Genome-Wide Association Study Reveals the Genetic Architecture of Stripe Rust Resistance at the Adult Plant Stage in Chinese Endemic Wheat
Jing Li, Yunfeng Jiang, Fangjie Yao, Li Long, Yuqi Wang, Yu Wu, Hao Li, Jirui Wang, Qiantao Jiang, Houyang Kang, Wei Li, Pengfei Qi, Jian Ma, Zhien Pu, Shoufen Dai, Yuming Wei, Youliang Zheng, Guoyue Chen
Abstract
Chinese endemic wheat, comprising Tibetan semi-wild wheat (Triticum aestivum ssp. tibetanum), Yunnan hulled wheat (T. aestivum ssp. yunnanense), and Xinjiang rice wheat (T. petropavlovskyi), are genetically and morphologically unique around the world. To clarify the adult-plant resistance to stripe rust among Chinese endemic wheat germplasm, a panel of 213 accessions were inoculated with mixed virulent races of Puccinia striiformis f. sp. tritici in four environments in the field. Four stripe-rust resistance-associated traits, infection type, final disease severity, disease index, and area under the disease progress curve, were used for evaluation of resistance. Phenotypic datasets and 55K single-nucleotide polymorphism (SNP) array-based genome-wide association analyses were performed to identify effective resistance loci. Eighty-nine accessions with stable resistance were identified by phenotypic evaluation in at least three environments. Eleven markers located on chromosomes 1A, 2B, 3D, 5B, 7A, and 7D in the GWAS analysis showed significant associations with at least two resistance-associated traits in two environments. These loci were divided into seven quantitative trait loci (QTLs) based on the linkage disequilibrium decay distance and explained 9.3% to 25.1% of the total phenotypic variation. Five QTLs on chromosomes 1A, 2B, 3D, and 7D overlapped or were in close proximity to previously reported QTL regions based on the consensus map and physical map using IWGSC RefSeq v1.0. The remaining two QTLs were potential novel QTLs given their physical positions. Haplotype variants of QYr.sicau-3DS showed peculiar subspecies-specific inheritance of the resistance loci. Resistant loci among Chinese endemic wheat germplasm could be assembled into common wheat cultivars, and high-confidence SNP markers would aid in marker-assisted selection in breeding of wheat for disease resistance.