Fine mapping of Wheat yellow mosaic virus resistance gene Ym5 and its application in breeding

Wheat yellow mosaic virus (WYMV) poses a significant threat to global autumn-sown wheat production. Growing wheat varieties with WYMV resistance is the most effective strategy for disease control. In this study, we fine-mapped a major WYMV resistance gene Ym5 (previously designated as QYm.njau-5A.1) in the Japanese wheat variety Xifeng. We delimited Ym5 to a 4.6 Mb linkage block (534.6–539.2 Mb in chromosome 5A) by genome-wide association study of 266 wheat accessions (excluding those carrying Ym1). Comparative genomic analyses revealed that resistant haplotypes, shared by Xifeng and European line ArinaLrFor, represent a putative alien introgression from Triticum monococcum. Twelve InDel and one KASP markers were developed and confirmed as diagnostic. Twenty-four recombinants were identified from a Xifeng × Yangmai 158 F₂ population consisting of 6882 individuals, and Ym5, flanked by markers ARI_106 and ARI_218, was narrowed down to a 1.1 Mb interval (534.8–535.9 Mb in ArinaLrFor). The use of Ym5 in Chinese breeding programs was traced to two sources: Xifeng and Australian variety Quality. Further investigation showed Ym5 introgression conferred no obvious yield penalty.