Genotyping-By-Sequencing Reveals Three QTL for Clubroot Resistance to Six Pathotypes of Plasmodiophora brassicae in Brassica rapa

Clubroot, caused by Plasmodiophora brassicae, poses a serious threat to canola and Brassica vegetable production worldwide. A B. rapa canola breeding line T19 was found to be highly resistant to six pathotypes (Williams’ system pathotypes 2 (P2), 3 (P3), 5 (P5), 6 (P6), 8 (P8) and a highly virulent variant of P5 (P5x) of P. brassicae identified from canola in Canada. Crosses of T19 with a susceptible double-haploid line ACDC were made and the resulting F₁ was backcrossed with ACDC to produce a BC₁ population. The 92 BC₁ plants were self-pollinated to produce 92 BC₁S₁ lines, which were evaluated for resistance to clubroot. Genotyping-by-sequencing (GBS) was performed on the parental lines and 92 plants in the BC₁. Short-read sequences were aligned into the chromosomes of the reference genome and genome-wide DNA variants were identified in the population and the parental lines. After filtering for false heterozygous, monomorphic and un-linked SNP loci, 1178 high quality SNP loci distributed on 10 chromosomes of B. rapa were obtained. A single co-localized QTL designated as Rcr4 on chromosome A03 conferred resistance to P2, P3, P5, P6 and P8. Two QTL designated as Rcr8 on chromosomes A02 and Rcr9 on A08 were detected for resistance to pathotype 5x. DNA variants in the respective QTL target regions were examined through bulked segregant DNA sequencing to identify possible candidate genes. Our results demonstrated the power of GBS-based QTL mapping for rapid and efficient QTL detection and provided reliable QTL regions for fine mapping.