Genome-Wide Identification of Wheat Gene Resources Conferring Resistance to Stripe Rust

Stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), threatens global wheat production. Breeding resistant varieties is a key to disease control. In this study, 198 modern wheat varieties were phenotyped with the prevalent Pst races CYR33 and CYR34 at the seedling stage and with mixed Pst races at the adult-plant stage. Seven stable resistance varieties with infection type (IT) ≤ 2 and disease severity (DS) ≤ 20% were found, including five Chinese accessions (Zhengpinmai8, Zhengmai1860, Zhoumai36, Lantian36, and Chuanmai32), one USA accession (GA081628-13E16), and one Pakistani accession (Pa12). The genotyping applied a 55K wheat single-nucleotide polymorphism (SNP) array. A genome-wide association study (GWAS) identified 14 QTL using a significance threshold of p ≤ 0.001, which distributed on chromosomes 1B (4), 1D (2), 2B (4), 6B, 6D, 7B, and 7D (4 for CYR33, 7 for CYR34, 3 for mixed Pst races), explaining 6.04% to 18.32% of the phenotypic variance. Nine of these QTL were potentially novel, as they did not overlap with the previously reported Yr or QTL loci within a ±5.0 Mb interval (consistent with genome-wide LD decay). The haplotypes and resistance effects were evaluated to identify the favorable haplotype for each QTL. Candidate genes within the QTL regions were inferred based on their transcription levels following the stripe rust inoculation. These resistant varieties, QTL haplotypes, and favorable alleles will aid in wheat breeding for stripe rust resistance.