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

• DOI: 10.1186/s12870-020-02693-w
• Publication Date: 2020-10-27T09:02:53Z
• Authors: Mengjie Jia; Lijun Yang; Wei Zhang; Garry Rosewarne; Junhui Li; Enian Yang; Ling Chen; Wenxue Wang; Yike Liu; Hanwen Tong; Weijie He; Yuqing Zhang; Zhanwang Zhu; Chunbao Gao
• Keywords: Marker-trait association; Genetic Markers; 2. Zero hunger; China; 0303 health sciences; Quantitative Trait Loci; Triticum aestivum; Botany; Genetic Variation; Yellow rust; Polymorphism, Single Nucleotide; 630; 03 medical and health sciences; Single nucleotide polymorphism (SNP); QK1-989; Puccinia; Alleles; Triticum; Research Article; Disease Resistance; Genome-Wide Association Study; Plant Diseases

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.