Genome-Wide Association Study Reveals the Genetic Architecture of Stripe Rust Resistance at the Adult Plant Stage in Chinese Endemic Wheat

Stripe rust is one of the most destructive diseases of wheat (Triticum aestivum L.), caused by Puccinia striiformis f. sp. tritici (Pst), and responsible for significant yield losses worldwide. Single-nucleotide polymorphism (SNP) diagnostic markers were used to identify new sources of resistance at adult plant stage to wheat stripe rust (YR) in 141 CIMMYT advanced bread wheat lines over 3 years in replicated trials at Borlaug Institute for South Asia (BISA), Ludhiana. We performed a genome-wide association study and genomic prediction to aid the genetic gain by accumulating disease resistance alleles. The responses to YR in 141 advanced wheat breeding lines at adult plant stage were used to generate G × E (genotype × environment)-dependent rust scores for prediction and genome-wide association study (GWAS), eliminating variation due to climate and disease pressure changes. The lowest mean prediction accuracies were 0.59 for genomic best linear unbiased prediction (GBLUP) and ridge-regression BLUP (RRBLUP), while the highest mean was 0.63 for extended GBLUP (EGBLUP) and random forest (RF), using 14,563 SNPs and the G × E rust score results. RF and EGBLUP predicted higher accuracies (∼3%) than did GBLUP and RRBLUP. Promising genomic prediction demonstrates the viability and efficacy of improving quantitative rust tolerance. The resistance to YR in these lines was attributed to eight quantitative trait loci (QTLs) using the FarmCPU algorithm. Four (Q.Yr.bisa-2A.1, Q.Yr.bisa-2D, Q.Yr.bisa-5B.2, and Q.Yr.bisa-7A) of eight QTLs linked to the diagnostic markers were mapped at unique loci (previously unidentified for Pst resistance) and possibly new loci. The statistical evidence of effectiveness and distribution of the new diagnostic markers for the resistance loci would help to develop new stripe rust resistance sources. These diagnostic markers along with previously established markers would be used to create novel DNA biosensor-based microarrays for rapid detection of the resistance loci on large panels upon functional validation of the candidate genes identified in the present study to aid in rapid genetic gain in the future breeding programs.

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Identifying Loci Conferring Resistance to Leaf and Stripe Rusts in a Spring Wheat Population (Triticum aestivum) via Genome-Wide Association Mapping

Phytopathology ◽

10.1094/phyto-04-19-0143-r ◽

2019 ◽

Vol 109 (11) ◽

pp. 1932-1940 ◽

Cited By ~ 1

Author(s):

Weizhen Liu ◽

James Kolmer ◽

Sheri Rynearson ◽

Xianming Chen ◽

Liangliang Gao ◽

...

Keyword(s):

Leaf Rust ◽

Stripe Rust ◽

Spring Wheat ◽

Rust Resistance ◽

Genome Wide Association Study ◽

Leaf Rust Resistance ◽

Genome Wide Association ◽

Stripe Rust Resistance ◽

Adult Plant ◽

Genome Wide

A previous genome-wide association study (GWAS) for leaf rust (caused by Puccinia triticina) resistance identified 46 resistance quantitative trait loci (QTL) in an elite spring wheat leaf rust resistance diversity panel. With the aim of characterizing the pleiotropic resistance sources to both leaf rust and stripe rust (caused by P. striiformis f. sp. tritici), stripe rust responses were tested in five U.S. environments at the adult-plant stage and to five U.S. races at the seedling stage. The data revealed balanced phenotypic distributions in this population except for the seedling response to P. striiformis f. sp. tritici race PSTv-37. GWAS for stripe rust resistance discovered a total of 21 QTL significantly associated with all-stage or field resistance on chromosomes 1B, 1D, 2B, 3B, 4A, 5A, 5B, 5D, 6A, 6B, 7A, and 7B. Previously documented pleiotropic resistance genes Yr18/Lr34 and Yr46/Lr67 and tightly linked genes Yr17-Lr37 and Yr30-Sr2-Lr27 were also detected in this population. In addition, stripe rust resistance QTL Yrswp-2B.1, Yrswp-3B, and Yrswp-7B colocated with leaf rust resistance loci 2B_3, 3B_t2, and 7B_4, respectively. Haplotype analysis uncovered that Yrswp-3B and 3B_t2 were either tightly linked genes or the same gene for resistance to both stripe and leaf rusts. Single nucleotide polymorphism markers IWB35950, IWB74350, and IWB72134 for the 3B QTL conferring resistance to both rusts should be useful in incorporating the resistance allele(s) in new cultivars.

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Genome-wide association studies revealed novel stripe rust resistance QTL in barley at seedling and adult-plant stages

Euphytica ◽

10.1007/s10681-020-02728-1 ◽

2021 ◽

Vol 217 (1) ◽

Author(s):

Sanjaya Gyawali ◽

Sujan Mamidi ◽

Shiaoman Chao ◽

Subhash C. Bhardwaj ◽

Pradeep S. Shekhawat ◽

...

Keyword(s):

Stripe Rust ◽

Rust Resistance ◽

Association Studies ◽

Genome Wide Association ◽

Stripe Rust Resistance ◽

Adult Plant ◽

Genome Wide Association Studies ◽

Resistance Qtl ◽

Genome Wide

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A combination of genome-wide association study and selection signature analysis dissects the genetic architecture underlying bone traits in chickens

animal ◽

10.1016/j.animal.2021.100322 ◽

2021 ◽

Vol 15 (8) ◽

pp. 100322

Author(s):

Y.D. Li ◽

X. Liu ◽

Z.W. Li ◽

W.J. Wang ◽

Y.M. Li ◽

...

Keyword(s):

Association Study ◽

Genetic Architecture ◽

Genome Wide Association Study ◽

Genome Wide Association ◽

Signature Analysis ◽

Selection Signature ◽

Genome Wide

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Genome-wide association analysis of stripe rust resistance in modern Chinese wheat

BMC Plant Biology ◽

10.1186/s12870-020-02693-w ◽

2020 ◽

Vol 20 (1) ◽

Author(s):

Mengjie Jia ◽

Lijun Yang ◽

Wei Zhang ◽

Garry Rosewarne ◽

Junhui Li ◽

...

Keyword(s):

Stripe Rust ◽

Rust Resistance ◽

Genome Wide Association ◽

Stripe Rust Resistance ◽

Adult Plant ◽

Amplification Refractory Mutation System ◽

Post Inoculation ◽

Genome Wide ◽

A Genome ◽

Chinese Wheat

Abstract Background Stripe rust (yellow rust) is a significant disease for bread wheat (Triticum aestivum L.) worldwide. A genome-wide association study was conducted on 240 Chinese wheat cultivars and elite lines genotyped with the wheat 90 K single nucleotide polymorphism (SNP) arrays to decipher the genetic architecture of stripe rust resistance in Chinese germplasm. Results Stripe rust resistance was evaluated at the adult plant stage in Pixian and Xindu in Sichuan province in the 2015–2016 cropping season, and in Wuhan in Hubei province in the 2013–2014, 2016–2017 and 2018–2019 cropping seasons. Twelve stable loci for stripe rust resistance were identified by GWAS using TASSEL and GAPIT software. These loci were distributed on chromosomes 1B, 1D, 2A, 2B, 3A, 3B, 4B (3), 4D, 6D, and 7B and explained 3.6 to 10.3% of the phenotypic variation. Six of the loci corresponded with previously reported genes/QTLs, including Sr2/Yr30/Lr27, while the other six (QYr.hbaas-1BS, QYr.hbaas-2BL, QYr.hbaas-3AL, QYr.hbaas-4BL.3, QYr.hbaas-4DL, and QYr.hbaas-6DS) are probably novel. The results suggest high genetic diversity for stripe rust resistance in this population. The resistance alleles of QYr.hbaas-2AS, QYr.hbaas-3BS, QYr.hbaas-4DL, and QYr.hbaas-7BL were rare in the present panel, indicating their potential use in breeding for stripe rust resistance in China. Eleven penta-primer amplification refractory mutation system (PARMS) markers were developed from SNPs significantly associated with seven mapped QTLs. Twenty-seven genes were predicted for mapped QTLs. Six of them were considered as candidates for their high relative expression levels post-inoculation. Conclusion The resistant germplasm, mapped QTLs, and PARMS markers developed in this study are resources for enhancing stripe rust resistance in wheat breeding.

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