Fine mapping of a clubroot resistance gene from turnip using SNP markers identified from bulked segregant RNA-Seq

Clubroot caused by Plasmodiophora brassicae poses a serious threat to canola production around the world, but sources of clubroot resistance in canola are limited. In this study, turnip cultivar Purple Top White Globe, which is highly resistant to pathotype 3 (Williams' system), was used as the source of resistance. Genetic studies showed that the resistance in this cultivar was controlled by a major gene, Rcr5. Bulked segregant RNA-Seq was used to map the gene. A total of 124.6 M raw reads were generated from the resistant (R) and susceptible (S) pooled samples, and 78 K polymorphic DNA variants between the pooled R and the pooled S samples were identified. The percentage of polymorphic variants (PPV) on A03 was much higher than that on the other chromosomes, which indicated that Rcr5 was located on A03. Rcr5 was further mapped into the 23-31 Mb region of A03 through analysis of PPV in the chromosome. A segregated population consisting of 824 plants was genotyped based on 15 SNP markers in the region using Kompetitive Allele Specific PCR. Rcr5 was finely mapped between SNP_A03_83 and SNP_ A03_100, with 0.2 and 0.3 cM from Rcr5, respectively. The markers were located between 23,339,019 and 23,465,030 bp on A03. Eighteen genes were annotated in the Rcr5 target region, seven genes were expressed, and DNA variants were identified in the genes. The SNP markers developed in this study could be used for marker-assisted selection for resistance to clubroot when the gene is transferred to canola.