RNA‐seq bulked segregant analysis combined with KASP genotyping rapidly identified PmCH7087 as responsible for powdery mildew resistance in wheat

Abstract

Powdery mildew causes considerable yield losses in common wheat (Triticum aestivum L.) production. Mapping and cloning powdery mildew-resistant quantitative trait loci can benefit stable yield production by facilitating the breeding of resistant varieties. In this study, we used the powdery mildew resistance introgression line 'CH7087' (harboring the resistance gene PmCH7087) and developed a large F 2 population and a corresponding F 2:3 segregation population containing 2,000 family lines for molecular mapping of PmCH7087. Genetic analysis demonstrated that the resistance phenotype was controlled by a single dominant gene. According to the performance exhibited by the F 2:3 lines, 50 resistant lines and 50 susceptible lines without phenotype segregation were chosen for pooling and bulked segregant RNA sequencing (BSR-Seq) analysis. A region spanning 42.77 Mb was identified, and genotyping of an additional 183 F 2:3 lines with extreme phenotypes using 20 kompetitive allele-specific polymerase chain reaction (KASP) markers in the BSR-Seq mapping regions confirmed this region and narrowed it to 9.68 Mb, in which 45 genes were identified and annotated. Five of these transcripts harbored nonsynonymous single nucleotide polymorphisms between the two parents, with the transcripts of TraesCS2B01G302800 being involved in signal transduction. Furthermore, TraesCS2B01G302800.2 was annotated as the closest homologue of serine/threonine-protein kinase PBS1, a typical participant in the plant disease immune response, indicating that TraesCS2B01G302800 was the candidate gene of PmCH7087. Our results may facilitate future research attempting to improve powdery mildew resistance in wheat and to identify candidate genes for further verification and gene cloning.

The putative vacuolar processing enzyme gene TaVPE3cB is a candidate gene for wheat stem pith-thickness

“…In addition, RNA-seq reveals DEGs between two bulked sample pools in the mapping interval and provides the necessary information for gene screening. Recently, several genes have been identified through BSR-seq in different plant species, including the genes related to powdery mildew resistance (Xie et al 2020 ; Zhan et al 2021 ), pest resistance (Hao et al 2019 ), male sterile (Tan et al 2019 ) and waterlogging-tolerance (Du et al 2017 ).…”