food Canada, Swift Current Research and Development Centre, Swift Current, SK, Canada
| | - Asheesh K. Singh
- Department of Agronomy, Iowa State University, Ames, IA, United States
| | - Fran R. Clarke
- Agriculture and Agri-Food Canada, Swift Current Research and Development Centre, Swift Current, SK, Canada
| | - John M. Clarke
- Department of Plant Sciences, Crop Development Centre, University of Saskatchewan, Saskatoon, SK, Canada
| | - Curtis J. Pozniak
- Department of Plant Sciences, Crop Development Centre, University of Saskatchewan, Saskatoon, SK, Canada
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1504
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Melino VJ, Casartelli A, George J, Rupasinghe T, Roessner U, Okamoto M, Heuer S. RNA Catabolites Contribute to the Nitrogen Pool and Support Growth Recovery of Wheat. FRONTIERS IN PLANT SCIENCE 2018; 9:1539. [PMID: 30455708 PMCID: PMC6230992 DOI: 10.3389/fpls.2018.01539] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 10/01/2018] [Indexed: 05/23/2023]
Abstract
Turn-over of RNA and catabolism of nucleotides releases one to four ammonia molecules; the released nutrients being reassimilated into primary metabolism. Preliminary evidence indicates that monocots store high levels of free nucleotides and nucleosides but their potential as a source of internal organic nitrogen for use and remobilization is uncharted. Early tillering wheat plants were therefore starved of N over a 5-day time-course with examination of nucleic acid yields in whole shoots, young and old leaves and roots. Nucleic acids constituted ∼4% of the total N pool of N starved wheat plants, which was comparable with the N available from nitrate (NO3 -) and greater than that available from the sum of 20 proteinogenic amino acids. Methods were optimized to detect nucleotide (purine and pyrimidine) metabolites, and wheat orthologs of RNA degradation (TaRNS), nucleoside transport (TaENT1, TaENT3) and salvage (TaADK) were identified. It was found that N starved wheat roots actively catabolised RNA and specific purines but accumulated pyrimidines. Reduced levels of RNA corresponded with induction of TaRNS2, TaENT1, TaENT3, and TaADK in the roots. Reduced levels of GMP, guanine, xanthine, allantoin, allantoate and glyoxylate in N starved roots correlated with accumulation of allantoate and glyoxylate in the oldest leaf, suggesting translocation of allantoin. Furthermore, N starved wheat plants exogenously supplied with N in the form of purine catabolites grew and photosynthesized as well as those plants re-supplied with NO3 -. These results support the hypothesis that the nitrogen and carbon recovered from purine metabolism can support wheat growth.
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Affiliation(s)
- Vanessa Jane Melino
- Waite Research Institute, University of Adelaide, Glen Osmond, SA, Australia
- School of Agriculture and Food, University of Melbourne, Parkville, VIC, Australia
| | - Alberto Casartelli
- Waite Research Institute, University of Adelaide, Glen Osmond, SA, Australia
| | - Jessey George
- Waite Research Institute, University of Adelaide, Glen Osmond, SA, Australia
| | - Thusitha Rupasinghe
- Metabolomics Australia, School of Biosciences, The University of Melbourne, Parkville, VIC, Australia
| | - Ute Roessner
- Metabolomics Australia, School of Biosciences, The University of Melbourne, Parkville, VIC, Australia
| | - Mamoru Okamoto
- Waite Research Institute, University of Adelaide, Glen Osmond, SA, Australia
| | - Sigrid Heuer
- Waite Research Institute, University of Adelaide, Glen Osmond, SA, Australia
- Department of Plant Biology and Crop Science, Rothamsted Research, Harpenden, United Kingdom
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1505
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Grewal S, Hubbart-Edwards S, Yang C, Scholefield D, Ashling S, Burridge A, Wilkinson PA, King IP, King J. Detection of T. urartu Introgressions in Wheat and Development of a Panel of Interspecific Introgression Lines. FRONTIERS IN PLANT SCIENCE 2018; 9:1565. [PMID: 30420865 PMCID: PMC6216105 DOI: 10.3389/fpls.2018.01565] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Accepted: 10/08/2018] [Indexed: 05/23/2023]
Abstract
Tritcum urartu (2n = 2x = 14, AuAu), the A genome donor of wheat, is an important source for new genetic variation for wheat improvement due to its high photosynthetic rate and disease resistance. By facilitating the generation of genome-wide introgressions leading to a variety of different wheat-T. urartu translocation lines, T. urartu can be practically utilized in wheat improvement. Previous studies that have generated such introgression lines have been unable to successfully use cytological methods to detect the presence of T. urartu in these lines. Many have, thus, used a variety of molecular markers with limited success due to the low-density coverage of these markers and time-consuming nature of the techniques rendering them unsuitable for large-scale breeding programs. In this study, we report the generation of a resource of single nucleotide polymorphic (SNP) markers, present on a high-throughput SNP genotyping array, that can detect the presence of T. urartu in a hexaploid wheat background making it a potentially valuable tool in wheat pre-breeding programs. A whole genome introgression approach has resulted in the transfer of different chromosome segments from T. urartu into wheat which have then been detected and characterized using these SNP markers. The molecular analysis of these wheat-T. urartu recombinant lines has resulted in the generation of a genetic map of T. urartu containing 368 SNP markers, spread across all seven chromosomes of T. urartu. Comparative analysis of the genetic map of T. urartu and the physical map of the hexaploid wheat genome showed that synteny between the two species is highly conserved at the macro-level and confirmed the presence of the 4/5 translocation in T. urartu also present in the A genome of wheat. A panel of 17 wheat-T. urartu recombinant lines, which consisted of introgressed segments that covered the whole genome of T. urartu, were also selected for self-fertilization to provide a germplasm resource for future trait analysis. This valuable resource of high-density molecular markers specifically designed for detecting wild relative chromosomes and a panel of stable interspecific introgression lines will greatly enhance the efficiency of wheat improvement through wild relative introgressions.
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Affiliation(s)
- Surbhi Grewal
- Nottingham BBSRC Wheat Research Centre, Plant and Crop Sciences, School of Biosciences, The University of Nottingham, Loughborough, United Kingdom
| | - Stella Hubbart-Edwards
- Nottingham BBSRC Wheat Research Centre, Plant and Crop Sciences, School of Biosciences, The University of Nottingham, Loughborough, United Kingdom
| | - Caiyun Yang
- Nottingham BBSRC Wheat Research Centre, Plant and Crop Sciences, School of Biosciences, The University of Nottingham, Loughborough, United Kingdom
| | - Duncan Scholefield
- Nottingham BBSRC Wheat Research Centre, Plant and Crop Sciences, School of Biosciences, The University of Nottingham, Loughborough, United Kingdom
| | - Stephen Ashling
- Nottingham BBSRC Wheat Research Centre, Plant and Crop Sciences, School of Biosciences, The University of Nottingham, Loughborough, United Kingdom
| | - Amanda Burridge
- Cereal Genomics Lab, Life Sciences Building, School of Biological Sciences, University of Bristol, Bristol, United Kingdom
| | - Paul Anthony Wilkinson
- Cereal Genomics Lab, Life Sciences Building, School of Biological Sciences, University of Bristol, Bristol, United Kingdom
| | - Ian P. King
- Nottingham BBSRC Wheat Research Centre, Plant and Crop Sciences, School of Biosciences, The University of Nottingham, Loughborough, United Kingdom
| | - Julie King
- Nottingham BBSRC Wheat Research Centre, Plant and Crop Sciences, School of Biosciences, The University of Nottingham, Loughborough, United Kingdom
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1506
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Genome-Wide Association Study Reveals Novel Genomic Regions Associated with 10 Grain Minerals in Synthetic Hexaploid Wheat. Int J Mol Sci 2018; 19:ijms19103237. [PMID: 30347689 PMCID: PMC6214031 DOI: 10.3390/ijms19103237] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Revised: 10/05/2018] [Accepted: 10/12/2018] [Indexed: 11/25/2022] Open
Abstract
Synthetic hexaploid wheat (SHW; Triticum durum L. × Aegilopstauschii Coss.) is a means of introducing novel genes/genomic regions into bread wheat (T. aestivum L.) and a potential genetic resource for improving grain mineral concentrations. We quantified 10 grain minerals (Ca, Cd, Cu, Co, Fe, Li, Mg, Mn, Ni, and Zn) using an inductively coupled mass spectrometer in 123 SHWs for a genome-wide association study (GWAS). A GWAS with 35,648 single nucleotide polymorphism (SNP) markers identified 92 marker-trait associations (MTAs), of which 60 were novel and 40 were within genes, and the genes underlying 20 MTAs had annotations suggesting a potential role in grain mineral concentration. Twenty-four MTAs on the D-genome were novel and showed the potential of Ae. tauschii for improving grain mineral concentrations such as Ca, Co, Cu, Li, Mg, Mn, and Ni. Interestingly, the large number of novel MTAs (36) identified on the AB genome of these SHWs indicated that there is a lot of variation yet to be explored and to be used in the A and B genome along with the D-genome. Regression analysis identified a positive correlation between a cumulative number of favorable alleles at MTA loci in a genotype and grain mineral concentration. Additionally, we identified multi-traits and stable MTAs and recommended 13 top 10% SHWs with a higher concentration of beneficial grain minerals (Cu, Fe, Mg, Mn, Ni, and Zn), a large number of favorable alleles compared to low ranking genotypes and checks that could be utilized in the breeding program for the genetic biofortification. This study will further enhance our understanding of the genetic architecture of grain minerals in wheat and related cereals.
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1507
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Fletcher JC. The CLV-WUS Stem Cell Signaling Pathway: A Roadmap to Crop Yield Optimization. PLANTS 2018; 7:plants7040087. [PMID: 30347700 PMCID: PMC6313860 DOI: 10.3390/plants7040087] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Revised: 10/09/2018] [Accepted: 10/10/2018] [Indexed: 12/22/2022]
Abstract
The shoot apical meristem at the growing shoot tip acts a stem cell reservoir that provides cells to generate the entire above-ground architecture of higher plants. Many agronomic plant yield traits such as tiller number, flower number, fruit number, and kernel row number are therefore defined by the activity of the shoot apical meristem and its derivatives, the floral meristems. Studies in the model plant Arabidopsis thaliana demonstrated that a molecular negative feedback loop called the CLAVATA (CLV)-WUSCHEL (WUS) pathway regulates stem cell maintenance in shoot and floral meristems. CLV-WUS pathway components are associated with quantitative trait loci (QTL) for yield traits in crop plants such as oilseed, tomato, rice, and maize, and may have played a role in crop domestication. The conservation of these pathway components across the plant kingdom provides an opportunity to use cutting edge techniques such as genome editing to enhance yield traits in a wide variety of agricultural plant species.
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Affiliation(s)
- Jennifer C Fletcher
- Plant Gene Expression Center, United States Department of Agriculture-Agricultural Research Service, Albany, CA 94710, USA.
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA.
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1508
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Gros-Balthazard M, Hazzouri KM, Flowers JM. Genomic Insights into Date Palm Origins. Genes (Basel) 2018; 9:genes9100502. [PMID: 30336633 PMCID: PMC6211059 DOI: 10.3390/genes9100502] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2018] [Revised: 10/03/2018] [Accepted: 10/03/2018] [Indexed: 11/16/2022] Open
Abstract
With the development of next-generation sequencing technology, the amount of date palm (Phoenix dactylifera L.) genomic data has grown rapidly and yielded new insights into this species and its origins. Here, we review advances in understanding of the evolutionary history of the date palm, with a particular emphasis on what has been learned from the analysis of genomic data. We first record current genomic resources available for date palm including genome assemblies and resequencing data. We discuss new insights into its domestication and diversification history based on these improved genomic resources. We further report recent discoveries such as the existence of wild ancestral populations in remote locations of Oman and high differentiation between African and Middle Eastern populations. While genomic data are consistent with the view that domestication took place in the Gulf region, they suggest that the process was more complex involving multiple gene pools and possibly a secondary domestication. Many questions remain unanswered, especially regarding the genetic architecture of domestication and diversification. We provide a road map to future studies that will further clarify the domestication history of this iconic crop.
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Affiliation(s)
- Muriel Gros-Balthazard
- Center for Genomics and Systems Biology, New York University Abu Dhabi, Saadiyat Island, P.O. Box 129188, Abu Dhabi, UAE.
| | - Khaled Michel Hazzouri
- Khalifa Center for Genetic Engineering and Biotechnology (KCGEB), United Arab Emirates University, P.O. Box 15551, Al Ain, UAE.
| | - Jonathan Mark Flowers
- Center for Genomics and Systems Biology, New York University Abu Dhabi, Saadiyat Island, P.O. Box 129188, Abu Dhabi, UAE.
- Department of Biology, Center for Genomics and Systems Biology, 12 Waverly Place, New York University, New York, NY 10003, USA.
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1509
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Klymiuk V, Yaniv E, Huang L, Raats D, Fatiukha A, Chen S, Feng L, Frenkel Z, Krugman T, Lidzbarsky G, Chang W, Jääskeläinen MJ, Schudoma C, Paulin L, Laine P, Bariana H, Sela H, Saleem K, Sørensen CK, Hovmøller MS, Distelfeld A, Chalhoub B, Dubcovsky J, Korol AB, Schulman AH, Fahima T. Cloning of the wheat Yr15 resistance gene sheds light on the plant tandem kinase-pseudokinase family. Nat Commun 2018; 9:3735. [PMID: 30282993 PMCID: PMC6170490 DOI: 10.1038/s41467-018-06138-9] [Citation(s) in RCA: 140] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Accepted: 07/26/2018] [Indexed: 01/11/2023] Open
Abstract
Yellow rust, caused by Puccinia striiformis f. sp. tritici (Pst), is a devastating fungal disease threatening much of global wheat production. Race-specific resistance (R)-genes are used to control rust diseases, but the rapid emergence of virulent Pst races has prompted the search for a more durable resistance. Here, we report the cloning of Yr15, a broad-spectrum R-gene derived from wild emmer wheat, which encodes a putative kinase-pseudokinase protein, designated as wheat tandem kinase 1, comprising a unique R-gene structure in wheat. The existence of a similar gene architecture in 92 putative proteins across the plant kingdom, including the barley RPG1 and a candidate for Ug8, suggests that they are members of a distinct family of plant proteins, termed here tandem kinase-pseudokinases (TKPs). The presence of kinase-pseudokinase structure in both plant TKPs and the animal Janus kinases sheds light on the molecular evolution of immune responses across these two kingdoms.
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Affiliation(s)
- Valentina Klymiuk
- Institute of Evolution, University of Haifa, 199 Abba-Hushi Avenue, Mt. Carmel, 3498838, Haifa, Israel
- Department of Evolutionary and Environmental Biology, University of Haifa, 199 Abba-Hushi Avenue, Mt. Carmel, 3498838, Haifa, Israel
| | - Elitsur Yaniv
- Institute of Evolution, University of Haifa, 199 Abba-Hushi Avenue, Mt. Carmel, 3498838, Haifa, Israel
- Department of Evolutionary and Environmental Biology, University of Haifa, 199 Abba-Hushi Avenue, Mt. Carmel, 3498838, Haifa, Israel
- Institute of Biotechnology, University of Helsinki, Viikinkaari 1, P.O. Box 65, FI-00014, Helsinki, Finland
- Viikki Plant Science Centre, University of Helsinki, Viikinkaari 1, P.O. Box 65, FI-00014, Helsinki, Finland
| | - Lin Huang
- Institute of Evolution, University of Haifa, 199 Abba-Hushi Avenue, Mt. Carmel, 3498838, Haifa, Israel
- Department of Evolutionary and Environmental Biology, University of Haifa, 199 Abba-Hushi Avenue, Mt. Carmel, 3498838, Haifa, Israel
- Triticeae Research Institute, Sichuan Agricultural University, 611130, Chengdu, China
| | - Dina Raats
- Institute of Evolution, University of Haifa, 199 Abba-Hushi Avenue, Mt. Carmel, 3498838, Haifa, Israel
- Department of Evolutionary and Environmental Biology, University of Haifa, 199 Abba-Hushi Avenue, Mt. Carmel, 3498838, Haifa, Israel
- Earlham Institute, Norwich Research Park, Colney Lane, Norwich, NR4 7UZ, UK
| | - Andrii Fatiukha
- Institute of Evolution, University of Haifa, 199 Abba-Hushi Avenue, Mt. Carmel, 3498838, Haifa, Israel
- Department of Evolutionary and Environmental Biology, University of Haifa, 199 Abba-Hushi Avenue, Mt. Carmel, 3498838, Haifa, Israel
| | - Shisheng Chen
- Department of Plant Sciences, University of California, One Shields Avenue, Davis, CA, 95616, USA
| | - Lihua Feng
- Institute of Evolution, University of Haifa, 199 Abba-Hushi Avenue, Mt. Carmel, 3498838, Haifa, Israel
- Department of Evolutionary and Environmental Biology, University of Haifa, 199 Abba-Hushi Avenue, Mt. Carmel, 3498838, Haifa, Israel
| | - Zeev Frenkel
- Institute of Evolution, University of Haifa, 199 Abba-Hushi Avenue, Mt. Carmel, 3498838, Haifa, Israel
| | - Tamar Krugman
- Institute of Evolution, University of Haifa, 199 Abba-Hushi Avenue, Mt. Carmel, 3498838, Haifa, Israel
| | - Gabriel Lidzbarsky
- Institute of Evolution, University of Haifa, 199 Abba-Hushi Avenue, Mt. Carmel, 3498838, Haifa, Israel
| | - Wei Chang
- Institute of Biotechnology, University of Helsinki, Viikinkaari 1, P.O. Box 65, FI-00014, Helsinki, Finland
- Viikki Plant Science Centre, University of Helsinki, Viikinkaari 1, P.O. Box 65, FI-00014, Helsinki, Finland
| | - Marko J Jääskeläinen
- Institute of Biotechnology, University of Helsinki, Viikinkaari 1, P.O. Box 65, FI-00014, Helsinki, Finland
- Viikki Plant Science Centre, University of Helsinki, Viikinkaari 1, P.O. Box 65, FI-00014, Helsinki, Finland
| | - Christian Schudoma
- Earlham Institute, Norwich Research Park, Colney Lane, Norwich, NR4 7UZ, UK
| | - Lars Paulin
- Institute of Biotechnology, University of Helsinki, Viikinkaari 1, P.O. Box 65, FI-00014, Helsinki, Finland
| | - Pia Laine
- Institute of Biotechnology, University of Helsinki, Viikinkaari 1, P.O. Box 65, FI-00014, Helsinki, Finland
| | - Harbans Bariana
- The University of Sydney Plant Breeding Institute, 107 Cobbitty Road, Cobbitty, NSW, 2570, Australia
| | - Hanan Sela
- Institute of Evolution, University of Haifa, 199 Abba-Hushi Avenue, Mt. Carmel, 3498838, Haifa, Israel
- The Institute for Cereal Crops Improvement, Tel Aviv University, P.O. Box 39040, 6139001, Tel Aviv, Israel
| | - Kamran Saleem
- Department of Agroecology, Aarhus University, Forsøgsvej 1, 4200, Slagelse, Denmark
| | | | - Mogens S Hovmøller
- Department of Agroecology, Aarhus University, Forsøgsvej 1, 4200, Slagelse, Denmark
| | - Assaf Distelfeld
- Institute of Evolution, University of Haifa, 199 Abba-Hushi Avenue, Mt. Carmel, 3498838, Haifa, Israel
- School of Plant Sciences and Food Security, Tel Aviv University, P.O. Box 39040, 6139001, Tel Aviv, Israel
| | - Boulos Chalhoub
- Institute of System and Synthetic Biology-Organization and Evolution of Complex Genomes, 2 rue Gaston Crémieux CP 5708, 91057, Evry Cedex, France
| | - Jorge Dubcovsky
- Department of Plant Sciences, University of California, One Shields Avenue, Davis, CA, 95616, USA
- Howard Hughes Medical Institute, 4000 Jones Bridge Road, Chevy Chase, MD, 20815, USA
| | - Abraham B Korol
- Institute of Evolution, University of Haifa, 199 Abba-Hushi Avenue, Mt. Carmel, 3498838, Haifa, Israel
- Department of Evolutionary and Environmental Biology, University of Haifa, 199 Abba-Hushi Avenue, Mt. Carmel, 3498838, Haifa, Israel
| | - Alan H Schulman
- Institute of Biotechnology, University of Helsinki, Viikinkaari 1, P.O. Box 65, FI-00014, Helsinki, Finland
- Viikki Plant Science Centre, University of Helsinki, Viikinkaari 1, P.O. Box 65, FI-00014, Helsinki, Finland
- Natural Resources Institute Finland (Luke), Latokartanonkaari 9, FI-00790, Helsinki, Finland
| | - Tzion Fahima
- Institute of Evolution, University of Haifa, 199 Abba-Hushi Avenue, Mt. Carmel, 3498838, Haifa, Israel.
- Department of Evolutionary and Environmental Biology, University of Haifa, 199 Abba-Hushi Avenue, Mt. Carmel, 3498838, Haifa, Israel.
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1510
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Crescente JM, Zavallo D, Helguera M, Vanzetti LS. MITE Tracker: an accurate approach to identify miniature inverted-repeat transposable elements in large genomes. BMC Bioinformatics 2018; 19:348. [PMID: 30285604 PMCID: PMC6171319 DOI: 10.1186/s12859-018-2376-y] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Accepted: 09/18/2018] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Miniature inverted-repeat transposable elements (MITEs) are short, non-autonomous class II transposable elements present in a high number of conserved copies in eukaryote genomes. An accurate identification of these elements can help to shed light on the mechanisms controlling genome evolution and gene regulation. The structure and distribution of these elements are well-defined and therefore computational approaches can be used to identify MITEs sequences. RESULTS Here we describe MITE Tracker, a novel, open source software program that finds and classifies MITEs using an efficient alignment strategy to retrieve nearby inverted-repeat sequences from large genomes. This program groups them into high sequence homology families using a fast clustering algorithm and finally filters only those elements that were likely transposed from different genomic locations because of their low scoring flanking sequence alignment. CONCLUSIONS Many programs have been proposed to find MITEs hidden in genomes. However, none of them are able to process large-scale genomes such as that of bread wheat. Furthermore, in many cases the existing methods perform high false-positive rates (or miss rates). The rice genome was used as reference to compare MITE Tracker against known tools. Our method turned out to be the most reliable in our tests. Indeed, it revealed more known elements, presented the lowest false-positive number and was the only program able to run with the bread wheat genome as input. In wheat, MITE Tracker discovered 6013 MITE families and allowed the first structural exploration of MITEs in the complete bread wheat genome.
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Affiliation(s)
- Juan Manuel Crescente
- Grupo Biotecnología y Recursos Genéticos, EEA INTA Marcos Juárez, Ruta 12 km 3, 2580, Marcos Juárez, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Diego Zavallo
- Instituto de Biotecnología, CNIA, Instituto Nacional de Tecnología Agropecuaria (INTA) Castelar, Los Reseros y Nicolas Repeto, Hurlingham, Buenos Aires, Argentina
| | - Marcelo Helguera
- Grupo Biotecnología y Recursos Genéticos, EEA INTA Marcos Juárez, Ruta 12 km 3, 2580, Marcos Juárez, Argentina
| | - Leonardo Sebastián Vanzetti
- Grupo Biotecnología y Recursos Genéticos, EEA INTA Marcos Juárez, Ruta 12 km 3, 2580, Marcos Juárez, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
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1511
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Bhatta M, Morgounov A, Belamkar V, Baenziger PS. Genome-Wide Association Study Reveals Novel Genomic Regions for Grain Yield and Yield-Related Traits in Drought-Stressed Synthetic Hexaploid Wheat. Int J Mol Sci 2018; 19:E3011. [PMID: 30279375 PMCID: PMC6212811 DOI: 10.3390/ijms19103011] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Revised: 09/27/2018] [Accepted: 09/29/2018] [Indexed: 01/09/2023] Open
Abstract
Synthetic hexaploid wheat (SHW; 2n = 6x = 42, AABBDD, Triticum aestivum L.) is produced from an interspecific cross between durum wheat (2n = 4x = 28, AABB, T. turgidum L.) and goat grass (2n = 2x = 14, DD, Aegilops tauschii Coss.) and is reported to have significant novel alleles-controlling biotic and abiotic stresses resistance. A genome-wide association study (GWAS) was conducted to unravel these loci [marker⁻trait associations (MTAs)] using 35,648 genotyping-by-sequencing-derived single nucleotide polymorphisms in 123 SHWs. We identified 90 novel MTAs (45, 11, and 34 on the A, B, and D genomes, respectively) and haplotype blocks associated with grain yield and yield-related traits including root traits under drought stress. The phenotypic variance explained by the MTAs ranged from 1.1% to 32.3%. Most of the MTAs (120 out of 194) identified were found in genes, and of these 45 MTAs were in genes annotated as having a potential role in drought stress. This result provides further evidence for the reliability of MTAs identified. The large number of MTAs (53) identified especially on the D-genome demonstrate the potential of SHWs for elucidating the genetic architecture of complex traits and provide an opportunity for further improvement of wheat under rapidly changing climatic conditions.
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Affiliation(s)
- Madhav Bhatta
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE 68583, USA.
| | - Alexey Morgounov
- International Maize and Wheat Improvement Center (CIMMYT), 06511 Emek, Ankara, Turkey.
| | - Vikas Belamkar
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE 68583, USA.
| | - P Stephen Baenziger
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE 68583, USA.
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1512
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Singh SP, Hurni S, Ruinelli M, Brunner S, Sanchez-Martin J, Krukowski P, Peditto D, Buchmann G, Zbinden H, Keller B. Evolutionary divergence of the rye Pm17 and Pm8 resistance genes reveals ancient diversity. PLANT MOLECULAR BIOLOGY 2018; 98:249-260. [PMID: 30244408 DOI: 10.1007/s11103-018-0780-3] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 09/12/2018] [Indexed: 05/18/2023]
Abstract
We have isolated a novel powdery mildew resistance gene in wheat that was originally introgressed from rye. Further analysis revealed evolutionary divergent history of wheat and rye orthologous resistance genes. Wheat production is under constant threat from a number of fungal pathogens, among them is wheat powdery mildew (Blumeria graminis f. sp. tritici). Deployment of resistance genes is the most economical and sustainable method for mildew control. However, domestication and selective breeding have narrowed genetic diversity of modern wheat germplasm, and breeders have relied on wheat relatives for enriching its gene pool through introgression. Translocations where the 1RS chromosome arm was introgressed from rye to wheat have improved yield and resistance against various pathogens. Here, we isolated the Pm17 mildew resistance gene located on the 1RS introgression in wheat cultivar 'Amigo' and found that it is an allele or a close paralog of the Pm8 gene isolated earlier from 'Petkus' rye. Functional validation using transient and stable transformation confirmed the identity of Pm17. Analysis of Pm17 and Pm8 coding regions revealed an overall identity of 82.9% at the protein level, with the LRR domains being most divergent. Our analysis also showed that the two rye genes are much more diverse compared to the variants encoded by the Pm3 gene in wheat, which is orthologous to Pm17/Pm8 as concluded from highly conserved upstream sequences in all these genes. Thus, the evolutionary history of these orthologous loci differs in the cereal species rye and wheat and demonstrates that orthologous resistance genes can take different routes towards functionally active genes. These findings suggest that the isolation of Pm3/Pm8/Pm17 orthologs from other grass species, additional alleles from the rye germplasm as well as possibly synthetic variants will result in novel resistance genes useful in wheat breeding.
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Affiliation(s)
- Simrat Pal Singh
- Department of Plant and Microbial Biology, University of Zurich, Zollikerstrasse 107, 8008, Zurich, Switzerland
- ETH Zürich, Universitätstrasse 2, 8092, Zurich, Switzerland
| | - Severine Hurni
- Department of Plant and Microbial Biology, University of Zurich, Zollikerstrasse 107, 8008, Zurich, Switzerland
| | - Michela Ruinelli
- Department of Plant and Microbial Biology, University of Zurich, Zollikerstrasse 107, 8008, Zurich, Switzerland
| | - Susanne Brunner
- Department of Plant and Microbial Biology, University of Zurich, Zollikerstrasse 107, 8008, Zurich, Switzerland
- Agroscope, Reckenholzstrasse 191, 8046, Zurich, Switzerland
| | - Javier Sanchez-Martin
- Department of Plant and Microbial Biology, University of Zurich, Zollikerstrasse 107, 8008, Zurich, Switzerland
| | - Patricia Krukowski
- Department of Plant and Microbial Biology, University of Zurich, Zollikerstrasse 107, 8008, Zurich, Switzerland
| | - David Peditto
- Department of Plant and Microbial Biology, University of Zurich, Zollikerstrasse 107, 8008, Zurich, Switzerland
| | - Gabriele Buchmann
- Department of Plant and Microbial Biology, University of Zurich, Zollikerstrasse 107, 8008, Zurich, Switzerland
| | - Helen Zbinden
- Department of Plant and Microbial Biology, University of Zurich, Zollikerstrasse 107, 8008, Zurich, Switzerland
| | - Beat Keller
- Department of Plant and Microbial Biology, University of Zurich, Zollikerstrasse 107, 8008, Zurich, Switzerland.
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1513
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Keller B, Wicker T, Krattinger SG. Advances in Wheat and Pathogen Genomics: Implications for Disease Control. ANNUAL REVIEW OF PHYTOPATHOLOGY 2018; 56:67-87. [PMID: 30149791 DOI: 10.1146/annurev-phyto-080516-035419] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
The gene pool of wheat and its wild and domesticated relatives contains a plethora of resistance genes that can be exploited to make wheat more resilient to pathogens. Only a few of these genes have been isolated and studied at the molecular level. In recent years, we have seen a shift from classical breeding to genomics-assisted breeding, which makes use of the enormous advancements in DNA sequencing and high-throughput molecular marker technologies for wheat improvement. These genomic advancements have the potential to transform wheat breeding in the near future and to significantly increase the speed and precision at which new cultivars can be bred. This review highlights the genomic improvements that have been made in wheat and its pathogens over the past years and discusses their implications for disease-resistance breeding.
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Affiliation(s)
- Beat Keller
- Department of Plant and Microbial Biology, University of Zurich, 8008 Zurich, Switzerland;
| | - Thomas Wicker
- Department of Plant and Microbial Biology, University of Zurich, 8008 Zurich, Switzerland;
| | - Simon G Krattinger
- Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia;
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1514
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Alaux M, Rogers J, Letellier T, Flores R, Alfama F, Pommier C, Mohellibi N, Durand S, Kimmel E, Michotey C, Guerche C, Loaec M, Lainé M, Steinbach D, Choulet F, Rimbert H, Leroy P, Guilhot N, Salse J, Feuillet C, Paux E, Eversole K, Adam-Blondon AF, Quesneville H. Linking the International Wheat Genome Sequencing Consortium bread wheat reference genome sequence to wheat genetic and phenomic data. Genome Biol 2018; 19:111. [PMID: 30115101 PMCID: PMC6097284 DOI: 10.1186/s13059-018-1491-4] [Citation(s) in RCA: 136] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Accepted: 07/23/2018] [Indexed: 01/24/2023] Open
Abstract
The Wheat@URGI portal has been developed to provide the international community of researchers and breeders with access to the bread wheat reference genome sequence produced by the International Wheat Genome Sequencing Consortium. Genome browsers, BLAST, and InterMine tools have been established for in-depth exploration of the genome sequence together with additional linked datasets including physical maps, sequence variations, gene expression, and genetic and phenomic data from other international collaborative projects already stored in the GnpIS information system. The portal provides enhanced search and browser features that will facilitate the deployment of the latest genomics resources in wheat improvement.
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Affiliation(s)
- Michael Alaux
- URGI, INRA, Université Paris-Saclay, 78026, Versailles, France.
| | - Jane Rogers
- International Wheat Genome Sequencing Consortium (IWGSC), 18 High Street, Little Eversden, Cambridge, CB23 1HE, UK
| | | | - Raphaël Flores
- URGI, INRA, Université Paris-Saclay, 78026, Versailles, France
| | | | - Cyril Pommier
- URGI, INRA, Université Paris-Saclay, 78026, Versailles, France
| | - Nacer Mohellibi
- URGI, INRA, Université Paris-Saclay, 78026, Versailles, France
| | - Sophie Durand
- URGI, INRA, Université Paris-Saclay, 78026, Versailles, France
| | - Erik Kimmel
- URGI, INRA, Université Paris-Saclay, 78026, Versailles, France
| | - Célia Michotey
- 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
| | - Mathilde Lainé
- URGI, INRA, Université Paris-Saclay, 78026, Versailles, France
| | - Delphine Steinbach
- URGI, INRA, Université Paris-Saclay, 78026, Versailles, France
- Present address: GQE-Le Moulon UMR 320, INRA, Université Paris-Sud, Université Paris-Saclay, CNRS, AgroParisTech, Ferme du Moulon, 91190, Gif-sur-Yvette, France
| | - Frédéric Choulet
- GDEC, INRA, Université Clermont Auvergne, 63000, Clermont-Ferrand, France
| | - Hélène Rimbert
- GDEC, INRA, Université Clermont Auvergne, 63000, Clermont-Ferrand, France
| | - Philippe Leroy
- GDEC, INRA, Université Clermont Auvergne, 63000, Clermont-Ferrand, France
| | - Nicolas Guilhot
- GDEC, INRA, Université Clermont Auvergne, 63000, Clermont-Ferrand, France
| | - Jérôme Salse
- GDEC, INRA, Université Clermont Auvergne, 63000, Clermont-Ferrand, France
| | - Catherine Feuillet
- GDEC, INRA, Université Clermont Auvergne, 63000, Clermont-Ferrand, France
- Present address: Inari Agriculture, 200 Sydney Street, Cambridge, MA, 02139, USA
| | - Etienne Paux
- GDEC, INRA, Université Clermont Auvergne, 63000, Clermont-Ferrand, France
| | - Kellye Eversole
- International Wheat Genome Sequencing Consortium (IWGSC), 5207 Wyoming Road, Bethesda, Maryland, 20816, USA
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1515
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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] [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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1516
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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: 530] [Impact Index Per Article: 88.3] [Reference Citation Analysis] [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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1517
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Wicker T, Gundlach H, Spannagl M, Uauy C, Borrill P, Ramírez-González RH, De Oliveira R, Mayer KFX, Paux E, Choulet F. Impact of transposable elements on genome structure and evolution in bread wheat. Genome Biol 2018; 19:103. [PMID: 30115100 PMCID: PMC6097303 DOI: 10.1186/s13059-018-1479-0] [Citation(s) in RCA: 157] [Impact Index Per Article: 26.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Accepted: 07/11/2018] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND Transposable elements (TEs) are major components of large plant genomes and main drivers of genome evolution. The most recent assembly of hexaploid bread wheat recovered the highly repetitive TE space in an almost complete chromosomal context and enabled a detailed view into the dynamics of TEs in the A, B, and D subgenomes. RESULTS The overall TE content is very similar between the A, B, and D subgenomes, although we find no evidence for bursts of TE amplification after the polyploidization events. Despite the near-complete turnover of TEs since the subgenome lineages diverged from a common ancestor, 76% of TE families are still present in similar proportions in each subgenome. Moreover, spacing between syntenic genes is also conserved, even though syntenic TEs have been replaced by new insertions over time, suggesting that distances between genes, but not sequences, are under evolutionary constraints. The TE composition of the immediate gene vicinity differs from the core intergenic regions. We find the same TE families to be enriched or depleted near genes in all three subgenomes. Evaluations at the subfamily level of timed long terminal repeat-retrotransposon insertions highlight the independent evolution of the diploid A, B, and D lineages before polyploidization and cases of concerted proliferation in the AB tetraploid. CONCLUSIONS Even though the intergenic space is changed by the TE turnover, an unexpected preservation is observed between the A, B, and D subgenomes for features like TE family proportions, gene spacing, and TE enrichment near genes.
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Affiliation(s)
- Thomas Wicker
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Heidrun Gundlach
- PGSB Plant Genome and Systems Biology, Helmholtz Center Munich, German Research Center for Environmental Health, Neuherberg, Germany
| | - Manuel Spannagl
- PGSB Plant Genome and Systems Biology, Helmholtz Center Munich, German Research Center for Environmental Health, Neuherberg, Germany
| | - Cristobal Uauy
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Colney, Norwich, NR4 7UH, UK
| | - Philippa Borrill
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Colney, Norwich, NR4 7UH, UK
| | | | - Romain De Oliveira
- GDEC, INRA, UCA (Université Clermont Auvergne), Clermont-Ferrand, France
| | - Klaus F X Mayer
- PGSB Plant Genome and Systems Biology, Helmholtz Center Munich, German Research Center for Environmental Health, Neuherberg, Germany
- School of Life Sciences, Technical University Munich, Munich, Germany
| | - Etienne Paux
- GDEC, INRA, UCA (Université Clermont Auvergne), Clermont-Ferrand, France
| | - Frédéric Choulet
- GDEC, INRA, UCA (Université Clermont Auvergne), Clermont-Ferrand, France.
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1518
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Liu J, Xu Z, Fan X, Zhou Q, Cao J, Wang F, Ji G, Yang L, Feng B, Wang T. A Genome-Wide Association Study of Wheat Spike Related Traits in China. FRONTIERS IN PLANT SCIENCE 2018; 9:1584. [PMID: 30429867 PMCID: PMC6220075 DOI: 10.3389/fpls.2018.01584] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Accepted: 10/11/2018] [Indexed: 05/22/2023]
Abstract
Rapid detection of allelic variation and identification of advantage haplotypes responsible for spike related traits play a crucial role in wheat yield improvement. The released genome sequence of hexaploid wheat (Chinese Spring) provides an extraordinary opportunity for rapid detection of natural variation and promotes breeding application. Here, selection signals detection and genome-wide association study (GWAS) were conducted for spike related traits. Based on the genotyping results by 90K SNP chip, 192 common wheat samples from southwest China were analyzed. One hundred and forty-six selective windows and one hundred and eighty-four significant SNPs (51 for spike length, 28 for kernels per spike, 39 for spikelet number, 30 for thousand kernel weight, and 36 for spike number per plant) were detected. Furthermore, tightly linkage and environmental stability window clusters and SNP clusters were also obtained. As a result, four SNP clusters associated with spike length were detected on chromosome 2A, 2B, 2D, and 6A. Two SNP clusters correlated to kernels per spike were detected on 2A and 2B. One pleiotropy SNP cluster correlated to spikelet number and kernels per spike was detected on 7B. According to the genome sequence, these SNP clusters and their overlapped/flanking QTLs which have been reported previously were integrated to a physical map. The candidate genes responsible for spike length, kernels per spike and spikelet number were predicted. Based on the genotypes of cultivars in south China, two advantage haplotypes associated with spike length and one advantage haplotype associated with kernels per spike/spikelet number were detected which have not been effectively transited into cultivars. According to these haplotypes, KASP markers were developed and diagnosed across landraces and cultivars which were selected from south and north China. Consequently, KASP assay, consistent with the GWAS results, provides reliable haplotypes for MAS in wheat yield improvement.
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Kyriakidou M, Tai HH, Anglin NL, Ellis D, Strömvik MV. Current Strategies of Polyploid Plant Genome Sequence Assembly. FRONTIERS IN PLANT SCIENCE 2018; 9:1660. [PMID: 30519250 PMCID: PMC6258962 DOI: 10.3389/fpls.2018.01660] [Citation(s) in RCA: 101] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Accepted: 10/25/2018] [Indexed: 05/14/2023]
Abstract
Polyploidy or duplication of an entire genome occurs in the majority of angiosperms. The understanding of polyploid genomes is important for the improvement of those crops, which humans rely on for sustenance and basic nutrition. As climate change continues to pose a potential threat to agricultural production, there will increasingly be a demand for plant cultivars that can resist biotic and abiotic stresses and also provide needed and improved nutrition. In the past decade, Next Generation Sequencing (NGS) has fundamentally changed the genomics landscape by providing tools for the exploration of polyploid genomes. Here, we review the challenges of the assembly of polyploid plant genomes, and also present recent advances in genomic resources and functional tools in molecular genetics and breeding. As genomes of diploid and less heterozygous progenitor species are increasingly available, we discuss the lack of complexity of these currently available reference genomes as they relate to polyploid crops. Finally, we review recent approaches of haplotyping by phasing and the impact of third generation technologies on polyploid plant genome assembly.
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Affiliation(s)
- Maria Kyriakidou
- Department of Plant Science, McGill University, Montreal, QC, Canada
| | - Helen H. Tai
- Fredericton Research and Development Centre, Agriculture and Agri-Food Canada, Fredericton, NB, Canada
| | | | | | - Martina V. Strömvik
- Department of Plant Science, McGill University, Montreal, QC, Canada
- *Correspondence: Martina V. Strömvik
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1520
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Roselló M, Royo C, Álvaro F, Villegas D, Nazco R, Soriano JM. Pasta-Making Quality QTLome From Mediterranean Durum Wheat Landraces. FRONTIERS IN PLANT SCIENCE 2018; 9:1512. [PMID: 30459781 PMCID: PMC6232839 DOI: 10.3389/fpls.2018.01512] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Accepted: 09/26/2018] [Indexed: 05/22/2023]
Abstract
In order to identify genome regions related to pasta-making quality traits, association mapping (AM) was performed in a set of 165 durum wheat landraces from 21 Mediterranean countries. The collection was genotyped using 1149 DArT markers and 872 of them with a known genetic position were used for AM. The collection was grown in north-east Spain during 3 years. Results of ANOVA showed that trait variation for quality traits, except for grain protein content (GPC), was mainly explained by genetic effects. Landraces showed higher GPC than modern cultivars but lower gluten strength (GS). Modern and eastern landraces showed the highest yellow color index (YI). Balkan landraces showed the lowest test weight (TW). A total of 92 marker-trait associations were detected, 20 corresponding to GS, 21 to GPC, 21 to YI and 30 to TW. With the aim of detecting new genomic regions involved in grain quality, the position of the associations was compared with previously mapped QTL by a meta-QTL analysis. A total of 249 QTLs were projected onto the same map used for AM, identifying 45 meta-QTL (MQTL) regions and the remaining 15 QTLs as singletons. The position of known genes involved in grain quality was also included, and gene annotation within the most significant regions detected by AM was carried out using the wheat genome sequence.
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