High density mapping of wheat stripe rust resistance gene QYrXN3517-1BL using QTL mapping, BSE-seq and candidate gene analysis

Abstract Identification and utilization of genetic resistance is an effective strategy to control stripe rust disease in wheat. Cultivar Xinong 3517 (XN3517) has remained highly resistant to stripe rust since its release in 2008. To understand the genetic architecture of stripe rust resistance, Avocet S (AvS) × XN3517 F6 RIL population was assessed for stripe rust severity in five field environments. The parnets and RILs were genotyped by using the GenoBaits Wheat 16K Panel. Four stable QTL from Xinong 3517 were detected on chromosome arms 1BL, 2AL, 2BL, and 6BS. Based on the Wheat 660K array and bulked segregant exome sequencing (BSE-seq), the most effective QTL on chromosome 1BL is most likely different for the known adult plant resistance gene Yr29 and was mapped to a 1.7 cM region [336 kb, including twelve candidate genes in International Wheat Genome Sequencing Consortium (IWGSC) RefSeq version 1.0]. The 6BS QTL was identified as Yr78, and the 2AL QTL was probably same as QYr.caas-2AL or QYrqin.nwafu-2AL. The novel QTL on 2BL was effective in seedling stage against the races used in phenotyping. Candidate gene analysis of 1BL overlapping region indicated TraesCS1B01G460000, TraesCS1B01G460100, TraesCS1B01G460200, TraesCS1B01G460300, and TraesCS1B01G460400 to be most likely genes associated with the stripe rust resistance. In addition, allele-specifc quantitative PCR (AQP) marker nwafu.a5 was developed for QYrXN3517-1BL to assist marker-assisted breeding.