Exome Sequencing from Bulked Segregant Analysis Identifies a Gene for All Stage Resistance to Stripe Rust on Chromosome 1AL in Chinese Wheat Landrace Xiaohemai.

Stripe rust caused by Puccinia striiformis f. sp. tritici (Pst) is one of the most destructive diseases of wheat. Identifying novel resistance genes applicable for developing disease resistant cultivars is important for the sustainable control of wheat stripe rust. Chinese wheat landrace Xiaohemai (XHM) is an elite germplasm line with all-stage resistance (ASR) effective against predominant Chinese Pst races. In this study, we performed a bulked segregant analysis coupled with exome capture sequencing (BSE-seq) to identify a candidate genomic region strongly associated with stripe rust resistance on chromosome 1AL in 173 F2:3 lines derived from cross XHM × Avocet S. The gene, designated as YrXH-1AL, was validated by a conventional quantitative trait locus analysis using newly developed Kompetitive allele-specific PCR (KASP) markers, explaining up to 48.50% of the phenotypic variance. By testing a secondary mapping population comprising 144 lines from the same cross at the seedling stage with prevalent Pst race CYR34, YrXH-1AL was identified as a single Mendelian factor in a 1.5 cM interval flanked by KASP markers KP1A_484.33 and KP1A_490.09. This region corresponded to a 5.76 Mb genomic interval on Chinese Spring chromosome 1AL. Furthermore, two co-segregating KASP markers showed high polymorphisms among 130 Chinese wheat cultivars and could be used for marker-assisted selection. Because no other Yr genes for ASR that originated from common wheat have been detected on chromosome 1AL, YrXH-1AL is likely a novel gene that can be incorporated into modern breeding materials to develop wheat cultivars with enhanced stripe rust resistance.