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Sehgal D, Rathan ND, Özdemir F, Keser M, Akin B, Dababat AA, Koc E, Dreisigacker S, Morgounov A. Genomic wide association study and selective sweep analysis identify genes associated with improved yield under drought in Turkish winter wheat germplasm. Sci Rep 2024; 14:8431. [PMID: 38600135 PMCID: PMC11006659 DOI: 10.1038/s41598-024-57469-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 03/18/2024] [Indexed: 04/12/2024] Open
Abstract
A panel comprising of 84 Turkish winter wheat landraces (LR) and 73 modern varieties (MV) was analyzed with genome wide association study (GWAS) to identify genes/genomic regions associated with increased yield under favorable and drought conditions. In addition, selective sweep analysis was conducted to detect signatures of selection in the winter wheat genome driving the differentiation between LR and MV, to gather an understanding of genomic regions linked to adaptation and yield improvement. The panel was genotyped with 25 K wheat SNP array and phenotyped for agronomic traits for two growing seasons (2018 and 2019) in Konya, Turkey. Year 2018 was treated as drought environment due to very low precipitation prior to heading whereas year 2019 was considered as a favorable season. GWAS conducted with SNPs and haplotype blocks using mixed linear model identified 18 genomic regions in the vicinities of known genes i.e., TaERF3-3A, TaERF3-3B, DEP1-5A, FRIZZY PANICLE-2D, TaSnRK23-1A, TaAGL6-A, TaARF12-2A, TaARF12-2B, WAPO1, TaSPL16-7D, TaTGW6-A1, KAT-2B, TaOGT1, TaSPL21-6B, TaSBEIb, trs1/WFZP-A, TaCwi-A1-2A and TaPIN1-7A associated with grain yield (GY) and yield related traits. Haplotype-based GWAS identified five haplotype blocks (H1A-42, H2A-71, H4A-48, H7B-123 and H7B-124), with the favorable haplotypes showing a yield increase of > 700 kg/ha in the drought season. SNP-based GWAS, detected only one larger effect genomic region on chromosome 7B, in common with haplotype-based GWAS. On an average, the percentage variation (PV) explained by haplotypes was 8.0% higher than PV explained by SNPs for all the investigated traits. Selective sweep analysis detected 39 signatures of selection between LR and MV of which 15 were within proximity of known functional genes controlling flowering (PRR-A1, PPR-D1, TaHd1-6B), GY and GY components (TaSus2-2B, TaGS2-B1, AG1-1A/WAG1-1A, DUO-A1, DUO-B1, AG2-3A/WAG2-3A, TaLAX1, TaSnRK210-4A, FBP, TaLAX1, TaPIL1 and AP3-1-7A/WPA3-7A) and 10 regions underlying various transcription factors and regulatory genes. The study outcomes contribute to utilization of LR in breeding winter wheat.
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Affiliation(s)
- Deepmala Sehgal
- International Maize and Wheat Improvement Center (CIMMYT), Km. 45, Carretera Mex-Veracruz, El Batan, CP 56237, Veracruz, Mexico.
- Syngenta, Jealott's Hill International Research Centre, Bracknell, Berkshire, RG42 6EY, UK.
| | | | - Fatih Özdemir
- Bahri Dagdas International Agricultural Research Institute, Konya, Turkey
| | - Mesut Keser
- International Center for Agricultural Research in Dry Areas (ICARDA), Ankara, Turkey
| | - Beyhan Akin
- International Maize and Wheat Improvement Center (CIMMYT), Ankara, Turkey
| | | | - Emrah Koc
- International Maize and Wheat Improvement Center (CIMMYT), Ankara, Turkey
| | - Susanne Dreisigacker
- International Maize and Wheat Improvement Center (CIMMYT), Km. 45, Carretera Mex-Veracruz, El Batan, CP 56237, Veracruz, Mexico
| | - Alexey Morgounov
- Scientific Production Center of Grain, Shortandy, Astana reg., 010000, Kazakhstan.
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Kumar M, Kumar S, Sandhu KS, Kumar N, Saripalli G, Prakash R, Nambardar A, Sharma H, Gautam T, Balyan HS, Gupta PK. GWAS and genomic prediction for pre-harvest sprouting tolerance involving sprouting score and two other related traits in spring wheat. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2023; 43:14. [PMID: 37313293 PMCID: PMC10248620 DOI: 10.1007/s11032-023-01357-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 01/26/2023] [Indexed: 06/15/2023]
Abstract
In wheat, a genome-wide association study (GWAS) and genomic prediction (GP) analysis were conducted for pre-harvest sprouting (PHS) tolerance and two of its related traits. For this purpose, an association panel of 190 accessions was phenotyped for PHS (using sprouting score), falling number, and grain color over two years and genotyped with 9904 DArTseq based SNP markers. GWAS for main-effect quantitative trait nucleotides (M-QTNs) using three different models (CMLM, SUPER, and FarmCPU) and epistatic QTNs (E-QTNs) using PLINK were performed. A total of 171 M-QTNs (CMLM, 47; SUPER, 70; FarmCPU, 54) for all three traits, and 15 E-QTNs involved in 20 first-order epistatic interactions were identified. Some of the above QTNs overlapped the previously reported QTLs, MTAs, and cloned genes, allowing delineating 26 PHS-responsive genomic regions that spread over 16 wheat chromosomes. As many as 20 definitive and stable QTNs were considered important for use in marker-assisted recurrent selection (MARS). The gene, TaPHS1, for PHS tolerance (PHST) associated with one of the QTNs was also validated using the KASP assay. Some of the M-QTNs were shown to have a key role in the abscisic acid pathway involved in PHST. Genomic prediction accuracies (based on the cross-validation approach) using three different models ranged from 0.41 to 0.55, which are comparable to the results of previous studies. In summary, the results of the present study improved our understanding of the genetic architecture of PHST and its related traits in wheat and provided novel genomic resources for wheat breeding based on MARS and GP. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-023-01357-5.
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Affiliation(s)
- Manoj Kumar
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, UP India
| | - Sachin Kumar
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, UP India
| | | | - Neeraj Kumar
- Department of Plant and Environmental Sciences, Clemson University, Clemson, SC USA
| | - Gautam Saripalli
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, UP India
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD USA
| | - Ram Prakash
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, UP India
| | - Akash Nambardar
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, UP India
| | - Hemant Sharma
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, UP India
| | - Tinku Gautam
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, UP India
| | - Harindra Singh Balyan
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, UP India
| | - Pushpendra Kumar Gupta
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, UP India
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Sehgal D, Dhakate P, Ambreen H, Shaik KHB, Rathan ND, Anusha NM, Deshmukh R, Vikram P. Wheat Omics: Advancements and Opportunities. PLANTS (BASEL, SWITZERLAND) 2023; 12:426. [PMID: 36771512 PMCID: PMC9919419 DOI: 10.3390/plants12030426] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 12/07/2022] [Accepted: 12/14/2022] [Indexed: 06/18/2023]
Abstract
Plant omics, which includes genomics, transcriptomics, metabolomics and proteomics, has played a remarkable role in the discovery of new genes and biomolecules that can be deployed for crop improvement. In wheat, great insights have been gleaned from the utilization of diverse omics approaches for both qualitative and quantitative traits. Especially, a combination of omics approaches has led to significant advances in gene discovery and pathway investigations and in deciphering the essential components of stress responses and yields. Recently, a Wheat Omics database has been developed for wheat which could be used by scientists for further accelerating functional genomics studies. In this review, we have discussed various omics technologies and platforms that have been used in wheat to enhance the understanding of the stress biology of the crop and the molecular mechanisms underlying stress tolerance.
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Affiliation(s)
- Deepmala Sehgal
- International Maize and Wheat Improvement Center (CIMMYT), El Batán, Texcoco 56237, Mexico
- Syngenta, Jealott’s Hill International Research Centre, Bracknell, Berkshire RG42 6EY, UK
| | - Priyanka Dhakate
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110076, India
| | - Heena Ambreen
- School of Life Sciences, University of Sussex, Brighton BN1 9RH, UK
| | - Khasim Hussain Baji Shaik
- Faculty of Agriculture Sciences, Georg-August-Universität, Wilhelmsplatz 1, 37073 Göttingen, Germany
| | - Nagenahalli Dharmegowda Rathan
- Indian Agricultural Research Institute (ICAR-IARI), New Delhi 110012, India
- Corteva Agriscience, Hyderabad 502336, Telangana, India
| | | | - Rupesh Deshmukh
- Department of Biotechnology, Central University of Haryana, Mahendragarh 123031, Haryana, India
| | - Prashant Vikram
- Bioseed Research India Ltd., Hyderabad 5023324, Telangana, India
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Yang CJ, Ladejobi O, Mott R, Powell W, Mackay I. Analysis of historical selection in winter wheat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:3005-3023. [PMID: 35864201 PMCID: PMC9482581 DOI: 10.1007/s00122-022-04163-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Accepted: 06/22/2022] [Indexed: 06/15/2023]
Abstract
KEY MESSAGE Modeling of the distribution of allele frequency over year of variety release identifies major loci involved in historical breeding of winter wheat. Winter wheat is a major crop with a rich selection history in the modern era of crop breeding. Genetic gains across economically important traits like yield have been well characterized and are the major force driving its production. Winter wheat is also an excellent model for analyzing historical genetic selection. As a proof of concept, we analyze two major collections of winter wheat varieties that were bred in Western Europe from 1916 to 2010, namely the Triticeae Genome (TG) and WAGTAIL panels, which include 333 and 403 varieties, respectively. We develop and apply a selection mapping approach, Regression of Alleles on Years (RALLY), in these panels, as well as in simulated populations. RALLY maps loci under sustained historical selection by using a simple logistic model to regress allele counts on years of variety release. To control for drift-induced allele frequency change, we develop a hybrid approach of genomic control and delta control. Within the TG panel, we identify 22 significant RALLY quantitative selection loci (QSLs) and estimate the local heritabilities for 12 traits across these QSLs. By correlating predicted marker effects with RALLY regression estimates, we show that alleles whose frequencies have increased over time are heavily biased toward conferring positive yield effect, but negative effects in flowering time, lodging, plant height and grain protein content. Altogether, our results (1) demonstrate the use of RALLY to identify selected genomic regions while controlling for drift, and (2) reveal key patterns in the historical selection in winter wheat and guide its future breeding.
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Affiliation(s)
- Chin Jian Yang
- Scotland's Rural College (SRUC), Kings Buildings, West Mains Road, Edinburgh, EH9 3JG, UK
| | - Olufunmilayo Ladejobi
- Department of Genetics, Evolution and Environment, University College London, London, WC1E 6BT, UK
| | - Richard Mott
- Department of Genetics, Evolution and Environment, University College London, London, WC1E 6BT, UK
| | - Wayne Powell
- Scotland's Rural College (SRUC), Kings Buildings, West Mains Road, Edinburgh, EH9 3JG, UK
| | - Ian Mackay
- Scotland's Rural College (SRUC), Kings Buildings, West Mains Road, Edinburgh, EH9 3JG, UK.
- IMplant Consultancy Ltd, Chelmsford, UK.
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Hussain S, Habib M, Ahmed Z, Sadia B, Bernardo A, Amand PS, Bai G, Ghori N, Khan AI, Awan FS, Maqbool R. Genotyping-by-Sequencing Based Molecular Genetic Diversity of Pakistani Bread Wheat ( Triticum aestivum L.) Accessions. Front Genet 2022; 13:772517. [PMID: 35464861 PMCID: PMC9019749 DOI: 10.3389/fgene.2022.772517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 01/07/2022] [Indexed: 11/29/2022] Open
Abstract
Spring wheat (Triticum aestivum L.) is one of the most imperative staple food crops, with an annual production of 765 million tons globally to feed ∼40% world population. Genetic diversity in available germplasm is crucial for sustainable wheat improvement to ensure global food security. A diversity panel of 184 Pakistani wheat accessions was genotyped using 123,596 high-quality single nucleotide polymorphism (SNP) markers generated by genotyping-by-sequencing with 42% of the SNPs mapped on B, 36% on A, and 22% on D sub-genomes of wheat. Chromosome 2B contains the most SNPs (9,126), whereas 4D has the least (2,660) markers. The mean polymorphic information content, genetic diversity, and major allele frequency of the population were 0.157, 0.1844, and 0.87, respectively. Analysis of molecular variance revealed a higher genetic diversity (80%) within the sub-population than among the sub-populations (20%). The genome-wide linkage disequilibrium was 0.34 Mbp for the whole wheat genome. Among the three subgenomes, A has the highest LD decay value (0.29 Mbp), followed by B (0.2 Mbp) and D (0.07 Mbp) genomes, respectively. The results of population structure, principal coordinate analysis, phylogenetic tree, and kinship analysis also divided the whole population into three clusters comprising 31, 33, and 120 accessions in group 1, group 2, and group 3, respectively. All groups were dominated by the local wheat accessions. Estimation of genetic diversity will be a baseline for the selection of breeding parents for mutations and the genome-wide association and marker-assisted selection studies.
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Affiliation(s)
- Shabbir Hussain
- Center of Agricultural Biochemistry and Biotechnology, University of Agriculture, Faisalabad, Pakistan
| | - Madiha Habib
- Center of Agricultural Biochemistry and Biotechnology, University of Agriculture, Faisalabad, Pakistan
| | - Zaheer Ahmed
- Department of Plant Breeding and Genetics, University of Agriculture, Faisalabad, Pakistan
| | - Bushra Sadia
- Center of Agricultural Biochemistry and Biotechnology, University of Agriculture, Faisalabad, Pakistan
| | - Amy Bernardo
- USDA, Hard Winter Wheat Genetics Research Unit, Manhattan, KS, United States
| | - Paul St Amand
- USDA, Hard Winter Wheat Genetics Research Unit, Manhattan, KS, United States
| | - Guihua Bai
- USDA, Hard Winter Wheat Genetics Research Unit, Manhattan, KS, United States
| | - Nida Ghori
- USDA, Hard Winter Wheat Genetics Research Unit, Manhattan, KS, United States
| | - Azeem I Khan
- Department of Plant Breeding and Genetics, University of Agriculture, Faisalabad, Pakistan
| | - Faisal S Awan
- Center of Agricultural Biochemistry and Biotechnology, University of Agriculture, Faisalabad, Pakistan
| | - Rizwana Maqbool
- Department of Plant Breeding and Genetics, University of Agriculture, Faisalabad, Pakistan
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Sharma R, Cockram J, Gardner KA, Russell J, Ramsay L, Thomas WTB, O'Sullivan DM, Powell W, Mackay IJ. Trends of genetic changes uncovered by Env- and Eigen-GWAS in wheat and barley. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:667-678. [PMID: 34778903 PMCID: PMC8866380 DOI: 10.1007/s00122-021-03991-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 11/02/2021] [Indexed: 05/26/2023]
Abstract
Variety age and population structure detect novel QTL for yield and adaptation in wheat and barley without the need to phenotype. The process of crop breeding over the last century has delivered new varieties with increased genetic gains, resulting in higher crop performance and yield. However, in many cases, the alleles and genomic regions underpinning this success remain unknown. This is partly due to the difficulty of generating sufficient phenotypic data on large numbers of historical varieties to enable such analyses. Here we demonstrate the ability to circumvent such bottlenecks by identifying genomic regions selected over 100 years of crop breeding using age of a variety as a surrogate for yield. Rather than collecting phenotype data, we deployed 'environmental genome-wide association scans' (EnvGWAS) based on variety age in two of the world's most important crops, wheat and barley, and detected strong signals of selection across both genomes. EnvGWAS identified 16 genomic regions in barley and 10 in wheat with contrasting patterns between spring and winter types of the two crops. To further examine changes in genome structure, we used the genomic relationship matrix of the genotypic data to derive eigenvectors for analysis in EigenGWAS. This detected seven major chromosomal introgressions that contributed to adaptation in wheat. EigenGWAS and EnvGWAS based on variety age avoid costly phenotyping and facilitate the identification of genomic tracts that have been under selection during breeding. Our results demonstrate the potential of using historical cultivar collections coupled with genomic data to identify chromosomal regions under selection and may help guide future plant breeding strategies to maximise the rate of genetic gain and adaptation.
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Affiliation(s)
- Rajiv Sharma
- Scotland's Rural College (SRUC), Kings Buildings, West Mains Road, Edinburgh, EH9 3JG, UK
| | - James Cockram
- The John Bingham Laboratory, NIAB, 93 Lawrence Weaver Road, Cambridge, CB3 0LE, UK
| | - Keith A Gardner
- The John Bingham Laboratory, NIAB, 93 Lawrence Weaver Road, Cambridge, CB3 0LE, UK
| | - Joanne Russell
- The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
| | - Luke Ramsay
- The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
| | | | - Donal M O'Sullivan
- School of Agriculture, Policy and Development, University of Reading, Reading, RG6 6AR, UK
| | - Wayne Powell
- Scotland's Rural College (SRUC), Kings Buildings, West Mains Road, Edinburgh, EH9 3JG, UK
| | - Ian J Mackay
- Scotland's Rural College (SRUC), Kings Buildings, West Mains Road, Edinburgh, EH9 3JG, UK.
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Langlands-Perry C, Cuenin M, Bergez C, Krima SB, Gélisse S, Sourdille P, Valade R, Marcel TC. Resistance of the Wheat Cultivar ‘Renan’ to Septoria Leaf Blotch Explained by a Combination of Strain Specific and Strain Non-Specific QTL Mapped on an Ultra-Dense Genetic Map. Genes (Basel) 2021; 13:genes13010100. [PMID: 35052440 PMCID: PMC8774678 DOI: 10.3390/genes13010100] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 12/22/2021] [Accepted: 12/22/2021] [Indexed: 11/16/2022] Open
Abstract
Quantitative resistance is considered more durable than qualitative resistance as it does not involve major resistance genes that can be easily overcome by pathogen populations, but rather a combination of genes with a lower individual effect. This durability means that quantitative resistance could be an interesting tool for breeding crops that would not systematically require phytosanitary products. Quantitative resistance has yet to reveal all of its intricacies. Here, we delve into the case of the wheat/Septoria tritici blotch (STB) pathosystem. Using a population resulting from a cross between French cultivar Renan, generally resistant to STB, and Chinese Spring, a cultivar susceptible to the disease, we built an ultra-dense genetic map that carries 148,820 single nucleotide polymorphism (SNP) markers. Phenotyping the interaction was done with two different Zymoseptoria tritici strains with contrasted pathogenicities on Renan. A linkage analysis led to the detection of three quantitative trait loci (QTL) related to resistance in Renan. These QTL, on chromosomes 7B, 1D, and 5D, present with an interesting diversity as that on 7B was detected with both fungal strains, while those on 1D and 5D were strain-specific. The resistance on 7B was located in the region of Stb8 and the resistance on 1D colocalized with Stb19. However, the resistance on 5D was new, so further designated Stb20q. Several wall-associated kinases (WAK), nucleotide-binding and leucine-rich repeats (NB-LRR) type, and kinase domain carrying genes were present in the QTL regions, and some of them were expressed during the infection. These results advocate for a role of Stb genes in quantitative resistance and for resistance in the wheat/STB pathosystem being as a whole quantitative and polygenic.
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Affiliation(s)
- Camilla Langlands-Perry
- Université Paris Saclay, INRAE, UR BIOGER, 78850 Thiverval-Grignon, France; (C.L.-P.); (M.C.); (C.B.); (S.B.K.); (S.G.)
- ARVALIS Institut du Végétal, 91720 Boigneville, France;
| | - Murielle Cuenin
- Université Paris Saclay, INRAE, UR BIOGER, 78850 Thiverval-Grignon, France; (C.L.-P.); (M.C.); (C.B.); (S.B.K.); (S.G.)
| | - Christophe Bergez
- Université Paris Saclay, INRAE, UR BIOGER, 78850 Thiverval-Grignon, France; (C.L.-P.); (M.C.); (C.B.); (S.B.K.); (S.G.)
| | - Safa Ben Krima
- Université Paris Saclay, INRAE, UR BIOGER, 78850 Thiverval-Grignon, France; (C.L.-P.); (M.C.); (C.B.); (S.B.K.); (S.G.)
| | - Sandrine Gélisse
- Université Paris Saclay, INRAE, UR BIOGER, 78850 Thiverval-Grignon, France; (C.L.-P.); (M.C.); (C.B.); (S.B.K.); (S.G.)
| | - Pierre Sourdille
- Université Clermont–Auvergne, INRAE, UMR GDEC, 63000 Clermont-Ferrand, France;
| | - Romain Valade
- ARVALIS Institut du Végétal, 91720 Boigneville, France;
| | - Thierry C. Marcel
- Université Paris Saclay, INRAE, UR BIOGER, 78850 Thiverval-Grignon, France; (C.L.-P.); (M.C.); (C.B.); (S.B.K.); (S.G.)
- Correspondence:
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Exploring the legacy of Central European historical winter wheat landraces. Sci Rep 2021; 11:23915. [PMID: 34903761 PMCID: PMC8668957 DOI: 10.1038/s41598-021-03261-4] [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: 06/18/2021] [Accepted: 11/29/2021] [Indexed: 11/14/2022] Open
Abstract
Historical wheat landraces are rich sources of genetic diversity offering untapped reservoirs for broadening the genetic base of modern varieties. Using a 20K SNP array, we investigated the accessible genetic diversity in a Central European bread wheat landrace collection with great drought, heat stress tolerance and higher tillering capacity. We discovered distinct differences in the number of average polymorphisms between landraces and modern wheat cultivars, and identified a set of novel rare alleles present at low frequencies in the landrace collection. The detected polymorphisms were unevenly distributed along the wheat genome, and polymorphic markers co-localized with genes of great agronomic importance. The geographical distribution of the inferred Bayesian clustering revealed six genetically homogenous ancestral groups among the collection, where the Central European core bared an admixed background originating from four ancestral groups. We evaluated the effective population sizes (Ne) of the Central European collection and assessed changes in diversity over time, which revealed a dramatic ~ 97% genetic erosion between 1955 and 2015.
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Siekmann D, Jansen G, Zaar A, Kilian A, Fromme FJ, Hackauf B. A Genome-Wide Association Study Pinpoints Quantitative Trait Genes for Plant Height, Heading Date, Grain Quality, and Yield in Rye ( Secale cereale L.). FRONTIERS IN PLANT SCIENCE 2021; 12:718081. [PMID: 34777409 PMCID: PMC8586073 DOI: 10.3389/fpls.2021.718081] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 09/22/2021] [Indexed: 06/03/2023]
Abstract
Rye is the only cross-pollinating Triticeae crop species. Knowledge of rye genes controlling complex-inherited traits is scarce, which, currently, largely disables the genomics assisted introgression of untapped genetic variation from self-incompatible germplasm collections in elite inbred lines for hybrid breeding. We report on the first genome-wide association study (GWAS) in rye based on the phenotypic evaluation of 526 experimental hybrids for plant height, heading date, grain quality, and yield in 2 years and up to 19 environments. We established a cross-validated NIRS calibration model as a fast, effective, and robust analytical method to determine grain quality parameters. We observed phenotypic plasticity in plant height and tiller number as a resource use strategy of rye under drought and identified increased grain arabinoxylan content as a striking phenotype in osmotically stressed rye. We used DArTseq™ as a genotyping-by-sequencing technology to reduce the complexity of the rye genome. We established a novel high-density genetic linkage map that describes the position of almost 19k markers and that allowed us to estimate a low genome-wide LD based on the assessed genetic diversity in elite germplasm. We analyzed the relationship between plant height, heading date, agronomic, as well as grain quality traits, and genotype based on 20k novel single-nucleotide polymorphism markers. In addition, we integrated the DArTseq™ markers in the recently established 'Lo7' reference genome assembly. We identified cross-validated SNPs in 'Lo7' protein-coding genes associated with all traits studied. These include associations of the WUSCHEL-related homeobox transcription factor DWT1 and grain yield, the DELLA protein gene SLR1 and heading date, the Ethylene overproducer 1-like protein gene ETOL1 and thousand-grain weight, protein and starch content, as well as the Lectin receptor kinase SIT2 and plant height. A Leucine-rich repeat receptor protein kinase and a Xyloglucan alpha-1,6-xylosyltransferase count among the cross-validated genes associated with water-extractable arabinoxylan content. This study demonstrates the power of GWAS, hybrid breeding, and the reference genome sequence in rye genetics research to dissect and identify the function of genes shaping genetic diversity in agronomic and grain quality traits of rye. The described links between genetic causes and phenotypic variation will accelerate genomics-enabled rye improvement.
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Affiliation(s)
- Dörthe Siekmann
- Julius Kühn Institute, Federal Research Centre for Cultivated Plants, Institute for Breeding Research on Agricultural Crops, Sanitz, Germany
- HYBRO Saatzucht GmbH & Co. KG, Schenkenberg, Germany
| | - Gisela Jansen
- Julius Kühn Institute, Federal Research Centre for Cultivated Plants, Institute for Resistance Research and Stress Tolerance, Sanitz, Germany
| | - Anne Zaar
- Julius Kühn Institute, Federal Research Centre for Cultivated Plants, Institute for Resistance Research and Stress Tolerance, Sanitz, Germany
| | | | | | - Bernd Hackauf
- Julius Kühn Institute, Federal Research Centre for Cultivated Plants, Institute for Breeding Research on Agricultural Crops, Sanitz, Germany
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Kaur J, Kaur J, Dhillon GS, Kaur H, Singh J, Bala R, Srivastava P, Kaur S, Sharma A, Chhuneja P. Characterization and Mapping of Spot Blotch in Triticum durum-Aegilops speltoides Introgression Lines Using SNP Markers. FRONTIERS IN PLANT SCIENCE 2021; 12:650400. [PMID: 34122476 PMCID: PMC8193842 DOI: 10.3389/fpls.2021.650400] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 04/20/2021] [Indexed: 05/17/2023]
Abstract
Spot blotch (SB) of wheat is emerging as a major threat to successful wheat production in warm and humid areas of the world. SB, also called leaf blight, is caused by Bipolaris sorokiniana, and is responsible for high yield losses in Eastern Gangetic Plains Zone in India. More recently, SB is extending gradually toward cooler, traditional wheat-growing North-Western part of the country which is a major contributor to the national cereal basket. Deployment of resistant cultivars is considered as the most economical and ecologically sound measure to avoid losses due to this disease. In the present study, 89 backcross introgression lines (DSBILs) derived from Triticum durum (cv. PDW274-susceptible) × Aegilops speltoides (resistant) were evaluated against SB for four consecutive years, 2016-2020. Phenotypic evaluation of these lines showed a continuous variation in disease severity indicating that the resistance to SB is certainly quantitative in nature. Phenotypic data of DSBILs were further used for mapping QTLs using SNPs obtained by genotyping by sequencing. To identify QTLs stable across the environments, Best Linear Unbiased Estimates (BLUEs) and Predictions (BLUPs) were used for mapping QTLs based on stepwise regression-based Likelihood Ratio Test (RSTEP-LRT) for additive effect of markers and single marker analysis (SMA). Five QTLs, Q.Sb.pau-2A, Q.Sb.pau-2B, Q.Sb.pau-3B, Q.Sb.pau-5B, and Q.Sb.pau-6A, linked to SB resistance were mapped across chromosomes 2A, 2B, 3B, 5B, and 6A. Genes found adjacent to the SNP markers linked to these QTLs were literature mined to identify possible candidate genes by studying their role in plant pathogenesis. Further, highly resistant DSBIL (DSBIL-13) was selected to cross with a susceptible hexaploidy cultivar (HD3086) generating BC2F1 population. The QTL Q.Sb.pau-5B, linked to SNP S5B_703858864, was validated on this BC2F1 population and thus, may prove to be a potential diagnostic marker for SB resistance.
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Affiliation(s)
- Jashanpreet Kaur
- Department of Plant Pathology, Punjab Agricultural University, Ludhiana, India
| | - Jaspal Kaur
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | | | - Harmandeep Kaur
- Department of Plant Pathology, Punjab Agricultural University, Ludhiana, India
| | - Jasvir Singh
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - Ritu Bala
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - Puja Srivastava
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - Satinder Kaur
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India
| | - Achla Sharma
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - Parveen Chhuneja
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India
- *Correspondence: Parveen Chhuneja,
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11
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Sehgal D, Mondal S, Crespo-Herrera L, Velu G, Juliana P, Huerta-Espino J, Shrestha S, Poland J, Singh R, Dreisigacker S. Haplotype-Based, Genome-Wide Association Study Reveals Stable Genomic Regions for Grain Yield in CIMMYT Spring Bread Wheat. Front Genet 2020; 11:589490. [PMID: 33335539 PMCID: PMC7737720 DOI: 10.3389/fgene.2020.589490] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 10/21/2020] [Indexed: 01/16/2023] Open
Abstract
We untangled key regions of the genetic architecture of grain yield (GY) in CIMMYT spring bread wheat by conducting a haplotype-based, genome-wide association study (GWAS), together with an investigation of epistatic interactions using seven large sets of elite yield trials (EYTs) consisting of a total of 6,461 advanced breeding lines. These lines were phenotyped under irrigated and stress environments in seven growing seasons (2011-2018) and genotyped with genotyping-by-sequencing markers. Genome-wide 519 haplotype blocks were constructed, using a linkage disequilibrium-based approach covering 14,036 Mb in the wheat genome. Haplotype-based GWAS identified 7, 4, 10, and 15 stable (significant in three or more EYTs) associations in irrigated (I), mild drought (MD), severe drought (SD), and heat stress (HS) testing environments, respectively. Considering all EYTs and the four testing environments together, 30 stable associations were deciphered with seven hotspots identified on chromosomes 1A, 1B, 2B, 4A, 5B, 6B, and 7B, where multiple haplotype blocks were associated with GY. Epistatic interactions contributed significantly to the genetic architecture of GY, explaining variation of 3.5-21.1%, 3.7-14.7%, 3.5-20.6%, and 4.4- 23.1% in I, MD, SD, and HS environments, respectively. Our results revealed the intricate genetic architecture of GY, controlled by both main and epistatic effects. The importance of these results for practical applications in the CIMMYT breeding program is discussed.
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Affiliation(s)
- Deepmala Sehgal
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
| | - Suchismita Mondal
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
| | | | - Govindan Velu
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
| | - Philomin Juliana
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
| | | | | | - Jesse Poland
- Kansas State University, Manhattan, KS, United States
| | - Ravi Singh
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
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