SNP-based linkage mapping for validation of adult plant stripe rust resistance QTL in common wheat cultivar Chakwal 86

Wheat crops in China are constantly challenged by stripe rust. Deployment of cultivars with diverse resistances is the best strategy to control the disease. A recombinant inbred line (RIL) population derived from a cross between the resistant cultivar Chakwal 86 and susceptible landrace Mingxian 169 was studied in multiple environments to examine the underlying genetics and to identify quantitative trait loci (QTL) for stripe rust resistance. One hundred and twenty-eight RILs were genotyped with wheat 35K SNP array and a genome-wide linkage map with 1480 polymorphic SNP markers, or bins, was constructed. Two major QTL on chromosomes 1BL and 3BS, and one minor QTL on 6BS had significant effects in reducing stripe rust severity. The QTL were validated using composite interval mapping (CIM) and inclusive composite interval mapping (ICIM). These methods explained 59.0%–74.1% of the phenotype variation in disease response. The QTL on chromosome 1BL was confirmed to be Yr29/Lr46 and the one on 3BS was the resistance allele identified in CIMMYT germplasm but was not Yr30/Sr2. The QTL on 6BS probably corresponded to previously known QTL. RILs with combined QTL were more resistant than those with single or no QTL. Kompetitive allele-specific PCR (KASP) assays for the QTL with largest effect QTL on chromosome 3BS were performed on a subset of RILs and 150 unrelated wheat lines. The QTL on 3BS with its linked KASP markers can be used in marker-assisted selection to improve stripe rust resistance in breeding programs.