Genome-wide association analysis permits characterization of\xa0Stagonospora nodorum blotch (SNB) resistance in hard winter wheat

Rami Altameemi,Harsimardeep S Gill,Brent Turnipseed,Jagdeep S Sidhu,Jyotirmoy Halder,Sunish K Sehgal,Upinder S Gill,Jose L Gonzalez Hernandez,Girma Ayana,Shaukat Ali

doi:10.1038/s41598-021-91515-6

Rami Altameemi, Harsimardeep S Gill + Show 8 more

Open Access

https://doi.org/10.1038/s41598-021-91515-6

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Abstract

Stagonospora nodorum blotch (SNB) is an economically important wheat disease caused by the necrotrophic fungus Parastagonospora nodorum. SNB resistance in wheat is controlled by several quantitative trait loci (QTLs). Thus, identifying novel resistance/susceptibility QTLs is crucial for continuous improvement of the SNB resistance. Here, the hard winter wheat association mapping panel (HWWAMP) comprising accessions from breeding programs in the Great Plains region of the US, was evaluated for SNB resistance and necrotrophic effectors (NEs) sensitivity at the seedling stage. A genome-wide association study (GWAS) was performed to identify single‐nucleotide polymorphism (SNP) markers associated with SNB resistance and effectors sensitivity. We found seven significant associations for SNB resistance/susceptibility distributed over chromosomes 1B, 2AL, 2DS, 4AL, 5BL, 6BS, and 7AL. Two new QTLs for SNB resistance/susceptibility at the seedling stage were identified on chromosomes 6BS and 7AL, whereas five QTLs previously reported in diverse germplasms were validated. Allele stacking analysis at seven QTLs explained the additive and complex nature of SNB resistance. We identified accessions (‘Pioneer-2180’ and ‘Shocker’) with favorable alleles at five of the seven identified loci, exhibiting a high level of resistance against SNB. Further, GWAS for sensitivity to NEs uncovered significant associations for SnToxA and SnTox3, co-locating with previously identified host sensitivity genes (Tsn1 and Snn3). Candidate region analysis for SNB resistance revealed 35 genes of putative interest with plant defense response-related functions. The QTLs identified and validated in this study could be easily employed in breeding programs using the associated markers to enhance the SNB resistance in hard winter wheat.

Highlights

Wheat (Triticum aestivum L.) is the largest grown cereal crop in the world and plays a crucial role in human food supply[1]
Genome-wide association studies (GWAS) or linkage disequilibrium-based mapping is another approach for dissecting the genetics of complex traits, which overcomes the major limitations of linkage mapping
Stagonospora nodorum blotch (SNB) resistance in 274 accessions of hard winter wheat association mapping panel (HWWAMP) was evaluated at the seedling stage in three independent experiments (Exp 1, Exp 2, and Exp 3)

Summary

Introduction

Wheat (Triticum aestivum L.) is the largest grown cereal crop in the world and plays a crucial role in human food supply[1]. Linkage analyses based on bi-parental populations have been useful in dissecting the genetic control of SNB resistance This approach has identified several QTLs for response to SNB on different wheat chromosomes[13,17,20,23,24,26,27,28,29,30]. Several GWA studies in wheat identified several QTLs for SNB resistance distributed over chromosomes 1A, 1B, 2A, 2D, 3A, 3B, 4A, 4B, 5A, 5B, 5D, 6A, 6B, 7A, and 7 D32,36,38–42 These studies employed association-mapping panels comprising a large number of wheat landraces[38,39], a set of modern cultivars[40,42], and a historical set of wheat lines[41]; most of these studies did not explore the US hard winter wheat cultivars/breeding materials

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