1
|
Patidar A, Yadav MC, Kumari J, Tiwari S, Chawla G, Paul V. Identification of Climate-Smart Bread Wheat Germplasm Lines with Enhanced Adaptation to Global Warming. PLANTS (BASEL, SWITZERLAND) 2023; 12:2851. [PMID: 37571005 PMCID: PMC10420658 DOI: 10.3390/plants12152851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 07/22/2023] [Accepted: 07/24/2023] [Indexed: 08/13/2023]
Abstract
Bread wheat (Triticum aestivum L.) is widely grown in sub-tropical and tropical areas and, as such, it is exposed to heatstress especially during the grain filling period (GFP). Global warming has further affected its production and productivity in these heat-stressed environments. We examined the effects of heatstress on 18 morpho-physiological and yield-related traits in 96 bread wheat accessions. Heat stress decreased crop growth and GFP, and consequently reduced morphological and yield-related traits in the delayed sown crop. A low heat susceptibility index and high yield stability were used for selecting tolerant accessions. Under heatstress, the days to 50% anthesis, flag-leaf area, chlorophyll content, normalized difference vegetation index (NDVI), thousand grain weight (TGW), harvest index and grain yield were significantly reduced both in tolerant and susceptible accessions. The reduction was severe in susceptible accessions (48.2% grain yield reduction in IC277741). The plant height, peduncle length and spike length showeda significant reduction in susceptible accessions, but a non-significant reduction in the tolerant accessions under the heatstress. The physiological traits like the canopy temperature depression (CTD), plant waxiness and leaf rolling were increased in tolerant accessions under heatstress. Scanning electron microscopy of matured wheat grains revealed ultrastructural changes in endosperm and aleurone cells due to heat stress. The reduction in size and density of large starch granules is the major cause of the yield and TGW decrease in the heat-stress-susceptible accessions. The most stable and high-yielding accessions, namely, IC566223, IC128454, IC335792, EC576707, IC535176, IC529207, IC446713 and IC416019 were identified as the climate-smart germplasm lines. We selected germplasm lines possessing desirable traits as potential parents for the development of bi-parent and multi-parent mapping populations.
Collapse
Affiliation(s)
- Anil Patidar
- Division of Genomic Resources, Indian Council of Agricultural Research (ICAR)-National Bureau of Plant Genetic Resources, New Delhi 110012, India; (A.P.); (S.T.)
- Post-Graduate School, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
| | - Mahesh C. Yadav
- Division of Genomic Resources, Indian Council of Agricultural Research (ICAR)-National Bureau of Plant Genetic Resources, New Delhi 110012, India; (A.P.); (S.T.)
| | - Jyoti Kumari
- Division of Germplasm Evaluation, ICAR-National Bureau of Plant Genetic Resources, New Delhi 110012, India;
| | - Shailesh Tiwari
- Division of Genomic Resources, Indian Council of Agricultural Research (ICAR)-National Bureau of Plant Genetic Resources, New Delhi 110012, India; (A.P.); (S.T.)
| | - Gautam Chawla
- Division of Nematology, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India;
| | - Vijay Paul
- Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
| |
Collapse
|
2
|
Mulugeta B, Ortiz R, Geleta M, Hailesilassie T, Hammenhag C, Hailu F, Tesfaye K. Harnessing genome-wide genetic diversity, population structure and linkage disequilibrium in Ethiopian durum wheat gene pool. FRONTIERS IN PLANT SCIENCE 2023; 14:1192356. [PMID: 37546270 PMCID: PMC10400094 DOI: 10.3389/fpls.2023.1192356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 07/05/2023] [Indexed: 08/08/2023]
Abstract
Yanyang Liu, Henan Academy of Agricultural Sciences (HNAAS), China; Landraces are an important genetic source for transferring valuable novel genes and alleles required to enhance genetic variation. Therefore, information on the gene pool's genetic diversity and population structure is essential for the conservation and sustainable use of durum wheat genetic resources. Hence, the aim of this study was to assess genetic diversity, population structure, and linkage disequilibrium, as well as to identify regions with selection signature. Five hundred (500) individuals representing 46 landraces, along with 28 cultivars were evaluated using the Illumina Infinium 25K wheat SNP array, resulting in 8,178 SNPs for further analysis. Gene diversity (GD) and the polymorphic information content (PIC) ranged from 0.13-0.50 and 0.12-0.38, with mean GD and PIC values of 0.34 and 0.27, respectively. Linkage disequilibrium (LD) revealed 353,600 pairs of significant SNPs at a cut-off (r2 > 0.20, P < 0.01), with an average r2 of 0.21 for marker pairs. The nucleotide diversity (π) and Tajima's D (TD) per chromosome for the populations ranged from 0.29-0.36 and 3.46-5.06, respectively, with genome level, mean π values of 0.33 and TD values of 4.43. Genomic scan using the Fst outlier test revealed 85 loci under selection signatures, with 65 loci under balancing selection and 17 under directional selection. Putative candidate genes co-localized with regions exhibiting strong selection signatures were associated with grain yield, plant height, host plant resistance to pathogens, heading date, grain quality, and phenolic content. The Bayesian Model (STRUCTURE) and distance-based (principal coordinate analysis, PCoA, and unweighted pair group method with arithmetic mean, UPGMA) methods grouped the genotypes into five subpopulations, where landraces from geographically non-adjoining environments were clustered in the same cluster. This research provides further insights into population structure and genetic relationships in a diverse set of durum wheat germplasm, which could be further used in wheat breeding programs to address production challenges sustainably.
Collapse
Affiliation(s)
- Behailu Mulugeta
- Institute of Biotechnology, Addis Ababa University, Addis Ababa, Ethiopia
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden
- Sinana Agricultural Research Center, Oromia Agricultural Research Institute, Bale-Robe, Ethiopia
| | - Rodomiro Ortiz
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | - Mulatu Geleta
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | | | - Cecilia Hammenhag
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | - Faris Hailu
- Bio and Emerging Technology Institute, Addis Ababa, Ethiopia
| | - Kassahun Tesfaye
- Institute of Biotechnology, Addis Ababa University, Addis Ababa, Ethiopia
- Department of Biology and Biotechnology, Wollo University, Dessie, Ethiopia
| |
Collapse
|
3
|
Maserumule M, Rauwane M, Madala NE, Ncube E, Figlan S. Defence-related metabolic changes in wheat ( Triticum aestivum L.) seedlings in response to infection by Puccinia graminis f. sp. tritici. FRONTIERS IN PLANT SCIENCE 2023; 14:1166813. [PMID: 37377801 PMCID: PMC10292758 DOI: 10.3389/fpls.2023.1166813] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 05/16/2023] [Indexed: 06/29/2023]
Abstract
Stem rust caused by the pathogen Puccinia graminis f. sp. tritici is a destructive fungal disease-causing major grain yield losses in wheat. Therefore, understanding the plant defence regulation and function in response to the pathogen attack is required. As such, an untargeted LC-MS-based metabolomics approach was employed as a tool to dissect and understand the biochemical responses of Koonap (resistant) and Morocco (susceptible) wheat varieties infected with two different races of P. graminis (2SA88 [TTKSF] and 2SA107 [PTKST]). Data was generated from the infected and non-infected control plants harvested at 14- and 21- days post-inoculation (dpi), with 3 biological replicates per sample under a controlled environment. Chemo-metric tools such as principal component analysis (PCA), orthogonal projection to latent structures-discriminant analysis (OPLS-DA) were used to highlight the metabolic changes using LC-MS data of the methanolic extracts generated from the two wheat varieties. Molecular networking in Global Natural Product Social (GNPS) was further used to analyse biological networks between the perturbed metabolites. PCA and OPLS-DA analysis showed cluster separations between the varieties, infection races and the time-points. Distinct biochemical changes were also observed between the races and time-points. Metabolites were identified and classified using base peak intensities (BPI) and single ion extracted chromatograms from samples, and the most affected metabolites included flavonoids, carboxylic acids and alkaloids. Network analysis also showed high expression of metabolites from thiamine and glyoxylate, such as flavonoid glycosides, suggesting multi-faceted defence response strategy by understudied wheat varieties towards P. graminis pathogen infection. Overall, the study provided the insights of the biochemical changes in the expression of wheat metabolites in response to stem rust infection.
Collapse
Affiliation(s)
- Mercy Maserumule
- Department of Agriculture and Animal Health, School of Agriculture and Life Sciences, College of Agriculture and Environmental Sciences, University of South Africa, Roodepoort, South Africa
| | - Molemi Rauwane
- Department of Agriculture and Animal Health, School of Agriculture and Life Sciences, College of Agriculture and Environmental Sciences, University of South Africa, Roodepoort, South Africa
- Department of Botany, Nelson Mandela University, South Campus, Port Elizabeth, South Africa
| | - Ntakadzeni E. Madala
- Department of Biochemistry and Microbiology, Faculty of Sciences, Agriculture and Engineering, University of Venda, Thohoyandou, Limpopo, South Africa
| | - Efficient Ncube
- Department of Agriculture and Animal Health, School of Agriculture and Life Sciences, College of Agriculture and Environmental Sciences, University of South Africa, Roodepoort, South Africa
| | - Sandiswa Figlan
- Department of Agriculture and Animal Health, School of Agriculture and Life Sciences, College of Agriculture and Environmental Sciences, University of South Africa, Roodepoort, South Africa
| |
Collapse
|
4
|
Dallacorte LV, Bosse MA, Capelin D, Paladini MV, Cattani F, Remor MB, Donizetti de Lima J, Perboni AT, Marchese JA. Economic versus technical efficiency in using ASM combined with fungicides to elicit wheat varieties with different disease susceptibilities. Heliyon 2023; 9:e17012. [PMID: 37484364 PMCID: PMC10361120 DOI: 10.1016/j.heliyon.2023.e17012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 05/29/2023] [Accepted: 06/04/2023] [Indexed: 07/25/2023] Open
Abstract
Despite the positive results of using elicitors to induce resistance against plant diseases, some factors have inhibited the popularization of their use in agriculture. There is an energetic cost related to the elicitors' induced response which can cause undesired effects on growth under low-pressure disease conditions. Elicitors can create phytotoxicity and show high variation in their efficiency between different genotypes within the same crop; in addition, the positive results related to the induced resistance may not repeat in field treatments, adding to the possibility that they are not economically viable. Thus, we carried out two experiments to investigate the technical and economic efficiency of acibenzolar-S-methyl (ASM) and its association with fungicides in the control of leaf diseases of susceptible and resistant wheat varieties, and as how it reflects on the photosynthetic and production performance of wheat. This study showed the limitations of incorporating ASM into foliar fungal disease control in economic terms. However, it was evident that ASM effectively induced plant resistance against Leaf Rust and Powdery Mildew in the field and can be considered a sustainable option for wheat cultivation. Even though its association with chemical control was not the best economic strategy the use of ASM is a tool that can be incorporated into wheat cultivation to minimize the emergence of fungicide-resistant pathogens due to the diversification of modes of action employed and reduce the toxic residue deposition to the environment and human health.
Collapse
Affiliation(s)
| | - Marco Antonio Bosse
- Agronomy Department, Federal University of Technology – Paraná, Pato Branco, PR, Brazil
| | - Diogo Capelin
- Agronomy Department, Federal University of Technology – Paraná, Pato Branco, PR, Brazil
| | - Marcos Vily Paladini
- Agronomy Department, Federal University of Technology – Paraná, Pato Branco, PR, Brazil
| | - Felipe Cattani
- Agronomy Department, Federal University of Technology – Paraná, Pato Branco, PR, Brazil
| | | | | | - Anelise Tessari Perboni
- Bioprocess and Biotechnology Engineering Department, Federal University of Technology – Paraná, Dois Vizinhos, PR, Brazil
| | - José Abramo Marchese
- Agronomy Department, Federal University of Technology – Paraná, Pato Branco, PR, Brazil
| |
Collapse
|
5
|
Kaur S, Gill HS, Breiland M, Kolmer JA, Gupta R, Sehgal SK, Gill U. Identification of leaf rust resistance loci in a geographically diverse panel of wheat using genome-wide association analysis. FRONTIERS IN PLANT SCIENCE 2023; 14:1090163. [PMID: 36818858 PMCID: PMC9929074 DOI: 10.3389/fpls.2023.1090163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Accepted: 01/16/2023] [Indexed: 06/18/2023]
Abstract
Leaf rust, caused by Puccinia triticina (Pt) is among the most devastating diseases posing a significant threat to global wheat production. The continuously evolving virulent Pt races in North America calls for exploring new sources of leaf rust resistance. A diversity panel of 365 bread wheat accessions selected from a worldwide population of landraces and cultivars was evaluated at the seedling stage against four Pt races (TDBJQ, TBBGS, MNPSD and, TNBJS). A wide distribution of seedling responses against the four Pt races was observed. Majority of the genotypes displayed a susceptible response with only 28 (9.8%), 59 (13.5%), 45 (12.5%), and 29 (8.1%) wheat accessions exhibiting a highly resistant response to TDBJQ, TBBGS, MNPSD and, TNBJS, respectively. Further, we conducted a high-resolution multi-locus genome-wide association study (GWAS) using a set of 302,524 high-quality single nucleotide polymorphisms (SNPs). The GWAS analysis identified 27 marker-trait associations (MTAs) for leaf rust resistance on different wheat chromosomes of which 20 MTAs were found in the vicinity of known Lr genes, MTAs, or quantitative traits loci (QTLs) identified in previous studies. The remaining seven significant MTAs identified represent genomic regions that harbor potentially novel genes for leaf rust resistance. Furthermore, the candidate gene analysis for the significant MTAs identified various genes of interest that may be involved in disease resistance. The identified resistant lines and SNPs linked to the QTLs in this study will serve as valuable resources in wheat rust resistance breeding programs.
Collapse
Affiliation(s)
- Shivreet Kaur
- Department of Plant Pathology, North Dakota State University, Fargo, ND, United States
| | - Harsimardeep S. Gill
- Department of Agronomy, Horticulture and Plant Science, South Dakota State University, Brookings, SD, United States
| | - Matthew Breiland
- Department of Plant Pathology, North Dakota State University, Fargo, ND, United States
| | - James A. Kolmer
- Cereal Disease Laboratory, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), St. Paul, MN, United States
| | - Rajeev Gupta
- Cereal Crops Research Unit, Edward T. Schafer Agricultural Research Center, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Fargo, ND, United States
| | - Sunish K. Sehgal
- Department of Agronomy, Horticulture and Plant Science, South Dakota State University, Brookings, SD, United States
| | - Upinder Gill
- Department of Plant Pathology, North Dakota State University, Fargo, ND, United States
| |
Collapse
|
6
|
Lhamo D, Sun Q, Zhang Q, Li X, Fiedler JD, Xia G, Faris JD, Gu YQ, Gill U, Cai X, Acevedo M, Xu SS. Genome-wide association analyses of leaf rust resistance in cultivated emmer wheat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:20. [PMID: 36683081 DOI: 10.1007/s00122-023-04281-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Accepted: 11/07/2022] [Indexed: 06/17/2023]
Abstract
Fifteen and eleven loci, with most loci being novel, were identified to associate with seedling and adult resistances, respectively, to the durum-specific races of leaf rust pathogen in cultivated emmer. Leaf rust, caused by Puccinia triticina (Pt), constantly threatens durum (Triticum turgidum ssp. durum) and bread wheat (Triticum aestivum) production worldwide. A Pt race BBBQD detected in California in 2009 poses a potential threat to durum production in North America because resistance source to this race is rare in durum germplasm. To find new resistance sources, we assessed a panel of 180 cultivated emmer wheat (Triticum turgidum ssp. dicoccum) accessions for seedling resistance to BBBQD and for adult resistance to a mixture of durum-specific races BBBQJ, CCMSS, and MCDSS in the field, and genotyped the panel using genotype-by-sequencing (GBS) and the 9 K SNP (Single Nucleotide Polymorphism) Infinium array. The results showed 24 and nine accessions consistently exhibited seedling and adult resistance, respectively, with two accessions providing resistance at both stages. We performed genome-wide association studies using 46,383 GBS and 4,331 9 K SNP markers and identified 15 quantitative trait loci (QTL) for seedling resistance located mostly on chromosomes 2B and 6B, and 11 QTL for adult resistance on 2B, 3B and 6A. Of these QTL, one might be associated with leaf rust resistance (Lr) gene Lr53, and two with the QTL previously reported in durum or hexaploid wheat. The remaining QTL are potentially associated with new Lr genes. Further linkage analysis and gene cloning are necessary to identify the causal genes underlying these QTL. The emmer accessions with high levels of resistance will be useful for developing mapping populations and adapted durum germplasm and varieties with resistance to the durum-specific races.
Collapse
Affiliation(s)
- Dhondup Lhamo
- USDA-ARS, Crop Improvement and Genetics Research Unit, Western Regional Research Center, Albany, CA, 94710, USA
| | - Qun Sun
- Department of Plant Sciences, North Dakota State University, Fargo, ND, 58108, USA
| | - Qijun Zhang
- Department of Plant Sciences, North Dakota State University, Fargo, ND, 58108, USA
| | - Xuehui Li
- Department of Plant Sciences, North Dakota State University, Fargo, ND, 58108, USA
| | - Jason D Fiedler
- USDA-ARS, Cereal Crops Research Unit, Edward T. Schafer Agricultural Research Center, Fargo, ND, 58102, USA
| | - Guangmin Xia
- Key Laboratory of Plant Development and Environmental Adaptation Biology, School of Life Science, Shandong University, Qingdao, 266237, China
| | - Justin D Faris
- USDA-ARS, Cereal Crops Research Unit, Edward T. Schafer Agricultural Research Center, Fargo, ND, 58102, USA
| | - Yong-Qiang Gu
- USDA-ARS, Crop Improvement and Genetics Research Unit, Western Regional Research Center, Albany, CA, 94710, USA
| | - Upinder Gill
- Department of Plant Pathology, North Dakota State University, Fargo, ND, 58108, USA
| | - Xiwen Cai
- USDA-ARS, Wheat, Sorghum and Forage Research Unit, and Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE, 68583, USA
| | - Maricelis Acevedo
- Department of Global Development, College of Agriculture and Life Sciences, Cornell University, Ithaca, NY, 14853, USA.
| | - Steven S Xu
- USDA-ARS, Crop Improvement and Genetics Research Unit, Western Regional Research Center, Albany, CA, 94710, USA.
| |
Collapse
|
7
|
Jankowicz-Cieslak J, Hofinger BJ, Jarc L, Junttila S, Galik B, Gyenesei A, Ingelbrecht IL, Till BJ. Spectrum and Density of Gamma and X-ray Induced Mutations in a Non-Model Rice Cultivar. PLANTS (BASEL, SWITZERLAND) 2022; 11:3232. [PMID: 36501272 PMCID: PMC9741009 DOI: 10.3390/plants11233232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 11/19/2022] [Accepted: 11/20/2022] [Indexed: 06/17/2023]
Abstract
Physical mutagens are a powerful tool used for genetic research and breeding for over eight decades. Yet, when compared to chemical mutagens, data sets on the effect of different mutagens and dosages on the spectrum and density of induced mutations remain lacking. To address this, we investigated the landscape of mutations induced by gamma and X-ray radiation in the most widely cultivated crop species: rice. A mutant population of a tropical upland rice, Oryza sativa L., was generated and propagated via self-fertilization for seven generations. Five dosages ranging from 75 Gy to 600 Gy in both X-ray and gamma-irradiated material were applied. In the process of a forward genetic screens, 11 unique rice mutant lines showing phenotypic variation were selected for mutation analysis via whole-genome sequencing. Thousands of candidate mutations were recovered in each mutant with single base substitutions being the most common, followed by small indels and structural variants. Higher dosages resulted in a higher accumulation of mutations in gamma-irradiated material, but not in X-ray-treated plants. The in vivo role of all annotated rice genes is yet to be directly investigated. The ability to induce a high density of single nucleotide and structural variants through mutagenesis will likely remain an important approach for functional genomics and breeding.
Collapse
Affiliation(s)
- Joanna Jankowicz-Cieslak
- Plant Breeding and Genetics Laboratory, FAO/IAEA Joint Division, International Atomic Energy Agency (IAEA), 2444 Seibersdorf, Austria
| | - Bernhard J. Hofinger
- Plant Breeding and Genetics Laboratory, FAO/IAEA Joint Division, International Atomic Energy Agency (IAEA), 2444 Seibersdorf, Austria
| | - Luka Jarc
- Plant Breeding and Genetics Laboratory, FAO/IAEA Joint Division, International Atomic Energy Agency (IAEA), 2444 Seibersdorf, Austria
| | - Sini Junttila
- Bioinformatics and Scientific Computing Core, Vienna Biocenter Core Facilities GmbH, Dr-Bohr-Gasse 3, 1030 Vienna, Austria
- Medical Bioinformatics Centre, Turku Bioscience Centre, University of Turku, Tykistökatu 6, 20520 Turku, Finland
- Medical Bioinformatics Centre, Turku Bioscience Centre, Åbo Akademi University, Tykistökatu 6, 20520 Turku, Finland
| | - Bence Galik
- Bioinformatics and Scientific Computing Core, Vienna Biocenter Core Facilities GmbH, Dr-Bohr-Gasse 3, 1030 Vienna, Austria
- Department of Clinical Molecular Biology, Medical University of Bialystok, 15-269 Bialystok, Poland
- Bioinformatics Research Group, Genomics and Bioinformatics Core Facility Szentágothai Research Centre, University of Pécs, H-7622 Pecs, Hungary
| | - Attila Gyenesei
- Bioinformatics and Scientific Computing Core, Vienna Biocenter Core Facilities GmbH, Dr-Bohr-Gasse 3, 1030 Vienna, Austria
- Bioinformatics Research Group, Genomics and Bioinformatics Core Facility Szentágothai Research Centre, University of Pécs, H-7622 Pecs, Hungary
| | - Ivan L. Ingelbrecht
- Plant Breeding and Genetics Laboratory, FAO/IAEA Joint Division, International Atomic Energy Agency (IAEA), 2444 Seibersdorf, Austria
| | - Bradley J. Till
- Plant Breeding and Genetics Laboratory, FAO/IAEA Joint Division, International Atomic Energy Agency (IAEA), 2444 Seibersdorf, Austria
- Veterinary Genetics Laboratory, University of California, Old Davis Road, Davis, CA 95616, USA
| |
Collapse
|
8
|
Tomaszewska P, Schwarzacher T, Heslop-Harrison JS(P. Oat chromosome and genome evolution defined by widespread terminal intergenomic translocations in polyploids. FRONTIERS IN PLANT SCIENCE 2022; 13:1026364. [PMID: 36483968 PMCID: PMC9725029 DOI: 10.3389/fpls.2022.1026364] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 10/14/2022] [Indexed: 06/17/2023]
Abstract
Structural chromosome rearrangements involving translocations, fusions and fissions lead to evolutionary variation between species and potentially reproductive isolation and variation in gene expression. While the wheats (Triticeae, Poaceae) and oats (Aveneae) all maintain a basic chromosome number of x=7, genomes of oats show frequent intergenomic translocations, in contrast to wheats where these translocations are relatively rare. We aimed to show genome structural diversity and genome relationships in tetraploid, hexaploid and octoploid Avena species and amphiploids, establishing patterns of intergenomic translocations across different oat taxa using fluorescence in situ hybridization (FISH) with four well-characterized repetitive DNA sequences: pAs120, AF226603, Ast-R171 and Ast-T116. In A. agadiriana (2n=4x=28), the selected probes hybridized to all chromosomes indicating that this species originated from one (autotetraploid) or closely related ancestors with the same genomes. Hexaploid amphiploids were confirmed as having the genomic composition AACCDD, while octoploid amphiploids showed three different genome compositions: AACCCCDD, AAAACCDD or AABBCCDD. The A, B, C, and D genomes of oats differ significantly in their involvement in non-centromeric, intercalary translocations. There was a predominance of distal intergenomic translocations from the C- into the D-genome chromosomes. Translocations from A- to C-, or D- to C-genome chromosomes were less frequent, proving that at least some of the translocations in oat polyploids are non-reciprocal. Rare translocations from A- to D-, D- to A- and C- to B-genome chromosomes were also visualized. The fundamental research has implications for exploiting genomic biodiversity in oat breeding through introgression from wild species potentially with contrasting chromosomal structures and hence deleterious segmental duplications or large deletions in amphiploid parental lines.
Collapse
Affiliation(s)
- Paulina Tomaszewska
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
- Department of Genetics and Cell Physiology, Faculty of Biological Sciences, University of Wrocław, Wrocław, Poland
| | - Trude Schwarzacher
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization/Guangdong Provincial, Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - J. S. (Pat) Heslop-Harrison
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization/Guangdong Provincial, Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| |
Collapse
|
9
|
Lehnert H, Berner T, Lang D, Beier S, Stein N, Himmelbach A, Kilian B, Keilwagen J. Insights into breeding history, hotspot regions of selection, and untapped allelic diversity for bread wheat breeding. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 112:897-918. [PMID: 36073999 DOI: 10.1111/tpj.15952] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 08/17/2022] [Accepted: 08/22/2022] [Indexed: 06/15/2023]
Abstract
Breeding has increasingly altered the genetics of crop plants since the domestication of their wild progenitors. It is postulated that the genetic diversity of elite wheat breeding pools is too narrow to cope with future challenges. In contrast, plant genetic resources (PGRs) of wheat stored in genebanks are valuable sources of unexploited genetic diversity. Therefore, to ensure breeding progress in the future, it is of prime importance to identify the useful allelic diversity available in PGRs and to transfer it into elite breeding pools. Here, a diverse collection consisting of modern winter wheat cultivars and genebank accessions was investigated based on reduced-representation genomic sequencing and an iSelect single nucleotide polymorphism (SNP) chip array. Analyses of these datasets provided detailed insights into population structure, levels of genetic diversity, sources of new allelic diversity, and genomic regions affected by breeding activities. We identified 57 regions representing genomic signatures of selection and 827 regions representing private alleles associated exclusively with genebank accessions. The presence of known functional wheat genes, quantitative trait loci, and large chromosomal modifications, i.e., introgressions from wheat wild relatives, provided initial evidence for putative traits associated within these identified regions. These findings were supported by the results of ontology enrichment analyses. The results reported here will stimulate further research and promote breeding in the future by allowing for the targeted introduction of novel allelic diversity into elite wheat breeding pools.
Collapse
Affiliation(s)
- Heike Lehnert
- Institute for Biosafety in Plant Biotechnology, Julius Kuehn Institute, Quedlinburg, Germany
| | - Thomas Berner
- Institute for Biosafety in Plant Biotechnology, Julius Kuehn Institute, Quedlinburg, Germany
| | - Daniel Lang
- PGSB, Helmholtz Center Munich, German Research Center for Environmental Health, Plant Genome and Systems Biology, Neuherberg, Germany
| | - Sebastian Beier
- Research Group Bioinformatics and Information Technology, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Nils Stein
- Research Group Genomics of Genetic Resources, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
- Center of integrated Breeding Research (CiBreed), Department of Crop Sciences, Georg-August-University, Göttingen, Germany
| | - Axel Himmelbach
- Research Group Genomics of Genetic Resources, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | | | - Jens Keilwagen
- Institute for Biosafety in Plant Biotechnology, Julius Kuehn Institute, Quedlinburg, Germany
| |
Collapse
|
10
|
Lu Y, Chen J, Chen B, Liu Q, Zhang H, Yang L, Chao Z, Tian E. High genetic diversity and low population differentiation of a medical plant Ficus hirta Vahl., uncovered by microsatellite loci: implications for conservation and breeding. BMC PLANT BIOLOGY 2022; 22:334. [PMID: 35820829 PMCID: PMC9277808 DOI: 10.1186/s12870-022-03734-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 07/04/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Wuzhimaotao (Radix Fici Hirtae) originates from the dry root of Ficus hirta (Moraceae), which is widely known as a medical and edible plant distributed in South China. As the increasing demand for Wuzhimaotao, the wild F. hirta has been extremely reduced during the past years. It is urgent to protect and rationally develop the wild resources of F. hirta for its sustainable utilization. However, a lack of genetic background of F. hirta makes it difficult to plan conservation and breeding strategies for this medical plant. In the present study, a total of 414 accessions of F. hirta from 7 provinces in southern China were evaluated for the population genetics using 9 polymorphic SSR markers. RESULTS A mean of 17.1 alleles per locus was observed. The expected heterozygosity (He) varied from 0.142 to 0.861 (mean = 0.706) in nine SSR loci. High genetic diversity (He = 0.706, ranged from 0.613 to 0.755) and low genetic differentiation among populations (G'ST = 0.147) were revealed at population level. In addition, analysis of molecular variance (AMOVA) indicated that the principal molecular variance existed within populations (96.2%) was significantly higher than that among populations (3.8%). Meanwhile, the three kinds of clustering methods analysis (STRUCTURE, PCoA and UPGMA) suggested that the sampled populations were clustered into two main genetic groups (K = 2). Mantel test showed a significant correlation between geographic and genetic distance among populations (R2 = 0.281, P < 0.001). Pollen flow, seed flow and/or geographical barriers might be the main factors that formed the current genetic patterns of F. hirta populations. CONCLUSIONS This is a comprehensive study of genetic diversity and population structure of F. hirta in southern China. We revealed the high genetic diversity and low population differentiation in this medicinal plant and clarified the causes of its current genetic patterns. Our study will provide novel insights into the exploitation and conservation strategies for F. hirta.
Collapse
Affiliation(s)
- Yi Lu
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou, 510515, China
| | - Jianling Chen
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou, 510515, China
| | - Bing Chen
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou, 510515, China
| | - Qianqian Liu
- Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou, 510095, China
| | - Hanlin Zhang
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou, 510515, China
| | - Liyuan Yang
- Department of Landscape Plants and Ornamental Horticulture, College of Landscape Architecture, Zhejiang Agriculture & Forestry University, Hangzhou, 311300, People's Republic of China.
- Zhejiang Provincial Key Laboratory of Germplasm Innovation and Utilization for Garden Plants, Zhejiang Agriculture & Forestry University, Hangzhou, 311300, People's Republic of China.
| | - Zhi Chao
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou, 510515, China.
| | - Enwei Tian
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou, 510515, China.
- Guangdong Provincial Key Laboratory of Chinese Medicine Pharmaceutics, Guangzhou, 510515, China.
- Guangdong Provincial Engineering Laboratory of Chinese Medicine Preparation Technology, Guangzhou, 510515, China.
| |
Collapse
|
11
|
Ben-Abu Y, Itsko M. Metabolome dynamics during wheat domestication. Sci Rep 2022; 12:8532. [PMID: 35595776 PMCID: PMC9122938 DOI: 10.1038/s41598-022-11952-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 04/25/2022] [Indexed: 11/09/2022] Open
Abstract
One of the most important crops worldwide is wheat. Wheat domestication took place about 10,000 years ago. Not only that its wild progenitors have been discovered and phenotypically characterized, but their genomes were also sequenced and compared to modern wheat. While comparative genomics is essential to track genes that contribute to improvement in crop yield, comparative analyses of functional biological end-products, such as metabolites, are still lacking. With the advent of rigorous mass-spectrometry technologies, it is now possible to address that problem on a big-data scale. In attempt to reveal classes of metabolites, which are associated with wheat domestication, we analyzed the metabolomes of wheat kernel samples from various wheat lines. These wheat lines represented subspecies of tetraploid wheat along primary and secondary domestications, including wild emmer, domesticated emmer, landraces durum, and modern durum. We detected that the groups of plant metabolites such as plant-defense metabolites, antioxidants and plant hormones underwent significant changes during wheat domestication. Our data suggest that these metabolites may have contributed to the improvement in the agricultural fitness of wheat. Closer evaluation of specific metabolic pathways may result in the future in genetically-engineered high-yield crops.
Collapse
Affiliation(s)
- Yuval Ben-Abu
- Department of Physics and Project Unit, Sapir Academic College, 79165, Sderot, Hof Ashkelon, Israel. .,Clarendon Laboratory, Department of Physics, University of Oxford, Oxford, UK.
| | - Mark Itsko
- WDS Inc., Contractor to Centers for Disease Control and Prevention, 1600 Clifton Road, Atlanta, GA, 30033, USA
| |
Collapse
|
12
|
Ferjaoui S, Aouini L, Slimane RB, Ammar K, Dreisigacker S, Schouten HJ, Sapkota S, Bahri BA, Ben M'Barek S, Visser RGF, Kema GHJ, Hamza S. Deciphering resistance to Zymoseptoria tritici in the Tunisian durum wheat landrace accession 'Agili39'. BMC Genomics 2022; 23:372. [PMID: 35581550 PMCID: PMC9112612 DOI: 10.1186/s12864-022-08560-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 04/14/2022] [Indexed: 01/28/2023] Open
Abstract
Background Septoria tritici blotch (STB), caused by Zymoseptoria tritici (Z. tritici), is an important biotic threat to durum wheat in the entire Mediterranean Basin. Although most durum wheat cultivars are susceptible to Z. tritici, research in STB resistance in durum wheat has been limited. Results In our study, we have identified resistance to a wide array of Z. tritici isolates in the Tunisian durum wheat landrace accession ‘Agili39’. Subsequently, a recombinant inbred population was developed and tested under greenhouse conditions at the seedling stage with eight Z. tritici isolates and for five years under field conditions with three Z. tritici isolates. Mapping of quantitative trait loci (QTL) resulted in the identification of two major QTL on chromosome 2B designated as Qstb2B_1 and Qstb2B_2. The Qstb2B_1 QTL was mapped at the seedling and the adult plant stage (highest LOD 33.9, explained variance 61.6%), conferring an effective resistance against five Z. tritici isolates. The Qstb2B_2 conferred adult plant resistance (highest LOD 32.9, explained variance 42%) and has been effective at the field trials against two Z. tritici isolates. The physical positions of the flanking markers linked to Qstb2B_1 and Qstb2B_2 indicate that these two QTL are 5 Mb apart. In addition, we identified two minor QTL on chromosomes 1A (Qstb1A) and chromosome 7A (Qstb7A) (highest LODs 4.6 and 4.0, and explained variances of 16% and 9%, respectively) that were specific to three and one Z. tritici isolates, respectively. All identified QTL were derived from the landrace accession Agili39 that represents a valuable source for STB resistance in durum wheat. Conclusion This study demonstrates that Z. tritici resistance in the ‘Agili39’ landrace accession is controlled by two minor and two major QTL acting in an additive mode. We also provide evidence that the broad efficacy of the resistance to STB in ‘Agili 39’ is due to a natural pyramiding of these QTL. A sustainable use of this Z. tritici resistance source and a positive selection of the linked markers to the identified QTL will greatly support effective breeding for Z. tritici resistance in durum wheat. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08560-2.
Collapse
Affiliation(s)
- Sahbi Ferjaoui
- Laboratory of Bioaggressors and Integrated Protection in Agriculture (BPIA), National Institute of Agronomy of Tunisia (INAT), 43 Avenue Charles Nicolle, 1082 El Mahrajène, Tunis, Tunisia.,Present Address Field Crops Laboratory, Regional Field Crops Research Center of Beja (CRRGC), P.O. Box 9000, Beja, Tunisia
| | - Lamia Aouini
- Bio-Interaction and Plant Health, Wageningen University and Research, PO Box 16, 6700AA, Wageningen, The Netherlands.,The Graduate School 'Experimental Plant Sciences' (EPS), Wageningen Campus, 6708 PB, Wageningen, The Netherlands.,Present Address Center for Desert Agriculture, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Rim B Slimane
- Laboratory of Bioaggressors and Integrated Protection in Agriculture (BPIA), National Institute of Agronomy of Tunisia (INAT), 43 Avenue Charles Nicolle, 1082 El Mahrajène, Tunis, Tunisia.,Present address Higher Institute of Agronomy of Chott Meriam (ISA-CM), 4042, Sousse, Tunisia
| | - Karim Ammar
- International Maize and Wheat Improvement Center (CIMMYT), Apdo. Postal 6‑641, 06600, Mexico, D.F., Mexico
| | - Suzanne Dreisigacker
- International Maize and Wheat Improvement Center (CIMMYT), Apdo. Postal 6‑641, 06600, Mexico, D.F., Mexico
| | - Henk J Schouten
- Plant Breeding, Wageningen University and Research, P.O. Box 386, 6700 AJ, Wageningen, The Netherlands
| | - Suraj Sapkota
- Institute of Plant Breeding, Genetics and Genomics, Department of Plant Pathology and Institute of Plant Breeding, University of Georgia, Griffin, GA, 30223, USA.,Present Address United States Department of Agriculture USDA, Crop Genetics and Breeding Research Unit, Tifton, GA, USA
| | - Bochra A Bahri
- Laboratory of Bioaggressors and Integrated Protection in Agriculture (BPIA), National Institute of Agronomy of Tunisia (INAT), 43 Avenue Charles Nicolle, 1082 El Mahrajène, Tunis, Tunisia.,Institute of Plant Breeding, Genetics and Genomics, Department of Plant Pathology and Institute of Plant Breeding, University of Georgia, Griffin, GA, 30223, USA
| | - Sarrah Ben M'Barek
- CRP-Wheat Septoria Phenotyping Platform (CIMMYT-IRESA), Regional Field Crops Research Center of Beja (CRRGC), BP 350, 9000, Beja, Tunisia
| | - Richard G F Visser
- Plant Breeding, Wageningen University and Research, P.O. Box 386, 6700 AJ, Wageningen, The Netherlands
| | - Gert H J Kema
- Bio-Interaction and Plant Health, Wageningen University and Research, PO Box 16, 6700AA, Wageningen, The Netherlands.,Laboratory of Phytopathology, Wageningen University and Research, PO box 16, 6700AA, Wageningen, The Netherlands
| | - Sonia Hamza
- Laboratory of Bioaggressors and Integrated Protection in Agriculture (BPIA), National Institute of Agronomy of Tunisia (INAT), 43 Avenue Charles Nicolle, 1082 El Mahrajène, Tunis, Tunisia.
| |
Collapse
|
13
|
Saxesena RR, Mishra VK, Chand R, Kumar U, Chowdhury AK, Bhati J, Budhlakoti N, Joshi AK. SNP Discovery Using BSR-Seq Approach for Spot Blotch Resistance in Wheat ( Triticum aestivum L.), an Essential Crop for Food Security. Front Genet 2022; 13:859676. [PMID: 35450212 PMCID: PMC9016274 DOI: 10.3389/fgene.2022.859676] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 02/17/2022] [Indexed: 11/13/2022] Open
Abstract
The pathogenic fungus, Bipolaris sorokiniana, that causes spot blotch (SB) disease of wheat, is a major production constraint in the Eastern Gangetic Plains of South Asia and other warm, humid regions of the world. A recombinant inbred line population was developed and phenotyped at three SB-prone locations in India. The single nucleotide polymorphism (SNP) for SB resistance was identified using a bulked segregant RNA-Seq-based approach, referred to as “BSR-Seq.” Transcriptome sequencing of the resistant parent (YS#24), the susceptible parent (YS#58), and their resistant and susceptible bulks yielded a total of 429.67 million raw reads. The bulk frequency ratio (BFR) of SNPs between the resistant and susceptible bulks was estimated, and selection of SNPs linked to resistance was done using sixfold enrichments in the corresponding bulks (BFR >6). With additional filtering criteria, the number of transcripts was further reduced to 506 with 1055 putative polymorphic SNPs distributed on 21 chromosomes of wheat. Based on SNP enrichment on chromosomal loci, five transcripts were found to be associated with SB resistance. Among the five SB resistance-associated transcripts, four were distributed on the 5B chromosome with putative 52 SNPs, whereas one transcript with eight SNPs was present on chromosome 3B. The SNPs linked to the trait were exposed to a tetra-primer ARMS-PCR assay, and an SNP-based allele-specific marker was identified for SB resistance. The in silico study of these five transcripts showed homology with pathogenesis-related genes; the metabolic pathway also exhibits similar results, suggesting their role in the plant defense mechanism.
Collapse
Affiliation(s)
- Ravi Ranjan Saxesena
- Department of Genetics and Plant Breeding, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi, India
| | - Vinod Kumar Mishra
- Department of Genetics and Plant Breeding, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi, India
| | - Ramesh Chand
- Department of Mycology and Plant Pathology, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi, India
| | - Uttam Kumar
- Borlaug Institute for South Asia (BISA), Ludhiana, India
| | | | - Jyotika Bhati
- ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Neeraj Budhlakoti
- ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Arun Kumar Joshi
- Borlaug Institute for South Asia (BISA), Ludhiana, India.,International Maize and Wheat Improvement Center (CIMMYT) and Borlaug Institute for South Asia (BISA), DPS Marg, New Delhi, India
| |
Collapse
|
14
|
Lyu Z, Hao Y, Chen L, Xu S, Wang H, Li M, Ge W, Hou B, Cheng X, Li X, Che N, Zhen T, Sun S, Bao Y, Yang Z, Jia J, Kong L, Wang H. Wheat- Thinopyrum Substitution Lines Imprint Compensation Both From Recipients and Donors. FRONTIERS IN PLANT SCIENCE 2022; 13:837410. [PMID: 35498638 PMCID: PMC9051513 DOI: 10.3389/fpls.2022.837410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 02/04/2022] [Indexed: 06/14/2023]
Abstract
Even frequently used in wheat breeding, we still have an insufficient understanding of the biology of the products via distant hybridization. In this study, a transcriptomic analysis was performed for six Triticum aestivum-Thinopyrum elongatum substitution lines in comparison with the host plants. All the six disomic substitution lines showed much stronger "transcriptomic-shock" occurred on alien genomes with 57.43-69.22% genes changed expression level but less on the recipient genome (2.19-8.97%). Genome-wide suppression of alien genes along chromosomes was observed with a high proportion of downregulated genes (39.69-48.21%). Oppositely, the wheat recipient showed genome-wide compensation with more upregulated genes, occurring on all chromosomes but not limited to the homeologous groups. Moreover, strong co-upregulation of the orthologs between wheat and Thinopyrum sub-genomes was enriched in photosynthesis with predicted chloroplastic localization, which indicates that the compensation happened not only on wheat host genomes but also on alien genomes.
Collapse
Affiliation(s)
- Zhongfan Lyu
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Taian, China
| | - Yongchao Hao
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Taian, China
| | - Liyang Chen
- Smartgenomics Technology Institute, Tianjin, China
| | - Shoushen Xu
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Taian, China
| | - Hongjin Wang
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, China
| | - Mengyao Li
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Taian, China
| | - Wenyang Ge
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Taian, China
| | - Bingqian Hou
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Taian, China
| | - Xinxin Cheng
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Taian, China
| | - Xuefeng Li
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Taian, China
| | - Naixiu Che
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Taian, China
| | - Tianyue Zhen
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Taian, China
| | - Silong Sun
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Taian, China
| | - Yinguang Bao
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Taian, China
| | - Zujun Yang
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, China
| | - Jizeng Jia
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Lingrang Kong
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Taian, China
| | - Hongwei Wang
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Taian, China
| |
Collapse
|
15
|
Adhikari L, Raupp J, Wu S, Wilson D, Evers B, Koo DH, Singh N, Friebe B, Poland J. Genetic characterization and curation of diploid A-genome wheat species. PLANT PHYSIOLOGY 2022; 188:2101-2114. [PMID: 35134208 PMCID: PMC8968256 DOI: 10.1093/plphys/kiac006] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 12/17/2021] [Indexed: 06/14/2023]
Abstract
A-genome diploid wheats represent the earliest domesticated and cultivated wheat species in the Fertile Crescent and include the donor of the wheat A sub-genome. The A-genome species encompass the cultivated einkorn (Triticum monococcum L. subsp. monococcum), wild einkorn (T. monococcum L. subsp. aegilopoides (Link) Thell.), and Triticum urartu. We evaluated the collection of 930 accessions in the Wheat Genetics Resource Center (WGRC) using genotyping by sequencing and identified 13,860 curated single-nucleotide polymorphisms. Genomic analysis detected misclassified and genetically identical (>99%) accessions, with most of the identical accessions originating from the same or nearby locations. About 56% (n = 520) of the WGRC A-genome species collections were genetically identical, supporting the need for genomic characterization for effective curation and maintenance of these collections. Population structure analysis confirmed the morphology-based classifications of the accessions and reflected the species geographic distributions. We also showed that T. urartu is the closest A-genome diploid to the A-subgenome in common wheat (Triticum aestivum L.) through phylogenetic analysis. Population analysis within the wild einkorn group showed three genetically distinct clusters, which corresponded with wild einkorn races α, β, and γ described previously. The T. monococcum genome-wide FST scan identified candidate genomic regions harboring a domestication selection signature at the Non-brittle rachis 1 (Btr1) locus on the short arm of chromosome 3Am at ∼70 Mb. We established an A-genome core set (79 accessions) based on allelic diversity, geographical distribution, and available phenotypic data. The individual species core set maintained at least 79% of allelic variants in the A-genome collection and constituted a valuable genetic resource to improve wheat and domesticated einkorn in breeding programs.
Collapse
Affiliation(s)
- Laxman Adhikari
- Department of Plant Pathology, Kansas State University, Manhattan, Kansas 66502, USA
- Wheat Genetic Resource Center (WGRC), Kansas State University, Manhattan, Kansas 66502, USA
- Center for Desert Agriculture, King Abdullah University of Science and Technology, Thuwal 23955, Saudi Arabia
| | - John Raupp
- Department of Plant Pathology, Kansas State University, Manhattan, Kansas 66502, USA
- Wheat Genetic Resource Center (WGRC), Kansas State University, Manhattan, Kansas 66502, USA
| | - Shuangye Wu
- Department of Plant Pathology, Kansas State University, Manhattan, Kansas 66502, USA
- Wheat Genetic Resource Center (WGRC), Kansas State University, Manhattan, Kansas 66502, USA
| | - Duane Wilson
- Department of Plant Pathology, Kansas State University, Manhattan, Kansas 66502, USA
- Wheat Genetic Resource Center (WGRC), Kansas State University, Manhattan, Kansas 66502, USA
| | - Byron Evers
- Department of Plant Pathology, Kansas State University, Manhattan, Kansas 66502, USA
- Wheat Genetic Resource Center (WGRC), Kansas State University, Manhattan, Kansas 66502, USA
| | - Dal-Hoe Koo
- Department of Plant Pathology, Kansas State University, Manhattan, Kansas 66502, USA
- Wheat Genetic Resource Center (WGRC), Kansas State University, Manhattan, Kansas 66502, USA
| | | | - Bernd Friebe
- Department of Plant Pathology, Kansas State University, Manhattan, Kansas 66502, USA
- Wheat Genetic Resource Center (WGRC), Kansas State University, Manhattan, Kansas 66502, USA
| | | |
Collapse
|
16
|
Yield-Related QTL Clusters and the Potential Candidate Genes in Two Wheat DH Populations. Int J Mol Sci 2021; 22:ijms222111934. [PMID: 34769361 PMCID: PMC8585063 DOI: 10.3390/ijms222111934] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 10/21/2021] [Accepted: 10/28/2021] [Indexed: 11/17/2022] Open
Abstract
In the present study, four large-scale field trials using two doubled haploid wheat populations were conducted in different environments for two years. Grain protein content (GPC) and 21 other yield-related traits were investigated. A total of 227 QTL were mapped on 18 chromosomes, which formed 35 QTL clusters. The potential candidate genes underlying the QTL clusters were suggested. Furthermore, adding to the significant correlations between yield and its related traits, correlation variations were clearly shown within the QTL clusters. The QTL clusters with consistently positive correlations were suggested to be directly utilized in wheat breeding, including 1B.2, 2A.2, 2B (4.9–16.5 Mb), 2B.3, 3B (68.9–214.5 Mb), 4A.2, 4B.2, 4D, 5A.1, 5A.2, 5B.1, and 5D. The QTL clusters with negative alignments between traits may also have potential value for yield or GPC improvement in specific environments, including 1A.1, 2B.1, 1B.3, 5A.3, 5B.2 (612.1–613.6 Mb), 7A.1, 7A.2, 7B.1, and 7B.2. One GPC QTL (5B.2: 671.3–672.9 Mb) contributed by cultivar Spitfire was positively associated with nitrogen use efficiency or grain protein yield and is highly recommended for breeding use. Another GPC QTL without negatively pleiotropic effects on 2A (50.0–56.3 Mb), 2D, 4D, and 6B is suggested for quality wheat breeding.
Collapse
|
17
|
Perronne R, Dubs F, de Vallavieille-Pope C, Leconte M, du Cheyron P, Cadot V, Vidal T, Enjalbert J. Spatiotemporal Changes in Varietal Resistance to Wheat Yellow Rust in France Reveal an Increase in Field Resistance Level During the Period 1985-2018. PHYTOPATHOLOGY 2021; 111:1602-1612. [PMID: 34695367 DOI: 10.1094/phyto-05-20-0187-r] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Monitoring spatiotemporal changes in varietal resistance and understanding its drivers seem essential to managing plant diseases but require having access to the genetic basis of disease resistance and to its deployment. In this study, we focused on yellow rust (Puccinia striiformis f. sp. tritici) for three decades in France, by using field adult plant resistance levels, Yr race-specific resistance genes of varieties, presence of Puccinia striiformis f. sp. tritici pathotypes and their virulence profiles, and systematic surveys of the acreages of bread wheat varieties available at a yearly survey time and at a district level. Based on these data, we studied spatiotemporal changes in varietal resistance over the period from 1985 to 2018 in 54 French administrative districts (hereafter "departments") by using a set of relevant indicators weighted by the relative acreage proportion of the varieties sown at the department level. Our analyses revealed an increase in varietal resistance over decades that would be due to the accumulation of both quantitative resistance and different race-specific resistance genes. We suggest that, beyond breeders, several actors, including examination offices, agricultural advisory services, and farmers, may have had a substantial influence on these spatiotemporal changes, promoting more resistant varieties and the rapid replacement of newly susceptible varieties by still resistant ones at the beginning of each epidemic.
Collapse
Affiliation(s)
- Rémi Perronne
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE-Le Moulon, 91190 Gif-sur-Yvette, France
- IGEPP, INRAE, Institut Agro, Université Rennes, 35653 Le Rheu, France
| | - Florence Dubs
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE-Le Moulon, 91190 Gif-sur-Yvette, France
| | | | - Marc Leconte
- Université Paris-Saclay, INRAE, AgroParisTech, UMR BIOGER, 78850 Thiverval-Grignon, France
| | | | | | - Tiphaine Vidal
- Université Paris-Saclay, INRAE, AgroParisTech, UMR BIOGER, 78850 Thiverval-Grignon, France
| | - Jérôme Enjalbert
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE-Le Moulon, 91190 Gif-sur-Yvette, France
| |
Collapse
|
18
|
Steadham J, Schulden T, Kalia B, Koo DH, Gill BS, Bowden R, Yadav IS, Chhuneja P, Erwin J, Tiwari V, Rawat N. An approach for high-resolution genetic mapping of distant wild relatives of bread wheat: example of fine mapping of Lr57 and Yr40 genes. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:2671-2686. [PMID: 34013456 DOI: 10.1007/s00122-021-03851-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 04/29/2021] [Indexed: 06/12/2023]
Abstract
The article reports a powerful but simple approach for high-resolution mapping and eventual map-based cloning of agronomically important genes from distant relatives of wheat, using the already existing germplasm resources. Wild relatives of wheat are a rich reservoir of genetic diversity for its improvement. The effective utilization of distant wild relatives in isolation of agronomically important genes is hindered by the lack of recombination between the homoeologous chromosomes. In this study, we propose a simple yet powerful approach that can be applied for high-resolution mapping of a targeted gene from wheat's distant gene pool members. A wheat-Aegilops geniculata translocation line TA5602 with a small terminal segment from chromosome 5 Mg of Ae. geniculata translocated to 5D of wheat contains genes Lr57 and Yr40 for leaf rust and stripe rust resistance, respectively. To map these genes, TA5602 was crossed with a susceptible Ae. geniculata 5 Mg addition line. Chromosome pairing between the 5 Mg chromosomes of susceptible and resistant parents resulted in the development of a high-resolution mapping panel for the targeted genes. Next-generation-sequencing data from flow-sorted 5 Mg chromosome of Ae. geniculata allowed us to generate 5 Mg-specific markers. These markers were used to delineate Lr57 and Yr40 genes each to distinct ~ 1.5 Mb physical intervals flanked by gene markers on 5 Mg. The method presented here will allow researchers worldwide to utilize existing germplasm resources in genebanks and seed repositories toward routinely performing map-based cloning of important genes from tertiary gene pools of wheat.
Collapse
Affiliation(s)
- James Steadham
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, 20742, USA
| | - Taylor Schulden
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, 20742, USA
| | - Bhanu Kalia
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA
| | - Dal-Hoe Koo
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA
| | - Bikram S Gill
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA
| | - Robert Bowden
- Hard Winter Wheat Genetics Research Unit, USDA-ARS, Manhattan, KS, 66506, USA
| | - Inderjit Singh Yadav
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, 20742, USA
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, Punjab, 141004, India
| | - Parveen Chhuneja
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, Punjab, 141004, India
| | - John Erwin
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, 20742, USA
| | - Vijay Tiwari
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, 20742, USA.
| | - Nidhi Rawat
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, 20742, USA.
| |
Collapse
|
19
|
Tomar V, Dhillon GS, Singh D, Singh RP, Poland J, Joshi AK, Tiwari BS, Kumar U. Elucidating SNP-based genetic diversity and population structure of advanced breeding lines of bread wheat ( Triticum aestivum L .). PeerJ 2021; 9:e11593. [PMID: 34221720 PMCID: PMC8231316 DOI: 10.7717/peerj.11593] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 05/20/2021] [Indexed: 11/20/2022] Open
Abstract
Genetic diversity and population structure information are crucial for enhancing traits of interest and the development of superlative varieties for commercialization. The present study elucidated the population structure and genetic diversity of 141 advanced wheat breeding lines using single nucleotide polymorphism markers. A total of 14,563 high-quality identified genotyping-by-sequencing (GBS) markers were distributed covering 13.9 GB wheat genome, with a minimum of 1,026 SNPs on the homoeologous group four and a maximum of 2,838 SNPs on group seven. The average minor allele frequency was found 0.233, although the average polymorphism information content (PIC) and heterozygosity were 0.201 and 0.015, respectively. Principal component analyses (PCA) and population structure identified two major groups (sub-populations) based on SNPs information. The results indicated a substantial gene flow/exchange with many migrants (Nm = 86.428) and a considerable genetic diversity (number of different alleles, Na = 1.977; the number of effective alleles, Ne = 1.519; and Shannon's information index, I = 0.477) within the population, illustrating a good source for wheat improvement. The average PIC of 0.201 demonstrates moderate genetic diversity of the present evaluated advanced breeding panel. Analysis of molecular variance (AMOVA) detected 1% and 99% variance between and within subgroups. It is indicative of excessive gene traffic (less genetic differentiation) among the populations. These conclusions deliver important information with the potential to contribute new beneficial alleles using genome-wide association studies (GWAS) and marker-assisted selection to enhance genetic gain in South Asian wheat breeding programs.
Collapse
Affiliation(s)
- Vipin Tomar
- Borlaug Institute for South Asia, New Delhi, Delhi, India.,Department of Biological Sciences and Biotechnology, Institute of Advanced Research, Gandhinagar, Gandhinagar, Gujarat, India.,International Maize and Wheat Improvement Centre, New Delhi, Delhi, India
| | - Guriqbal Singh Dhillon
- Department of Biotechnology, Thapar Institute of Engineering and Technology, Patiala, Punjab, India
| | - Daljit Singh
- The Climate Corporation, Bayer Crop Science, Creve Coeur, MO, USA
| | - Ravi Prakash Singh
- Global Wheat Program, International Maize and Wheat Improvement Centre, Texcoco, Mexico
| | - Jesse Poland
- Department of Plant Pathology, Kansas State University, Manhattan, KS, United States of America
| | - Arun Kumar Joshi
- Borlaug Institute for South Asia, New Delhi, Delhi, India.,International Maize and Wheat Improvement Centre, New Delhi, Delhi, India.,Global Wheat Program, International Maize and Wheat Improvement Centre, Texcoco, Mexico
| | - Budhi Sagar Tiwari
- Department of Biological Sciences and Biotechnology, Institute of Advanced Research, Gandhinagar, Gandhinagar, Gujarat, India
| | - Uttam Kumar
- Borlaug Institute for South Asia, New Delhi, Delhi, India.,International Maize and Wheat Improvement Centre, New Delhi, Delhi, India.,Global Wheat Program, International Maize and Wheat Improvement Centre, Texcoco, Mexico
| |
Collapse
|
20
|
Kuzmanović L, Giovenali G, Ruggeri R, Rossini F, Ceoloni C. Small "Nested" Introgressions from Wild Thinopyrum Species, Conferring Effective Resistance to Fusarium Diseases, Positively Impact Durum Wheat Yield Potential. PLANTS (BASEL, SWITZERLAND) 2021; 10:579. [PMID: 33808545 PMCID: PMC8003120 DOI: 10.3390/plants10030579] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Revised: 03/15/2021] [Accepted: 03/17/2021] [Indexed: 11/16/2022]
Abstract
Today wheat cultivation is facing rapidly changing climate scenarios and yield instability, aggravated by the spreading of severe diseases such as Fusarium head blight (FHB) and Fusarium crown rot (FCR). To obtain productive genotypes resilient to stress pressure, smart breeding approaches must be envisaged, including the exploitation of wild relatives. Here we report on the assessment of the breeding potential of six durum wheat-Thinopyrum spp. recombinant lines (RLs) obtained through chromosome engineering. They are characterized by having 23% or 28% of their 7AL chromosome arm replaced by a "nested" alien segment, composed of homoeologous group 7 chromosome fractions from Th. ponticum and Th. elongatum (=7el1L + 7EL) or from different Th. ponticum accessions (=7el1L + 7el2L). In addition to the 7el1L genes Lr19 + Yp (leaf rust resistance, and yellow pigment content, respectively), these recombinant lines (RLs) possess a highly effective QTL for resistance to FHB and FCR within their 7el2L or 7EL portion. The RLs, their null segregants and well-adapted and productive durum wheat cultivars were evaluated for 16 yield-related traits over two seasons under rainfed and irrigated conditions. The absence of yield penalties and excellent genetic stability of RLs was revealed in the presence of all the alien segment combinations. Both 7el2L and 7EL stacked introgressions had positive impacts on source and sink yield traits, as well as on the overall performance of RLs in conditions of reduced water availability. The four "nested" RLs tested in 2020 were among the top five yielders, overall representing good candidates to be employed in breeding programs to enhance crop security and safety.
Collapse
Affiliation(s)
- Ljiljana Kuzmanović
- Department of Agriculture and Forestry Science, University of Tuscia, 01100 Viterbo, Italy; (G.G.); (R.R.); (F.R.); (C.C.)
| | | | | | | | | |
Collapse
|
21
|
Motta-Romero H, Niyongira F, Boehm JD, Rose DJ. Effects of foliar fungicide on yield, micronutrients, and cadmium in grains from historical and modern hard winter wheat genotypes. PLoS One 2021; 16:e0247809. [PMID: 33662021 PMCID: PMC7932086 DOI: 10.1371/journal.pone.0247809] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 02/16/2021] [Indexed: 11/19/2022] Open
Abstract
Plant breeding and disease management practices have increased the grain yield of hard winter wheat (Triticum aestivum L.) adapted to the Great Plains of the United States during the last century. However, the effect of genetic gains for seed yield and the application of fungicide on the micronutrient and cadmium (Cd) concentration in wheat grains is still unclear. The objectives of this study were to evaluate the effects of fungicide application on the productivity and nutritional quality of wheat cultivars representing 80 years of plant breeding efforts. Field experiments were conducted over two crop years (2017 and 2018) with eighteen hard winter wheat genotypes released between 1933 and 2013 in the presence or absence of fungicide application. For each growing season, the treatments were arranged in a split-plot design with the fungicide levels (treated and untreated) as the whole plot treatments and the genotypes as split-plot treatments in triplicate. The effects on seed yield, grain protein concentration (GPC), micronutrients, phytic acid, and Cd in grains were measured. While the yield of wheat was found to increase at annualized rates of 26.5 and 13.0 kg ha-1 yr-1 in the presence and absence of fungicide (P < 0.001), respectively, GPC (-190 and -180 mg kg-1 yr-1, P < 0.001), Fe (-35.0 and -44.0 μg kg-1 yr-1, P < 0.05), and Zn (-68.0 and -57.0 μg kg-1 yr-1, P < 0.01) significantly decreased during the period studied. In contrast to the other mineral elements, grain Cd significantly increased over time (0.4 μg kg-1 yr-1, P < 0.01) in the absence of fungicide. The results from this study are of great concern, as many mineral elements essential for human nutrition have decreased over time while the toxic heavy metal, Cd, has increased, indicating modern wheats are becoming a better vector of dietary Cd.
Collapse
Affiliation(s)
- Hollman Motta-Romero
- Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, NE, United States of America
| | - Ferdinand Niyongira
- Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, NE, United States of America
| | - Jeffrey D. Boehm
- Wheat, Sorghum and Forage Research Unit, US Department of Agriculture-Agricultural Research Service, Lincoln, NE, United States of America
| | - Devin J. Rose
- Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, NE, United States of America
- Department of Agronomy & Horticulture, University of Nebraska-Lincoln, NE, United States of America
| |
Collapse
|
22
|
Rai A, Ahlawat AK, Shukla RB, Jain N, Kumar RR, Mahendru-Singh A. Quality evaluation of near-isogenic line of the wheat variety HD2733 carrying the Lr24/Sr24 genomic region. 3 Biotech 2021; 11:130. [PMID: 33680695 DOI: 10.1007/s13205-021-02679-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 02/04/2021] [Indexed: 01/23/2023] Open
Abstract
A near-isogenic line (NIL) of the Indian wheat variety HD2733, carrying an introgressed Lr24/Sr24 genomic region was used for studying the effect of this introgression on quality traits. Data on the grain yield and 21 quality traits were recorded in this NIL and its recurrent parent (RP), both of which were grown in a randomized block design for two consecutive years. The statistical analysis revealed that grain yield was on par between the NIL and the RP. The NIL and its RP were both hard grained but the NIL showed a grain hardness index reduced by 9.7%. However, quality traits such as grain weight, protein content, sedimentation value, gluten traits, and solvent retention capacity were significantly higher in the NIL. The NIL also showed an increase in dough stability, a lower degree of softening and a higher farinograph quality number. These results indicated that the NIL could be utilized for hard grain, high protein and strong gluten-based products. An overall improvement in the quality of the NIL over its recurrent parent and without any yield penalty suggests that the Lr24/Sr24 genomic region could be gainfully utilized in wheat breeding for improving the industrial quality of wheat without jeopardising grain yield. The authors suggest that the improved quality of the NIL may be due to the genomic segment carried along with the Lr24/Sr24 genes. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s13205-021-02679-x.
Collapse
Affiliation(s)
- Anjali Rai
- Department of Biotechnology, Amity Institute of Biotechnology, Amity University, Noida, 201313 India
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, 110012 India
| | - Arvind K Ahlawat
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, 110012 India
| | - R B Shukla
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, 110012 India
| | - Neelu Jain
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, 110012 India
| | - Rajeev Ranjan Kumar
- Division of Forecasting and Agricultural System Modelling, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, 110012 India
| | - Anju Mahendru-Singh
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, 110012 India
| |
Collapse
|
23
|
Tomar V, Singh D, Dhillon GS, Singh RP, Poland J, Joshi AK, Singh PK, Bhati PK, Kumar S, Rahman M, Tiwari BS, Kumar U. New QTLs for Spot Blotch Disease Resistance in Wheat ( Triticum aestivum L.) Using Genome-Wide Association Mapping. Front Genet 2021; 11:613217. [PMID: 33519916 PMCID: PMC7841440 DOI: 10.3389/fgene.2020.613217] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 12/10/2020] [Indexed: 11/13/2022] Open
Abstract
Spot blotch disease caused by Bipolaris sorokiniana is a major constraint for wheat production in tropics and subtropics. The introgression of spot blotch resistance alleles to the disease susceptible lines is critical to securing the wheat production in these regions. Although genome-wide association studies (GWASs) for spot blotch were attempted earlier, the present study focused on identifying new quantitative trait loci (QTLs) for spot blotch under natural disease pressure in diverse field conditions. A total of 139 advanced spring wheat lines were evaluated in three environments (three years and two locations) in India and Bangladesh. The GWAS using 14,063 polymorphic genotyping-by-sequencing (GBS) markers identified eight QTLs associated with spot blotch disease resistance belonging to eight chromosomes across the wheat genome. Here, we report the identified marker–trait associations (MTAs), along with the allele effects associated with the disease. The functional annotation of the significant markers identified NBS-LRR, MADS-box transcription factor, and 34 other plant-related protein families across multiple chromosomal regions. The results indicate four promising new QTLs on chromosomes 1A (497.2 Mb), 1D (89.84 Mb), 2B (421.92 Mb), and 6D (6.84 Mb) associated with several disease resistance protein families. These results provide insights into new genomic regions associated with spot blotch disease, and with additional validation, could be utilized in disease resistance breeding efforts in wheat development.
Collapse
Affiliation(s)
- Vipin Tomar
- Borlaug Institute for South Asia, Ludhiana, India.,Institute of Advanced Research, Gandhinagar, Gujarat, India
| | - Daljit Singh
- The Climate Corporation, Bayer Crop Science, Creve Coeur, MO, United States
| | - Guriqbal Singh Dhillon
- Department of Biotechnology, Thapar Institute of Engineering and Technology, Patiala, India
| | - Ravi Prakash Singh
- Global Wheat Program, International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
| | - Jesse Poland
- Department of Plant Pathology, Kansas State University, Manhattan, KS, United States
| | - Arun Kumar Joshi
- Borlaug Institute for South Asia, Ludhiana, India.,International Maize and Wheat Improvement Centre, New Delhi, India
| | - Pawan Kumar Singh
- Global Wheat Program, International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
| | | | - Suneel Kumar
- Borlaug Institute for South Asia, Ludhiana, India
| | - Mokhlesur Rahman
- Wheat Research Center, Regional Agricultural Research Station, Bangladesh Agricultural Research Institute, Jamalpur, Bangladesh
| | | | - Uttam Kumar
- Borlaug Institute for South Asia, Ludhiana, India.,Global Wheat Program, International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
| |
Collapse
|
24
|
Hawliczek A, Bolibok L, Tofil K, Borzęcka E, Jankowicz-Cieślak J, Gawroński P, Kral A, Till BJ, Bolibok-Brągoszewska H. Deep sampling and pooled amplicon sequencing reveals hidden genic variation in heterogeneous rye accessions. BMC Genomics 2020; 21:845. [PMID: 33256606 PMCID: PMC7706248 DOI: 10.1186/s12864-020-07240-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Accepted: 11/18/2020] [Indexed: 01/16/2023] Open
Abstract
BACKGROUND Loss of genetic variation negatively impacts breeding efforts and food security. Genebanks house over 7 million accessions representing vast allelic diversity that is a resource for sustainable breeding. Discovery of DNA variations is an important step in the efficient use of these resources. While technologies have improved and costs dropped, it remains impractical to consider resequencing millions of accessions. Candidate genes are known for most agronomic traits, providing a list of high priority targets. Heterogeneity in seed stocks means that multiple samples from an accession need to be evaluated to recover available alleles. To address this we developed a pooled amplicon sequencing approach and applied it to the out-crossing cereal rye (Secale cereale L.). RESULTS Using the amplicon sequencing approach 95 rye accessions of different improvement status and worldwide origin, each represented by a pooled sample comprising DNA of 96 individual plants, were evaluated for sequence variation in six candidate genes with significant functions on biotic and abiotic stress resistance, and seed quality. Seventy-four predicted deleterious variants were identified using multiple algorithms. Rare variants were recovered including those found only in a low percentage of seed. CONCLUSIONS We conclude that this approach provides a rapid and flexible method for evaluating stock heterogeneity, probing allele diversity, and recovering previously hidden variation. A large extent of within-population heterogeneity revealed in the study provides an important point for consideration during rye germplasm conservation and utilization efforts.
Collapse
Affiliation(s)
- Anna Hawliczek
- Department of Plant Genetics, Breeding and Biotechnology, Institute of Biology, Warsaw University of Life Sciences - SGGW, Warsaw, Poland
| | - Leszek Bolibok
- Department of Silviculture, Institute of Forest Sciences, Warsaw University of Life Sciences - SGGW, Warsaw, Poland
| | - Katarzyna Tofil
- Department of Plant Genetics, Breeding and Biotechnology, Institute of Biology, Warsaw University of Life Sciences - SGGW, Warsaw, Poland
| | - Ewa Borzęcka
- Department of Plant Genetics, Breeding and Biotechnology, Institute of Biology, Warsaw University of Life Sciences - SGGW, Warsaw, Poland
| | - Joanna Jankowicz-Cieślak
- Plant Breeding and Genetics Laboratory, Joint FAO/IAEA Division of Nuclear Techniques in Food and Agriculture, IAEA Laboratories Seibersdorf, International Atomic Energy Agency, Vienna International Centre, Vienna, Austria
| | - Piotr Gawroński
- Department of Plant Genetics, Breeding and Biotechnology, Institute of Biology, Warsaw University of Life Sciences - SGGW, Warsaw, Poland
| | - Adam Kral
- Department of Plant Genetics, Breeding and Biotechnology, Institute of Biology, Warsaw University of Life Sciences - SGGW, Warsaw, Poland
| | - Bradley J Till
- Plant Breeding and Genetics Laboratory, Joint FAO/IAEA Division of Nuclear Techniques in Food and Agriculture, IAEA Laboratories Seibersdorf, International Atomic Energy Agency, Vienna International Centre, Vienna, Austria.
- Veterinary Genetics Laboratory, University of California, Davis, Davis, California, USA.
| | - Hanna Bolibok-Brągoszewska
- Department of Plant Genetics, Breeding and Biotechnology, Institute of Biology, Warsaw University of Life Sciences - SGGW, Warsaw, Poland.
| |
Collapse
|
25
|
Pronin D, Börner A, Weber H, Scherf KA. Wheat ( Triticum aestivum L.) Breeding from 1891 to 2010 Contributed to Increasing Yield and Glutenin Contents but Decreasing Protein and Gliadin Contents. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:13247-13256. [PMID: 32648759 DOI: 10.1021/acs.jafc.0c02815] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Epidemiologic studies suggest an increasing prevalence of celiac disease and non-celiac gluten/wheat sensitivity. With wheat proteins being the main triggers, changes in wheat protein composition are discussed as a potential cause. The goals of breeding toward increased yield and resistance might have inadvertently contributed to a higher immunostimulatory potential of modern wheat cultivars compared to old wheat cultivars. Therefore, agronomic characteristics, protein content, and gluten composition of 60 German winter wheat cultivars first registered between 1891 and 2010 grown in 3 years were analyzed. While plant height and spike density decreased over time, yield and harvest index increased. The protein and gliadin contents showed a decreasing trend, whereas glutenin contents increased, but there were no changes in albumin/globulin and gluten contents. Overall, the harvest year had a more significant effect on protein composition than the cultivar. At the protein level, we found no evidence to support an increased immunostimulatory potential of modern winter wheat.
Collapse
Affiliation(s)
- Darina Pronin
- Leibniz-Institute for Food Systems Biology at the Technical University of Munich, Lise-Meitner-Straße 34, 85354 Freising, Germany
| | - Andreas Börner
- Genebank Department, Leibniz Institute of Plant Genetics and Crop Plant Research, Corrensstraße 3, 06466 Seeland/OT Gatersleben, Germany
| | - Hans Weber
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research, Corrensstraße 3, 06466 Seeland/OT Gatersleben, Germany
| | - Katharina Anne Scherf
- Leibniz-Institute for Food Systems Biology at the Technical University of Munich, Lise-Meitner-Straße 34, 85354 Freising, Germany
- Department of Bioactive and Functional Food Chemistry, Institute of Applied Biosciences, Karlsruhe Institute of Technology (KIT), Adenauerring 20a, 76131 Karlsruhe, Germany
| |
Collapse
|
26
|
Abstract
Wheat-based foods have been staple foods since about 10,000 years and constitute a major source of energy, dietary fiber, and micronutrients for the world population. The role of wheat in our diet, however, has recently been scrutinized by pseudoscientific books and media reports promoting the overall impression that wheat consumption makes people sick, stupid, fat, and addicted. Consequently, numerous consumers in Western countries have started to question their dietary habits related to wheat consumption and voluntarily decided to adopt a wheat-free diet without a medical diagnosis of any wheat-related disorder (WRD), such as celiac disease, wheat allergy, or non-celiac gluten sensitivity. The aim of this review is to achieve an objective judgment of the positive aspects of wheat consumption as well as adverse effects for individuals suffering from WRDs. The first part presents wheat constituents and their positive nutritional value, in particular, the consumption of products from whole-grain flours. The second part is focused on WRDs that affect predisposed individuals and can be treated with a gluten-free or -reduced diet. Based on all available scientific knowledge, wheat consumption is safe and healthy for the vast majority of people. There is no scientific evidence to support that the general population would benefit from a wheat-free diet.
Collapse
Affiliation(s)
| | | | - Katharina A. Scherf
- Department of Bioactive and Functional Food Chemistry, Institute of Applied Biosciences, Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
| |
Collapse
|
27
|
Yakymchuk RА, Sobolenko LY, Sorokina SІ. Genetic analysis of morphological traits of the spike and reproductivity elements of speltoid chemomutant Triticum aestivum. REGULATORY MECHANISMS IN BIOSYSTEMS 2020. [DOI: 10.15421/022072] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Long use of the methods of direct intraspecies hybridization in the selective breeding of varieties of Triticum aestivum L. has led to narrowing of their gene fund and close similarity of the genetic potential of their selective breeding traits. Using the method of experimental mutagenesis, one can induce systemic mutants with features of other hexaploid Triticum species which can freely cross-breed with other hybridization offspring, contributing to extension of genetic potential of cultivated wheat and creation of varieties with new levels of manifestation of economically beneficial traits. We studied the pattern of inheritance of morphological traits of the ear, length of the stem and the elements of productivity of speltoid chemomutant of T. aestivum. For the genetic analysis we used hybrids F1 and F2 of soft wheat obtained by cross-breeding speltoid macromutant (Smuhlianka speltoid), induced by the impact of aqueous solution of N-nitroso-N-methylurea (NMU) in the concentration of 0.025% on the seeds of Smuhlianka variety, with plants of Smuhlianka variety (Erythrospermum variety) and Podoloanka (Lutescens variety). To determine the pattern of inheritance the spike morphology, length of the stem and the elements of productivity in F1 hybrids, we calculated the extent of phenotype domination. In populations of F2, we examined plants with different combinations of phenotype manifestation of ear morphology. In F1 hybrids, the speltoid shape of the ear, absence of awns and red colour of the glumes indicated the dominant pattern of inheritance. The high level of phenotype domination of length of the stem and ear, number of spikelets in the main ear indicates the inheritance of the features according to intermediate, partly dominant and over-dominant types. Taking into account the segregation according to the features of spike morphology, awnedness and colour of glumes, the plants of F2 population were divided into phenotype classes, that is 12 and 6 in the combinations of respectively Smuhlianka speltoid × Smuhlianka and Smuhlianka speltoid × Podolianka. We determined that the obtained results are the consequences of dihybrid linkage which corresponds to the theoretical proportion of 12 : 3 : 1. Segregation into non-aristate and aristate plants corresponds to the proportion of monogene segregation of 3 : 1. Within separately distinguished phenotype classes, no independent inheritance of the shape of the ear and awnedness was observed. Dihybrid segregation of F2 plants into speltoid, squarehead and varieties Lutescence/Erythrospermum with quantitative superiority of speltoid plants suggests the control of the trait by two non-allele genes with epistatic interaction. The red colour of the glumes indicates the dominant monogenic pattern of inheritance. Absence of independent inheritance of the shape of the ear and awnedness indicates localization of genes which determine these features in one chromosome.
Collapse
|
28
|
Bhandari A, Sandhu N, Bartholome J, Cao-Hamadoun TV, Ahmadi N, Kumari N, Kumar A. Genome-Wide Association Study for Yield and Yield Related Traits under Reproductive Stage Drought in a Diverse indica-aus Rice Panel. RICE (NEW YORK, N.Y.) 2020; 13:53. [PMID: 32761553 PMCID: PMC7410978 DOI: 10.1186/s12284-020-00406-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Accepted: 07/02/2020] [Indexed: 05/08/2023]
Abstract
BACKGROUND Reproductive-stage drought stress is a major impediment to rice production in rainfed areas. Conventional and marker-assisted breeding strategies for developing drought-tolerant rice varieties are being optimized by mining and exploiting adaptive traits, genetic diversity; identifying the alleles, and understanding their interactions with genetic backgrounds for their increased contribution to drought tolerance. Field experiments were conducted in this study to identify marker-trait associations (MTAs) involved in response to yield under reproductive-stage (RS) drought. A diverse set of 280 indica-aus accessions was phenotyped for ten agronomic traits including yield and yield-related traits under normal irrigated condition and under two managed reproductive-stage drought environments. The accessions were genotyped with 215,250 single nucleotide polymorphism markers. RESULTS The study identified a total of 219 significant MTAs for 10 traits and candidate gene analysis within a 200 kb window centred from GWAS identified SNP peaks detected these MTAs within/ in close proximity to 38 genes, 4 earlier reported major grain yield QTLs and 6 novel QTLs for 7 traits out of the 10. The significant MTAs were mainly located on chromosomes 1, 2, 5, 6, 9, 11 and 12 and the percent phenotypic variance captured for these traits ranged from 5 to 88%. The significant positive correlation of grain yield with yield-related and other agronomic traits except for flowering time, observed under different environments point towards their contribution in improving rice yield under drought. Seven promising accessions were identified for use in future genomics-assisted breeding programs targeting grain yield improvement under drought. CONCLUSION These results provide a promising insight into the complex genetic architecture of grain yield under reproductive-stage drought in different environments. Validation of major genomic regions reported in the study will enable their effectiveness to develop drought-tolerant varieties following marker-assisted selection as well as to identify genes and understanding the associated physiological mechanisms.
Collapse
Affiliation(s)
- Aditi Bhandari
- Rice Breeding Platform, International Rice Research Institute, DAPO Box, 7777, Metro Manila, Philippines
- Banasthali Vidyapith, Banasthali, 304022, India
| | - Nitika Sandhu
- Rice Breeding Platform, International Rice Research Institute, DAPO Box, 7777, Metro Manila, Philippines
- Punjab Agricultural University, Ludhiana, 141004, India
| | - Jérôme Bartholome
- Rice Breeding Platform, International Rice Research Institute, DAPO Box, 7777, Metro Manila, Philippines
- CIRAD, UMR, AGAP, Montpellier, France
- AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, Montepellier, France
| | - Tuong-Vi Cao-Hamadoun
- CIRAD, UMR, AGAP, Montpellier, France
- AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, Montepellier, France
| | - Nourollah Ahmadi
- CIRAD, UMR, AGAP, Montpellier, France
- AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, Montepellier, France
| | | | - Arvind Kumar
- Rice Breeding Platform, International Rice Research Institute, DAPO Box, 7777, Metro Manila, Philippines.
- IRRI South Asia Regional Centre, Varanasi, 221006, India.
| |
Collapse
|
29
|
Kumar D, Kumar A, Chhokar V, Gangwar OP, Bhardwaj SC, Sivasamy M, Prasad SVS, Prakasha TL, Khan H, Singh R, Sharma P, Sheoran S, Iquebal MA, Jaiswal S, Angadi UB, Singh G, Rai A, Singh GP, Kumar D, Tiwari R. Genome-Wide Association Studies in Diverse Spring Wheat Panel for Stripe, Stem, and Leaf Rust Resistance. FRONTIERS IN PLANT SCIENCE 2020; 11:748. [PMID: 32582265 PMCID: PMC7286347 DOI: 10.3389/fpls.2020.00748] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 05/12/2020] [Indexed: 05/20/2023]
Abstract
Among several important wheat foliar diseases, Stripe rust (YR), Leaf rust (LR), and Stem rust (SR) have always been an issue of concern to the farmers and wheat breeders. Evolution of virulent pathotypes of these rusts has posed frequent threats to an epidemic. Pyramiding rust-resistant genes are the most economical and environment-friendly approach in postponing this inevitable threat. To achieve durable long term resistance against the three rusts, an attempt in this study was made searching for novel sources of resistant alleles in a panel of 483 spring wheat genotypes. This is a unique and comprehensive study where evaluation of a diverse panel comprising wheat germplasm from various categories and adapted to different wheat agro-climatic zones was challenged with 18 pathotypes of the three rusts with simultaneous screening in field conditions. The panel was genotyped using 35K SNP array and evaluated for each rust at two locations for two consecutive crop seasons. High heritability estimates of disease response were observed between environments for each rust type. A significant effect of population structure in the panel was visible in the disease response. Using a compressed mixed linear model approach, 25 genomic regions were found associated with resistance for at least two rusts. Out of these, seven were associated with all the three rusts on chromosome groups 1 and 6 along with 2B. For resistance against YR, LR, and SR, there were 16, 18, and 27 QTL (quantitative trait loci) identified respectively, associated at least in two out of four environments. Several of these regions got annotated with resistance associated genes viz. NB-LRR, E3-ubiquitin protein ligase, ABC transporter protein, etc. Alien introgressed (on 1B and 3D) and pleiotropic (on 7D) resistance genes were captured in seedling and adult plant disease responses, respectively. The present study demonstrates the use of genome-wide association for identification of a large number of favorable alleles for leaf, stripe, and stem rust resistance for broadening the genetic base. Quick conversion of these QTL into user-friendly markers will accelerate the deployment of these resistance loci in wheat breeding programs.
Collapse
Affiliation(s)
- Deepender Kumar
- Department of Bio and Nanotechnology, Guru Jambheshwar University of Science and Technology, Hisar, India
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, India
| | - Animesh Kumar
- ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Vinod Chhokar
- Department of Bio and Nanotechnology, Guru Jambheshwar University of Science and Technology, Hisar, India
| | - Om Prakash Gangwar
- ICAR-Indian Institute of Wheat and Barley Research, Regional Station, Shimla, India
| | | | - M. Sivasamy
- ICAR-Indian Agricultural Research Institute, Regional Station, Wellington, India
| | - S. V. Sai Prasad
- ICAR-Indian Agricultural Research Institute, Regional Station, Indore, India
| | - T. L. Prakasha
- ICAR-Indian Agricultural Research Institute, Regional Station, Indore, India
| | - Hanif Khan
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, India
| | - Rajender Singh
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, India
| | - Pradeep Sharma
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, India
| | - Sonia Sheoran
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, India
| | - Mir Asif Iquebal
- ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Sarika Jaiswal
- ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Ulavappa B. Angadi
- ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Gyanendra Singh
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, India
| | - Anil Rai
- ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | | | - Dinesh Kumar
- ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Ratan Tiwari
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, India
| |
Collapse
|
30
|
Discovery and characterisation of a new leaf rust resistance gene introgressed in wheat from wild wheat Aegilops peregrina. Sci Rep 2020; 10:7573. [PMID: 32371881 PMCID: PMC7200655 DOI: 10.1038/s41598-020-64166-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Accepted: 04/08/2020] [Indexed: 12/03/2022] Open
Abstract
Wild wheat species Aegilops peregrina (UpUpSpSp), harbours resistance to various diseases including leaf rust and stripe rust. Inheritance studies in a recombinant inbred line population of wheat-Ae. peregrina introgression line IL pau16061 revealed the transfer of a single major dominant gene conditioning all stage resistance, herein temporarily designated as LrAp. Genomic in situ hybridisation of IL pau16061, resistant and susceptible RILs with U- and S-genome DNA probes confirmed that the introgression with leaf rust resistance is from the Up genome of Ae. peregrina. Fluorescence in situ hybridisation using chromosome specific probes identified Up genome introgression to be on the long arm of wheat chromosome 6B. To genetically map LrAp, bulked segregant analysis was combined with resistance gene enrichment sequencing (MapRenSeq). Five nucleotide binding leucine-rich repeat contigs distinguished resistant and susceptible bulks and single nucleotide polymorphism (SNP) markers from these contigs co-segregated with LrAp. All five RenSeq NB_ARC contigs showed identity with the long arm of wheat chromosome 6B confirming the introgression on 6BL which we propose is a compensating translocation from Ae. peregrina chromosome 6UpL due to homoeology between the alien and wheat chromosomes. The SNP markers developed in this study will aid in cloning and marker assisted gene pyramiding of LrAp.
Collapse
|
31
|
Bansal M, Adamski NM, Toor PI, Kaur S, Molnár I, Holušová K, Vrána J, Doležel J, Valárik M, Uauy C, Chhuneja P. Aegilops umbellulata introgression carrying leaf rust and stripe rust resistance genes Lr76 and Yr70 located to 9.47-Mb region on 5DS telomeric end through a combination of chromosome sorting and sequencing. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:903-915. [PMID: 31894365 DOI: 10.1007/s00122-019-03514-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2019] [Accepted: 12/17/2019] [Indexed: 05/13/2023]
Abstract
Lr76 and Yr70 have been fine mapped using the sequence of flow-sorted recombinant 5D chromosome from wheat-Ae. umbellulata introgression line. The alien introgression has been delineated to 9.47-Mb region on short arm of wheat chromosome 5D. Leaf rust and stripe rust are among the most damaging diseases of wheat worldwide. Wheat cultivation based on limited number of rust resistance genes deployed over vast areas expedites the emergence of new pathotypes warranting a continuous deployment of new resistance genes. In this paper, fine mapping of Aegilops umbellulata-derived leaf rust and stripe rust resistance genes Lr76 and Yr70 is being reported. We flow sorted and paired-end sequenced 5U chromosome of Ae. umbellulata, recombinant chromosome 5D (5DIL) from wheat-Ae. umbellulata introgression line pau16057 and 5DRP of recurrent parent WL711. Chromosome 5U reads were mapped against the reference Chinese Spring chromosome 5D sequence, and alien-specific SNPs were identified. Chromosome 5DIL and 5DRP sequences were de novo assembled, and alien introgression-specific markers were designed by selecting 5U- and 5D-specific SNPs. Overall, 27 KASP markers were mapped in high-resolution population consisting of 1404 F5 RILs. The mapping population segregated for single gene each for leaf rust and stripe rust resistance. The physical order of the SNPs in pau16057 was defined by projecting the 27 SNPs against the IWGSC RefSeq v1.0 sequence. Based on this physical map, the size of Ae. umbellulata introgression was determined to be 9.47 Mb on the distal most end of the short arm of chromosome 5D. This non-recombining alien segment carries six NB-LRR encoding genes based on NLR annotation of assembled chromosome 5DIL sequence and IWGSC RefSeq v1.1 gene models. The presence of SNPs and other sequence variations in these genes between pau16057 and WL711 suggested that they are candidates for Lr76 and Yr70.
Collapse
Affiliation(s)
- Mitaly Bansal
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, Punjab, 141 004, India
| | | | - Puneet Inder Toor
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, Punjab, 141 004, India
| | - Satinder Kaur
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, Punjab, 141 004, India
| | - István Molnár
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, 783 71, Olomouc, Czech Republic
- Centre for Agricultural Research, Agricultural Institute, Hungarian Academy of Sciences, Brunszvik u. 2, Martonvásár, 2462, Hungary
| | - Kateřina Holušová
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, 783 71, Olomouc, Czech Republic
| | - Jan Vrána
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, 783 71, Olomouc, Czech Republic
| | - Jaroslav Doležel
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, 783 71, Olomouc, Czech Republic
| | - Miroslav Valárik
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, 783 71, Olomouc, Czech Republic
| | | | - Parveen Chhuneja
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, Punjab, 141 004, India.
| |
Collapse
|
32
|
Philipp N, Weise S, Oppermann M, Börner A, Keilwagen J, Kilian B, Arend D, Zhao Y, Graner A, Reif JC, Schulthess AW. Historical phenotypic data from seven decades of seed regeneration in a wheat ex situ collection. Sci Data 2019; 6:137. [PMID: 31358775 PMCID: PMC6662709 DOI: 10.1038/s41597-019-0146-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 07/08/2019] [Indexed: 11/16/2022] Open
Abstract
Genebanks are valuable sources of genetic diversity, which can help to cope with future problems of global food security caused by a continuously growing population, stagnating yields and climate change. However, the scarcity of phenotypic and genotypic characterization of genebank accessions severely restricts their use in plant breeding. To warrant the seed integrity of individual accessions during periodical regeneration cycles in the field phenotypic characterizations are performed. This study provides non-orthogonal historical data of 12,754 spring and winter wheat accessions characterized for flowering time, plant height, and thousand grain weight during 70 years of seed regeneration at the German genebank. Supported by historical weather observations outliers were removed following a previously described quality assessment pipeline. In this way, ready-to-use processed phenotypic data across regeneration years were generated and further validated. We encourage international and national genebanks to increase their efforts to transform into bio-digital resource centers. A first important step could consist in unlocking their historical data treasures that allows an educated choice of accessions by scientists and breeders.
Collapse
Affiliation(s)
- Norman Philipp
- Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, 06466 Seeland/OT, Gatersleben, Germany
| | - Stephan Weise
- Department of Genebank, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, 06466 Seeland/OT, Gatersleben, Germany
| | - Markus Oppermann
- Department of Genebank, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, 06466 Seeland/OT, Gatersleben, Germany
| | - Andreas Börner
- Department of Genebank, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, 06466 Seeland/OT, Gatersleben, Germany
| | - Jens Keilwagen
- Institute for Biosafety in Plant Biotechnology, Julius Kühn-Institut (JKI) - Federal Research Centre for Cultivated Plants, 06484, Quedlinburg, Germany
| | - Benjamin Kilian
- Global Crop Diversity Trust, Platz der Vereinten Nationen 7, 53113, Bonn, Germany
| | - Daniel Arend
- Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, 06466 Seeland/OT, Gatersleben, Germany
| | - Yusheng Zhao
- Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, 06466 Seeland/OT, Gatersleben, Germany
| | - Andreas Graner
- Department of Genebank, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, 06466 Seeland/OT, Gatersleben, Germany
| | - Jochen C Reif
- Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, 06466 Seeland/OT, Gatersleben, Germany.
| | - Albert W Schulthess
- Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, 06466 Seeland/OT, Gatersleben, Germany
| |
Collapse
|
33
|
Zhao Y, Fan Z, Hu F, Yin W, Zhao C, Yu A, Chai Q. Source-to-Sink Translocation of Carbon and Nitrogen Is Regulated by Fertilization and Plant Population in Maize-Pea Intercropping. FRONTIERS IN PLANT SCIENCE 2019; 10:891. [PMID: 31354765 PMCID: PMC6629956 DOI: 10.3389/fpls.2019.00891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 06/21/2019] [Indexed: 06/10/2023]
Abstract
Translocation of carbon (C) and nitrogen (N) from vegetative tissues to the grain sinks is critical for grain yield (GY). However, it is unclear how these processes respond to crop management practices when two crops are planted in relay-planting system. In this study, we characterized the C and N accumulation and translocation and their effects on yield formation in a pea (Pisum sativum L.)-maize (Zea mays L.) relay-planting system under different levels of source availabilities. Field experiment was conducted at Wuwei, northwest China, in 2012, 2013, and 2014. Two N fertilizer rates (low - N0 and high - N1) and three maize plant densities (low - D1, medium - D2, and high - D3) were designed to create the different levels of source availabilities. During the co-growth period, the rate of C accumulation in intercropped maize was 7.4-10.8%, 13.8-22.9%, and 13.5-32.0% lower than those in monoculture maize, respectively, under the D1, D2, and D3 treatments; however, after pea harvest, these values were 1.1-23.7%, 33.5-78.9%, and 36.8-123.7% greater than those in monoculture maize. At maturity, intercropped maize accumulated 11.4, 11.5, and 19.4% more N than monoculture maize, respectively, under the D1, D2, and D3 treatments. Compared to the monoculture crops, intercropped pea increased C accumulation in stems by 40.3% with N-application and by 19.5% without N application; intercropping maize increased these values by 16 and 11%, respectively. Overall, increasing N fertilization improved the rates of C and N remobilization from the vegetative tissues to the grain sinks across the different density treatments. In intercropped maize, the stems contributed 22, 33, and 44% more photosynthate to the grain sinks than the leaves, respectively, under the D1, D2, and D3 treatments. Quantitative assessments showed that the enhanced C and N remobilization due to high N fertilization and high plant density led to an increase of GY in the intercropping system by 35% compared with monoculture. We conclude that the enhanced productivity in maize-pea intercropping is a function of the source availability which is regulated by plant density and N fertilization.
Collapse
Affiliation(s)
- Yanhua Zhao
- College of Resources and Environmental Sciences, Gansu Agricultural University, Lanzhou, China
- Gansu Provincial Key Laboratory of Aridland Crop Science, Lanzhou, China
| | - Zhilong Fan
- Gansu Provincial Key Laboratory of Aridland Crop Science, Lanzhou, China
- College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Falong Hu
- Gansu Provincial Key Laboratory of Aridland Crop Science, Lanzhou, China
- College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Wen Yin
- Gansu Provincial Key Laboratory of Aridland Crop Science, Lanzhou, China
- College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Cai Zhao
- Gansu Provincial Key Laboratory of Aridland Crop Science, Lanzhou, China
- College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Aizhong Yu
- Gansu Provincial Key Laboratory of Aridland Crop Science, Lanzhou, China
- College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Qiang Chai
- Gansu Provincial Key Laboratory of Aridland Crop Science, Lanzhou, China
- College of Agronomy, Gansu Agricultural University, Lanzhou, China
| |
Collapse
|
34
|
Rai A, Mahendru-Singh A, Ahlawat AK, Kumar RR, K R, Saini S, Ganjewala D, Shukla R. Quality evaluation of near isogenic lines of the wheat variety carrying Sr26, Lr19 and Yr10 genes. J Cereal Sci 2019. [DOI: 10.1016/j.jcs.2019.05.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
35
|
Rai A, Mahendru-Singh A, Raghunandan K, Kumar TPJ, Sharma P, Ahlawat AK, Singh SK, Ganjewala D, Shukla RB, Sivasamy M. Marker-assisted transfer of PinaD1a gene to develop soft grain wheat cultivars. 3 Biotech 2019; 9:183. [PMID: 31065483 PMCID: PMC6476891 DOI: 10.1007/s13205-019-1717-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 04/13/2019] [Indexed: 11/24/2022] Open
Abstract
Grain softness has been a major trait of interest in wheat because of its role in producing flour suitable for making high-quality biscuits, cookies, cakes and some other products. In the present study, marker-assisted backcross breeding scheme was deployed to develop advanced wheat lines with soft grains. The Australian soft-grained variety Barham was used as the donor parent to transfer the puroindoline grain softness gene Pina-D1a to the Indian variety, DBW14, which is hard grained and has PinaD1bPinbD1a genes. Foreground selection with allele-specific PCR-based primer for Pina-D1a (positive selection) was used to identify heterozygous BC1F1 plants. Background selection with 173 polymorphic SSR primers covering all the 21 chromosomes was also carried out, in the foreground-selected BC1F1 plants. BC1F2 plants were selected by ascertaining the presence of Pina-D1a (positive selection) and absence of Pina-D1b (negative selection). Using the approach of positive, negative and background selection with molecular markers, 15 BC1F2 and 31 BC2F1 plants were finally selected. The 15 BC1F2 plants were selfed and the 31 BC2F1 plants were further backcrossed and selfed to raise BC3F1 and BC2F2 progenies, respectively. A part of the BC2F2 seed of each of the 31 plants was analyzed for grain hardness index (GHI) with single-kernel characterization system. The GHI varied from 12.1 to 37.1 in the seeds borne on the 31 BC2F1 plants. The reasons for this variation and further course of action are discussed.
Collapse
Affiliation(s)
- Anjali Rai
- Department of Biotechnology, Amity Institute of Biotechnology, Amity University, Noida, 201313 India
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, 110012 India
| | - Anju Mahendru-Singh
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, 110012 India
| | - K. Raghunandan
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, 110012 India
| | | | - Poornima Sharma
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, 110012 India
| | - Arvind K. Ahlawat
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, 110012 India
| | - Sumit K. Singh
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, 110012 India
| | - Deepak Ganjewala
- Department of Biotechnology, Amity Institute of Biotechnology, Amity University, Noida, 201313 India
| | - R. B. Shukla
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, 110012 India
| | - M. Sivasamy
- ICAR-Indian Agricultural Research Institute, Regional Station, Wellington, Tamilnadu 643231 India
| |
Collapse
|
36
|
Jamil M, Ali A, Gul A, Ghafoor A, Napar AA, Ibrahim AMH, Naveed NH, Yasin NA, Mujeeb-Kazi A. Genome-wide association studies of seven agronomic traits under two sowing conditions in bread wheat. BMC PLANT BIOLOGY 2019; 19:149. [PMID: 31003597 PMCID: PMC6475106 DOI: 10.1186/s12870-019-1754-6] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Accepted: 04/02/2019] [Indexed: 05/18/2023]
Abstract
BACKGROUND Wheat is a cool seasoned crop requiring low temperature during grain filling duration and therefore increased temperature causes significant yield reduction. A set of 125 spring wheat genotypes from International Maize and Wheat Improvement Centre (CIMMYT-Mexico) was evaluated for phenological and yield related traits at three locations in Pakistan under normal sowing time and late sowing time for expose to prolonged high temperature. With the help of genome-wide association study using genotyping-by-sequencing, marker trait associations (MTAs) were observed separately for the traits under normal and late sown conditions. RESULTS Significant reduction ranging from 9 to 74% was observed in all traits under high temperature. Especially 30, 25, 41 and 66% reduction was observed for days to heading (DH), plant height (PH), spikes per plant (SPP) and yield respectively. We identified 55,954 single nucleotide polymorphisms (SNPs) using genotyping by sequencing of these 125 hexaploid spring wheat genotypes and conducted genome-wide association studies (GWAS) for days to heading (DH), grain filled duration (GFD), plant height (PH), spikes per plant (SPP), grain number per spike (GNS), thousand kernel weight (TKW) and grain yield per plot (GY). Genomic regions identified through GWAS explained up to 13% of the phenotypic variance, on average. A total of 139 marker-trait associations (MTAs) across three wheat genomes (56 on genome A, 55 on B and 28 on D) were identified for all the seven traits studied. For days to heading, 20; grain filled duration, 21; plant height, 23; spikes per plant, 13; grain numbers per spike, 8; thousand kernel weight, 21 and for grain yield, 33 MTAs were detected under normal and late sown conditions. CONCLUSIONS This study identifies the essential resource of genetics research and underpins the chromosomal regions of seven agronomic traits under normal and high temperature. Significant relationship was observed between the number of favored alleles and trait observations. Fourteen protein coding genes with their respective annotations have been searched with the sequence of seven MTAs which were identified in this study. These findings will be helpful in the development of a breeder friendly platform for the selection of high yielding wheat lines at high temperature areas.
Collapse
Affiliation(s)
- Muhammad Jamil
- Department of Botany, University of Sargodha, Sargodha, Punjab Pakistan
| | - Aamir Ali
- Department of Botany, University of Sargodha, Sargodha, Punjab Pakistan
| | - Alvina Gul
- Atta-ur-Rehman School of Applied Biosciences (ASAB), National University of Science and Technology (NUST), Islamabad, Pakistan
| | - Abdul Ghafoor
- Plant Genetic Resources Institute (PGRI), National Agriculture Research Center (NARC), Islamabad, Pakistan
| | - Abdul Aziz Napar
- Institute of Plant Sciences, University of Sind Jamshoro, Sind, Pakistan
| | - Amir M. H. Ibrahim
- Soil and Crop Sciences Department, Texas A&M University, College Station, USA
| | - Naima Huma Naveed
- Department of Botany, University of Sargodha, Sargodha, Punjab Pakistan
| | | | | |
Collapse
|
37
|
Cereal Root Interactions with Soilborne Pathogens—From Trait to Gene and Back. AGRONOMY-BASEL 2019. [DOI: 10.3390/agronomy9040188] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Realizing the yield potential of crop plants in the presence of shifting pathogen populations, soil quality, rainfall, and other agro-environmental variables remains a challenge for growers and breeders worldwide. In this review, we discuss current approaches for combatting the soilborne phytopathogenic nematodes, Pratylenchus and Heterodera of wheat and barley, and Meloidogyne graminicola Golden and Birchfield, 1965 of rice. The necrotrophic fungal pathogens, Rhizoctonia solani Kühn 1858 AG-8 and Fusarium spp. of wheat and barley, also are discussed. These pathogens constitute major causes of yield loss in small-grain cereals of the Pacific Northwest, USA and throughout the world. Current topics include new sources of genetic resistance, molecular leads from whole genome sequencing and genome-wide patterns of hosts, nematode or fungal gene expression during root-pathogen interactions, host-induced gene silencing, and building a molecular toolbox of genes and regulatory sequences for deployment of resistance genes. In conclusion, improvement of wheat, barley, and rice will require multiple approaches.
Collapse
|
38
|
Janáková E, Jakobson I, Peusha H, Abrouk M, Škopová M, Šimková H, Šafář J, Vrána J, Doležel J, Järve K, Valárik M. Divergence between bread wheat and Triticum militinae in the powdery mildew resistance QPm.tut-4A locus and its implications for cloning of the resistance gene. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:1061-1072. [PMID: 30535646 PMCID: PMC6449310 DOI: 10.1007/s00122-018-3259-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Accepted: 12/03/2018] [Indexed: 06/09/2023]
Abstract
A segment of Triticum militinae chromosome 7G harbors a gene(s) conferring powdery mildew resistance which is effective at both the seedling and the adult plant stages when transferred into bread wheat (T. aestivum). The introgressed segment replaces a piece of wheat chromosome arm 4AL. An analysis of segregating materials generated to positionally clone the gene highlighted that in a plant heterozygous for the introgression segment, only limited recombination occurs between the introgressed region and bread wheat 4A. Nevertheless, 75 genetic markers were successfully placed within the region, thereby confining the gene to a 0.012 cM window along the 4AL arm. In a background lacking the Ph1 locus, the localized rate of recombination was raised 33-fold, enabling the reduction in the length of the region containing the resistance gene to a 480 kbp stretch harboring 12 predicted genes. The substituted segment in the reference sequence of bread wheat cv. Chinese Spring is longer (640 kbp) and harbors 16 genes. A comparison of the segments' sequences revealed a high degree of divergence with respect to both their gene content and nucleotide sequence. Of the 12 T. militinae genes, only four have a homolog in cv. Chinese Spring. Possible candidate genes for the resistance have been identified based on function predicted from their sequence.
Collapse
Affiliation(s)
- Eva Janáková
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, 78371, Olomouc, Czech Republic
| | - Irena Jakobson
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Akadeemia tee 15, 19086, Tallinn, Estonia
| | - Hilma Peusha
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Akadeemia tee 15, 19086, Tallinn, Estonia
| | - Michael Abrouk
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, 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
| | - Monika Škopová
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, 78371, Olomouc, Czech Republic
- Limagrain Central Europe Cereals, s.r.o., Hrubčice 111, 79821, Bedihošť, Czech Republic
| | - Hana Šimková
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, 78371, Olomouc, Czech Republic
| | - Jan Šafář
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, 78371, Olomouc, Czech Republic
| | - Jan Vrána
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, 78371, Olomouc, Czech Republic
| | - Jaroslav Doležel
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, 78371, Olomouc, Czech Republic
| | - Kadri Järve
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Akadeemia tee 15, 19086, Tallinn, Estonia
| | - Miroslav Valárik
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, 78371, Olomouc, Czech Republic.
| |
Collapse
|
39
|
Pan WL, Kidwell KK, McCracken VA, Bolton RP, Allen M. Economically Optimal Wheat Yield, Protein and Nitrogen Use Component Responses to Varying N Supply and Genotype. FRONTIERS IN PLANT SCIENCE 2019; 10:1790. [PMID: 32158450 PMCID: PMC7052120 DOI: 10.3389/fpls.2019.01790] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Accepted: 12/20/2019] [Indexed: 05/16/2023]
Abstract
Improvements in market value of hard red spring wheat (HRS, Triticum aestivum L.) are linked to breeding efforts to increase grain protein concentration (GPC). Numerous studies have been conducted on the identification, isolation of a chromosome region (Gpc-B1) of Wild emmer wheat (Triticum turgidum spp. dicoccoides) and its introgression into commercial hard wheat to GPC. Yet there has been limited research published on the comparative responsiveness of these altered lines and their parents to varied N supply. There is increased awareness that wheat genetic improvements must be assessed over a range of environmental and agronomic management conditions to assess stability. We report herein on economically optimal yield, protein and nitrogen use efficiency (NUE) component responses of two Pacific Northwestern USA cultivars, Tara and Scarlet compared to backcrossed derived near isolines with or without the Gpc-B1 allele. A field experiment with 5 N rates as whole plots and 8 genotypes as subplots was conducted over two years under semi-arid, dryland conditions. One goal was to evaluate the efficacy of the Gpc-B1 allele under a range of low to high N supply. Across all genotypes, grain yield responses to N supply followed the classic Mitscherlich response model, whereas GPC followed inverse quadratic or linear responses. The Gpc-B1 introgression had no major impact on grain protein, but grain N and total above ground crop N yields demonstrated quadratic responses to total N supply. Generally, higher maximum grain yields and steeper rise to the maxima (Mitscherlich c values) were obtained in the first site-year. Tara required less N supply to achieve GPC goals than Scarlet in both site-years. Genotypes with Gpc-B1 produced comparable or slightly lower Mitscherlich A values than unmodified genotypes, but displayed similar Mitscherlich c values. Target GPC goals were not achieved at economic optimal yields based on set wheat pricing. Economic optimization of N inputs to achieve protein goals showed positive revenue from additional N inputs for most genotypes. While N uptake efficiency did not drop below 0.40, N fertilizer-induced increases in grain N harvest correlated well with unused post-harvest soil N that is potentially susceptible to environmental loss.
Collapse
Affiliation(s)
- William L. Pan
- Nutrient Cycling, Rhizosphere Ecology Laboratory, Department of Crop and Soil Sciences, Washington State University, Pullman, WA, United States
- *Correspondence: William L. Pan,
| | - Kimberlee K. Kidwell
- College of Agricultural, Consumer, and Environmental Sciences, Urbana, IL, United States
| | - Vicki A. McCracken
- School of Economic Sciences, Washington State University, Pullman, WA, United States
| | - Ronald P. Bolton
- Nutrient Cycling, Rhizosphere Ecology Laboratory, Department of Crop and Soil Sciences, Washington State University, Pullman, WA, United States
| | - Monica Allen
- Nutrient Cycling, Rhizosphere Ecology Laboratory, Department of Crop and Soil Sciences, Washington State University, Pullman, WA, United States
| |
Collapse
|
40
|
Parmley K, Nagasubramanian K, Sarkar S, Ganapathysubramanian B, Singh AK. Development of Optimized Phenomic Predictors for Efficient Plant Breeding Decisions Using Phenomic-Assisted Selection in Soybean. PLANT PHENOMICS (WASHINGTON, D.C.) 2019; 2019:5809404. [PMID: 33313530 PMCID: PMC7706298 DOI: 10.34133/2019/5809404] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2019] [Accepted: 07/06/2019] [Indexed: 05/19/2023]
Abstract
The rate of advancement made in phenomic-assisted breeding methodologies has lagged those of genomic-assisted techniques, which is now a critical component of mainstream cultivar development pipelines. However, advancements made in phenotyping technologies have empowered plant scientists with affordable high-dimensional datasets to optimize the operational efficiencies of breeding programs. Phenomic and seed yield data was collected across six environments for a panel of 292 soybean accessions with varying genetic improvements. Random forest, a machine learning (ML) algorithm, was used to map complex relationships between phenomic traits and seed yield and prediction performance assessed using two cross-validation (CV) scenarios consistent with breeding challenges. To develop a prescriptive sensor package for future high-throughput phenotyping deployment to meet breeding objectives, feature importance in tandem with a genetic algorithm (GA) technique allowed selection of a subset of phenotypic traits, specifically optimal wavebands. The results illuminated the capability of fusing ML and optimization techniques to identify a suite of in-season phenomic traits that will allow breeding programs to decrease the dependence on resource-intensive end-season phenotyping (e.g., seed yield harvest). While we illustrate with soybean, this study establishes a template for deploying multitrait phenomic prediction that is easily amendable to any crop species and any breeding objective.
Collapse
Affiliation(s)
- Kyle Parmley
- Department of Agronomy, Iowa State University, Ames, IA, USA
| | | | - Soumik Sarkar
- Department of Mechanical Engineering, Iowa State University, Ames, IA, USA
| | | | | |
Collapse
|
41
|
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: 8] [Impact Index Per Article: 1.3] [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.
Collapse
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
| |
Collapse
|
42
|
Adhikari S, Seipel T, Menalled FD, Weaver DK. Farming system and wheat cultivar affect infestation of, and parasitism on, Cephus cinctus in the Northern Great Plains. PEST MANAGEMENT SCIENCE 2018; 74:2480-2487. [PMID: 29582553 DOI: 10.1002/ps.4925] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Revised: 02/23/2018] [Accepted: 03/23/2018] [Indexed: 06/08/2023]
Abstract
BACKGROUND Cephus cinctus infestation causes $350 million in annual losses in the Northern Great Plains. We compared infestation and parasitism of C. cinctus in spring (including Kamut; Triticum turgidum ssp. turanicum) and winter wheat cultivars grown in organic and conventional fields in Montana, USA. In the greenhouse, we compared C. cinctus preference and survival in Kamut, Gunnison, and Reeder spring wheat cultivars. RESULTS Stems cut by C. cinctus varied by farming system and the seasonality of the wheat crop. No stems of Kamut in organic fields were cut by C. cinctus, but 1.5% [±0.35% standard error (SE)] of stems in conventional spring wheat, 5% (±0.70% SE) of stems in organic winter wheat, and 20% (±0.93% SE) of stems in conventional winter wheat fields were cut by C. cinctus. More larvae of C. cinctus were parasitized in organic (27 ± 0.03% SE) compared with conventional (5 ± 0.01% SE) winter wheat fields. Cephus cinctus oviposition, survival, and the number of stems cut were lowest in Kamut compared with Gunnison and Reeder. CONCLUSION Cephus cinctus infestation was more common in winter wheat than in spring wheat. Organic fields with fewer cut stems also supported more parasitoids. Kamut is a genetic resource for developing C. cinctus-resistant cultivars. © 2018 Society of Chemical Industry.
Collapse
Affiliation(s)
- Subodh Adhikari
- Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, MT, USA
| | - Tim Seipel
- Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, MT, USA
| | - Fabian D Menalled
- Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, MT, USA
| | - David K Weaver
- Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, MT, USA
| |
Collapse
|
43
|
Brar GS, Fuentes-Dávila G, He X, Sansaloni CP, Singh RP, Singh PK. Genetic Mapping of Resistance in Hexaploid Wheat for a Quarantine Disease: Karnal Bunt. FRONTIERS IN PLANT SCIENCE 2018; 9:1497. [PMID: 30386358 PMCID: PMC6198147 DOI: 10.3389/fpls.2018.01497] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Accepted: 09/25/2018] [Indexed: 05/11/2023]
Abstract
Karnal bunt (KB) of wheat, caused by Tilletia indica, is one of the greatest challenges to grain industry, not because of yield loss, but quarantine regulations that restrict international movement and trade of affected stocks. Genetic resistance is the best way to manage this disease. Although several different sources of resistance have been identified to date, very few of those have been subjected to genetic analyses. Understanding the genetics of resistance, characterization and mapping of new resistance loci can help in development of improved germplasm. The objective of this study was to identify and characterize resistance loci (QTL) in two independent recombinant inbred lines (RILs) populations utilizing different wheat lines as resistance donors. Elite CIMMYT wheat lines Blouk#1 and Huirivis#1 were used as susceptible female parents and WHEAR/KUKUNA/3/C80.1/3∗BATAVIA//2∗WBLL1 (WKCBW) and Mutus as moderately resistant male parents in Pop1 and Pop2 populations, respectively. Populations were evaluated for KB resistance in 2015-16 and 2016-17 cropping seasons at two seeding dates (total four environments) in Cd. Obregon, Mexico. Two stable QTL from each population were identified in each environment: QKb.cim-2B and QKb.cim-3D (Pop1), QKb.cim-3B1 and QKb.cim-5B2 (Pop2). Other than those four QTL, other QTL were detected in each population which were specific to environments: QKb.cim-5B1, QKb.cim-6A, and QKb.cim-7A (Pop1), QKb.cim-3B2, QKb.cim-4A1, QKb.cim-4A2, QKb.cim-4B, QKb.cim-5A1, QKb.cim-5A2, and QKb.cim-7A2 (Pop2). Among the four stable QTL, all but QKb.cim-3B1 were derived from the resistant parent. QKb.cim-2B and QKb.cim-3D in Pop1 and QKb.cim-3B1 and QKb.cim-5B2 in Pop2 explained 5.0-11.4% and 3.3-7.1% phenotypic variance, respectively. A combination of two stable QTL in each population reduced KB infection by 24-33%, respectively. Transgressive resistant segregants lines derived with resistance alleles from both parents in each population were identified. Single nucleotide polymorphism (SNP) markers flanking these QTL regions may be amenable to marker-assisted selection. The best lines from both populations (in agronomy, end-use quality and KB resistance) carrying resistance alleles at all identified loci, may be used for inter-crossing and selection of improved germplasm in future. Markers flanking these QTL may assist in selection of such lines.
Collapse
Affiliation(s)
- Gurcharn S. Brar
- International Maize and Wheat Improvement Centre (CIMMYT), Texcoco, Mexico
- Department of Plant Science, Crop Development Centre, University of Saskatchewan, Saskatoon, SK, Canada
| | | | - Xinyao He
- International Maize and Wheat Improvement Centre (CIMMYT), Texcoco, Mexico
| | | | - Ravi P. Singh
- International Maize and Wheat Improvement Centre (CIMMYT), Texcoco, Mexico
| | - Pawan K. Singh
- International Maize and Wheat Improvement Centre (CIMMYT), Texcoco, Mexico
| |
Collapse
|
44
|
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 BIOTECHNOLOGY JOURNAL 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] [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.
Collapse
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
| |
Collapse
|
45
|
Skoracka A, Rector BG, Hein GL. The Interface Between Wheat and the Wheat Curl Mite, Aceria tosichella, the Primary Vector of Globally Important Viral Diseases. FRONTIERS IN PLANT SCIENCE 2018; 9:1098. [PMID: 30100916 PMCID: PMC6072864 DOI: 10.3389/fpls.2018.01098] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2018] [Accepted: 07/09/2018] [Indexed: 05/08/2023]
Abstract
Wheat production and sustainability are steadily threatened by pests and pathogens in both wealthy and developing countries. This review is focused on the wheat curl mite (WCM), Aceria tosichella, and its relationship with wheat. WCM is a major pest of wheat and other cereals and a vector of at least four damaging plant viruses (Wheat streak mosaic virus, High plains wheat mosaic virus, Brome streak mosaic virus, and Triticum mosaic virus). The WCM-virus pathosystem causes considerable yield losses worldwide and its severity increases significantly when mixed-virus infections occur. Chemical control strategies are largely ineffective because WCM occupies secluded niches on the plant, e.g., leaf sheaths or curled leaves in the whorl. The challenge of effectively managing this pest-virus complex is exacerbated by the existence of divergent WCM lineages that differ in host-colonization and virus-transmission abilities. We highlight research progress in mite ecology and virus epidemiology that affect management and development of cereal cultivars with WCM- and virus-resistance genes. We also address the challenge of avoiding both agronomically deleterious side effects and selection for field populations of WCM that can overcome these resistance genes. This report integrates the current state of knowledge of WCM-virus-plant interactions and addresses knowledge gaps regarding the mechanisms driving WCM infestation, viral epidemics, and plant responses. We discuss the potential application of molecular methods (e.g., transcriptomics, epigenetics, and whole-genome sequencing) to understand the chemical and cellular interface between the wheat plant and WCM-virus complexes.
Collapse
Affiliation(s)
- Anna Skoracka
- Population Ecology Lab, Faculty of Biology, Adam Mickiewicz University, Poznań, Poland
| | - Brian G. Rector
- Great Basin Rangelands Research Unit, United States Department of Agriculture – Agricultural Research Service, Reno, NV, United States
| | - Gary L. Hein
- Department of Entomology, University of Nebraska-Lincoln, Lincoln, NE, United States
| |
Collapse
|
46
|
Elbasyoni IS, Morsy SM, Ramamurthy RK, Nassar AM. Identification of Genomic Regions Contributing to Protein Accumulation in Wheat under Well-Watered and Water Deficit Growth Conditions. PLANTS (BASEL, SWITZERLAND) 2018; 7:E56. [PMID: 29997356 PMCID: PMC6160930 DOI: 10.3390/plants7030056] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Revised: 06/28/2018] [Accepted: 07/04/2018] [Indexed: 11/16/2022]
Abstract
Sustaining wheat production under low-input conditions through development and identifying genotypes with enhanced nutritional quality are two current concerns of wheat breeders. Wheat grain total protein content, to no small extent, determines the economic and nutritive value of wheat. Therefore, the objectives of this study are to identify accessions with high and low grain protein content (GPC) under well-watered and water-deficit growth conditions and to locate genomic regions that contribute to GPC accumulation. Spring wheat grains obtained from 2111 accessions that were grown under well-watered and water-deficit conditions were assessed for GPC using near-infrared spectroscopy (NIR). Results indicated significant influences of moisture, genotype, and genotype × environment interaction on the GPC accumulation. Furthermore, genotypes exhibited a wide range of variation for GPC, indicating the presence of high levels of genetic variability among the studied accessions. Around 366 (166 with high GPC and 200 with low GPC) wheat genotypes performed relatively the same across environments, which implies that GPC accumulation in these genotypes was less responsive to water deficit. Genome-wide association mapping results indicated that seven single nucleotide polymorphism (SNPs) were linked with GPC under well-watered growth conditions, while another six SNPs were linked with GPC under water-deficit conditions only. Moreover, 10 SNPs were linked with GPC under both well-watered and water-deficit conditions. These results emphasize the importance of using diverse, worldwide germplasm to dissect the genetic architecture of GPC in wheat and identify accessions that might be potential parents for high GPC in wheat breeding programs.
Collapse
Affiliation(s)
- Ibrahim S Elbasyoni
- Crop Science Department, Faculty of Agriculture, Damanhour University, Damanhour 22516, Egypt.
| | - Sabah M Morsy
- Crop Science Department, Faculty of Agriculture, Damanhour University, Damanhour 22516, Egypt.
| | | | - Atef M Nassar
- Plant Protection Department, Faculty of Agriculture, Damanhour University, Damanhour 22516, Egypt.
| |
Collapse
|
47
|
Kumar A, Sandhu N, Dixit S, Yadav S, Swamy BPM, Shamsudin NAA. Marker-assisted selection strategy to pyramid two or more QTLs for quantitative trait-grain yield under drought. RICE (NEW YORK, N.Y.) 2018; 11:35. [PMID: 29845495 PMCID: PMC5975061 DOI: 10.1186/s12284-018-0227-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 05/21/2018] [Indexed: 05/06/2023]
Abstract
BACKGROUND Marker-assisted breeding will move forward from introgressing single/multiple genes governing a single trait to multiple genes governing multiple traits to combat emerging biotic and abiotic stresses related to climate change and to enhance rice productivity. MAS will need to address concerns about the population size needed to introgress together more than two genes/QTLs. In the present study, grain yield and genotypic data from different generations (F3 to F8) for five marker-assisted breeding programs were analyzed to understand the effectiveness of synergistic effect of phenotyping and genotyping in early generations on selection of better progenies. RESULTS Based on class analysis of the QTL combinations, the identified superior QTL classes in F3/BC1F3/BC2F3 generations with positive QTL x QTL and QTL x background interactions that were captured through phenotyping maintained its superiority in yield under non-stress (NS) and reproductive-stage drought stress (RS) across advanced generations in all five studies. The marker-assisted selection breeding strategy combining both genotyping and phenotyping in early generation significantly reduced the number of genotypes to be carried forward. The strategy presented in this study providing genotyping and phenotyping cost savings of 25-68% compared with the traditional marker-assisted selection approach. The QTL classes, Sub1 + qDTY 1.1 + qDTY 2.1 + qDTY 3.1 and Sub1 + qDTY 2.1 + qDTY 3.1 in Swarna-Sub1, Sub1 + qDTY 1.1 + qDTY 1.2 , Sub1 + qDTY 1.1 + qDTY 2.2 and Sub1 + qDTY 2.2 + qDTY 12.1 in IR64-Sub1, qDTY 2.2 + qDTY 4.1 in Samba Mahsuri, Sub1 + qDTY 3.1 + qDTY 6.1 + qDTY 6.2 and Sub1 + qDTY 6.1 + qDTY 6.2 in TDK1-Sub1 and qDTY 12.1 + qDTY 3.1 and qDTY 2.2 + qDTY 3.1 in MR219 had shown better and consistent performance under NS and RS across generations over other QTL classes. CONCLUSION "Deployment of this procedure will save time and resources and will allow breeders to focus and advance only germplasm with high probability of improved performance. The identification of superior QTL classes and capture of positive QTL x QTL and QTL x background interactions in early generation and their consistent performance in subsequent generations across five backgrounds supports the efficacy of a combined MAS breeding strategy".
Collapse
Affiliation(s)
- Arvind Kumar
- International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| | - Nitika Sandhu
- International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| | - Shalabh Dixit
- International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| | - Shailesh Yadav
- International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| | - B. P. M. Swamy
- International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| | - Noraziyah Abd Aziz Shamsudin
- International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
- Current address: Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor Malaysia
| |
Collapse
|
48
|
Koller T, Brunner S, Herren G, Hurni S, Keller B. Pyramiding of transgenic Pm3 alleles in wheat results in improved powdery mildew resistance in the field. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2018; 131:861-871. [PMID: 29302719 PMCID: PMC5852180 DOI: 10.1007/s00122-017-3043-9] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2017] [Accepted: 12/17/2017] [Indexed: 05/22/2023]
Abstract
The combined effects of enhanced total transgene expression level and allele-specificity combination in transgenic allele-pyramided Pm3 wheat lines result in improved powdery mildew field resistance without negative pleiotropic effects. Allelic Pm3 resistance genes of wheat confer race-specific resistance to powdery mildew (Blumeria graminis f. sp. tritici, Bgt) and encode nucleotide-binding domain, leucine-rich repeat (NLR) receptors. Transgenic wheat lines overexpressing alleles Pm3a, b, c, d, f, and g have previously been generated by transformation of cultivar Bobwhite and tested in field trials, revealing varying degrees of powdery mildew resistance conferred by the transgenes. Here, we tested four transgenic lines each carrying two pyramided Pm3 alleles, which were generated by crossbreeding of lines transformed with single Pm3 alleles. All four allele-pyramided lines showed strongly improved powdery mildew resistance in the field compared to their parental lines. The improved resistance results from the two effects of enhanced total transgene expression levels and allele-specificity combinations. In contrast to leaf segment tests on greenhouse-grown seedlings, no allelic suppression was observed in the field. Plant development and yield scores of the pyramided lines were similar to the mean scores of the corresponding parental lines, and thus, the allele pyramiding did not cause any negative effects. On the contrary, in pyramided line, Pm3b × Pm3f normal plant development was restored compared to the delayed development and reduced seed set of parental line Pm3f. Allele-specific RT qPCR revealed additive transgene expression levels of the two Pm3 alleles in the pyramided lines. A positive correlation between total transgene expression level and powdery mildew field resistance was observed. In summary, allele pyramiding of Pm3 transgenes proved to be successful in enhancing powdery mildew field resistance.
Collapse
Affiliation(s)
- Teresa Koller
- Department of Plant and Microbial Biology, University of Zurich, Zollikerstrasse 107, 8008 Zurich, Switzerland
| | | | - Gerhard Herren
- Department of Plant and Microbial Biology, University of Zurich, Zollikerstrasse 107, 8008 Zurich, Switzerland
| | - Severine Hurni
- 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
| |
Collapse
|
49
|
Kroeger CM, Garza C, Lynch CJ, Myers E, Rowe S, Schneeman BO, Sharma AM, Allison DB. Scientific rigor and credibility in the nutrition research landscape. Am J Clin Nutr 2018; 107:484-494. [PMID: 29566196 PMCID: PMC6248649 DOI: 10.1093/ajcn/nqx067] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Revised: 11/30/2017] [Accepted: 12/04/2017] [Indexed: 12/27/2022] Open
Abstract
Scientific progress depends on the quality and credibility of research methods. As discourse on rigor, transparency, and reproducibility joins the cacophony of nutrition information and misinformation in mass media, buttressing the real and perceived reliability of nutrition science is more important than ever. This broad topic was the focus of a 2016 plenary session, "Scientific Rigor and Competing Interests in the Nutrition Research Landscape." This article summarizes and expands on this session in an effort to increase understanding and dialogue with regard to factors that limit the real and perceived reliability of nutrition science and steps that can be taken to mitigate those factors. The end goal is to both earn and merit greater trust in nutrition science by both the scientific community and the general public. The authors offer suggestions in each of the domains of education and training, communications, research conduct, and procedures and policies to help achieve this goal. The authors emphasize the need for adequate funding to support these efforts toward greater rigor and transparency, which will be resource demanding and may require either increased research funding or the recognition that a greater proportion of research funding may need to be allocated to these tasks.
Collapse
Affiliation(s)
- Cynthia M Kroeger
- Department of Epidemiology and Biostatistics, Indiana University School of
Public Health-Bloomington, Bloomington, IN
| | | | - Christopher J Lynch
- National Institutes of Diabetes and Digestive and Kidney Diseases, NIH,
Bethesda, MD
| | | | | | | | | | - David B Allison
- Department of Epidemiology and Biostatistics, Indiana University School of
Public Health-Bloomington, Bloomington, IN
| |
Collapse
|
50
|
McCormick RF, Truong SK, Sreedasyam A, Jenkins J, Shu S, Sims D, Kennedy M, Amirebrahimi M, Weers BD, McKinley B, Mattison A, Morishige DT, Grimwood J, Schmutz J, Mullet JE. The Sorghum bicolor reference genome: improved assembly, gene annotations, a transcriptome atlas, and signatures of genome organization. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 93:338-354. [PMID: 29161754 DOI: 10.1111/tpj.13781] [Citation(s) in RCA: 262] [Impact Index Per Article: 43.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Revised: 11/05/2017] [Accepted: 11/14/2017] [Indexed: 05/20/2023]
Abstract
Sorghum bicolor is a drought tolerant C4 grass used for the production of grain, forage, sugar, and lignocellulosic biomass and a genetic model for C4 grasses due to its relatively small genome (approximately 800 Mbp), diploid genetics, diverse germplasm, and colinearity with other C4 grass genomes. In this study, deep sequencing, genetic linkage analysis, and transcriptome data were used to produce and annotate a high-quality reference genome sequence. Reference genome sequence order was improved, 29.6 Mbp of additional sequence was incorporated, the number of genes annotated increased 24% to 34 211, average gene length and N50 increased, and error frequency was reduced 10-fold to 1 per 100 kbp. Subtelomeric repeats with characteristics of Tandem Repeats in Miniature (TRIM) elements were identified at the termini of most chromosomes. Nucleosome occupancy predictions identified nucleosomes positioned immediately downstream of transcription start sites and at different densities across chromosomes. Alignment of more than 50 resequenced genomes from diverse sorghum genotypes to the reference genome identified approximately 7.4 M single nucleotide polymorphisms (SNPs) and 1.9 M indels. Large-scale variant features in euchromatin were identified with periodicities of approximately 25 kbp. A transcriptome atlas of gene expression was constructed from 47 RNA-seq profiles of growing and developed tissues of the major plant organs (roots, leaves, stems, panicles, and seed) collected during the juvenile, vegetative and reproductive phases. Analysis of the transcriptome data indicated that tissue type and protein kinase expression had large influences on transcriptional profile clustering. The updated assembly, annotation, and transcriptome data represent a resource for C4 grass research and crop improvement.
Collapse
Affiliation(s)
- Ryan F McCormick
- Interdisciplinary Program in Genetics, Texas A&M University, College Station, TX, 77843, USA
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843, USA
| | - Sandra K Truong
- Interdisciplinary Program in Genetics, Texas A&M University, College Station, TX, 77843, USA
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843, USA
| | | | - Jerry Jenkins
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
| | - Shengqiang Shu
- Department of Energy, Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - David Sims
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
| | - Megan Kennedy
- Department of Energy, Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | | | - Brock D Weers
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843, USA
| | - Brian McKinley
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843, USA
| | - Ashley Mattison
- Interdisciplinary Program in Genetics, Texas A&M University, College Station, TX, 77843, USA
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843, USA
| | - Daryl T Morishige
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843, USA
| | - Jane Grimwood
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
- Department of Energy, Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Jeremy Schmutz
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
- Department of Energy, Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - John E Mullet
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843, USA
| |
Collapse
|