Molecular mapping of all stage stripe rust resistance gene YrPak in wheat landrace PI388231

Stripe (yellow) rust caused by Puccinia striiformis f. sp. tritici (Pst) is a major disease in many wheat growing regions. The objective of this study was to characterise stripe rust resistance in a common wheat landrace PI388231, originated from Sindh province of Pakistan, which confers high to moderate levels of resistance against Pst pathotypes prevalent in Pakistan. A recombinant inbred line (RIL) population was developed by crossing PI388231 with the susceptible parent Avocet ‘s’. Screening of this population with Pakistani Pst pathotype 574212 in glasshouse indicated the presence of a single gene and the locus was temporarily named YrPak. Bulked segregant analysis using the targeted genotyping-by-sequencing (tGBS) platform located YrPak on the short arm of chromosome 5B. YrPak-linked SNPs were converted into kompetitive-allele specific PCR (KASP) markers and were genotyped on the parents. Five KASP markers sunKASP_330, sunKASP_334, sunKASP_335, sunKASP_338 and sunKASP_341 that showed clear clustering between parents were tested on the entire RIL population. Markers sunKASP_338 and sunKASP_341 flanked YrPak. The markers sunKASP_338 and sunKASP_341 amplified alleles alternate to those linked with YrPak in 86% and 83% of wheat cultivars tested, respectively. This population segregated for two adult plant resistance genes in addition to YrPak. The presence of pleiotropic locus Yr46/Lr67/Sr55 was confirmed using the gene specific marker TM10_67T and the second gene remains unknown.