Development of linkage markers for stripe rust resistance gene Yr69 in Triticum aestivum L.

Stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is one of the most devastating wheat diseases in China. The Yr69 gene confers resistance to almost all Chinese P. striiformis stripe rust races, and thus has important value in the breeding of Triticum aestivum L. stripe rust resistance. To improve the efficiency of molecular marker-assisted selection and accelerate the application of Yr69 in wheat resistance breeding, this study used stripe rust race CYR34 to inoculate and identify the F₉ recombinant inbred line (RIL) population of ‘Taichung29/CH7086’ containing 340 families. Bulked segregant analysis-single nucleotide polymorphism (BSA-SNP) was used to remap the stripe rust resistance gene in ‘CH7086’. Based on the disease resistance identification results, the number of resistant families and susceptible families in the RIL population exhibited a bimodal distribution, suggesting that the resistance of ‘CH7086’ to stripe rust was controlled by a major locus. The BSA-SNP results showed that the polymorphic SNPs were mainly concentrated in a 0-30 Mb section at the end of the wheat 2AS chromosome. In this segment, 208 simple sequence repeat (SSR) molecular markers were identified. Among these, 14 molecular markers linked to Yr69 were screened using a small population of resistant plants and susceptible plants. The 14 linked markers were used for linkage mapping with 340 F₉ RIL population, with two markers found to be co-segregated with the Yr69 gene. Based on the Chinese spring wheat genome IWGSC Ref Seq v1.0, Yr69 was mapped to a 7.76 Mb interval between the two molecular markers 2AS111 and 2AS171, and their linkage distances with Yr69 were both 0.4 cM. Thus, two molecular markers (2AS117 and 2AS127) co-segregated with Yr69 were obtained, which not only can be used for molecular marker-assisted selection of Yr69, but also have important significance for fine mapping and cloning of the gene.