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

doi:10.3389/fpls.2020.00625

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

Front Plant Sci. 2020 Jun 5:11:625. doi: 10.3389/fpls.2020.00625. eCollection 2020.

Authors

Jing Li^{1

2}, Yunfeng Jiang^{1

2}, Fangjie Yao^{1

2}, Li Long^{1

2}, Yuqi Wang^{1

2}, Yu Wu^{1

2}, Hao Li¹, Jirui Wang^{1

2}, Qiantao Jiang^{1

2}, Houyang Kang^{1

2}, Wei Li³, Pengfei Qi¹, Jian Ma¹, Zhien Pu³, Shoufen Dai¹, Yuming Wei^{1

2}, Youliang Zheng^{1

2}, Guoyue Chen^{1

2}

Affiliations

¹ Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China.
² State Key Laboratory of Crop Gene Exploitation and Utilization in Southwest China, Chengdu, China.
³ College of Agronomy, Sichuan Agricultural University, Chengdu, China.

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. To examine the adult plant resistance to stripe rust among Chinese endemic wheat germplasms, a panel of 213 accessions was inoculated with mixed virulent races of wheat stripe rust (Puccinia striiformis f. sp. tritici) in four different field environments. Four traits associated with stripe rust resistance, infection type, final disease severity, disease index, and area under the disease progress curve, were used to evaluate the accessions. The phenotypic datasets were used for 55K single-nucleotide polymorphism (SNP) array-based genome-wide association studies to identify effective resistance loci. Eighty-nine accessions with stable resistance were identified in at least three of the four environments by phenotypic evaluation. Eleven markers located on chromosomes 1A, 2B, 5A, 5D, 7B, and 7D by the genome-wide association studies analysis showed significant associations with at least two resistance-associated traits in two of the environments. These loci, corresponding to seven genomic regions based on linkage disequilibrium decay distance, explained 9.3 to 26.0% of the total phenotypic variation. Five quantitative trait loci (QTLs) on chromosomes 1A, 2B, 7B, and 7D overlapped or were in close proximity to previously reported QTLs based on the consensus and physical maps using the reference sequence of bread wheat (IWGSC RefSeq v1.0). The other two QTLs were potential novel QTLs given their physical positions. Haplotype variants of QTL QYr.sicau-2BS showed subspecies-specific inheritance of the stripe rust resistance locus. Resistant loci among Chinese endemic wheat germplasms could be introduced into common wheat cultivars, and the high-confidence SNP markers will aid in marker-assisted selection in breeding for stripe rust disease resistance.

Keywords: Chinese endemic wheat; GWAS; Tibetan semi-wild wheat; Xinjiang rice wheat; Yunnan hulled wheat; stripe rust.