Identification of new QTLs for resistance to Plasmodiophora brassicae in Brassica napus using genome wide association mapping

Abstract Background Clubroot of canola ( Brassica napus ), caused by the obligate pathogen Plasmodiophora brassicae Woronin, is a major disease worldwide. Genetic resistance remains the best strategy to manage this disease. The objective of the study was to identify and map new sources of resistance to clubroot in B. napus using genome-wide association mapping. The reaction of a collection of 177 accessions to four highly virulent pathotypes of P. brassicae was assessed. These pathotypes were selected because they were most recently identified and showed different virulence patterns on the Canadian clubroot differential (CCD) lines. The collection was then genotyped using genotyping by sequencing (GBS) method. Multi-locus mixed linear model (MMLM) was used to perform the association analysis. Results The majority of accessions were highly susceptible (70 –100 DSI), while few individual accessions showed strong resistance (0–20 DSI) to 5X (2 accessions), 2B (7 accessions), 3A (8 accessions) and 3D (15 accessions). In total, 301,753 SNPs were mapped to 19 chromosomes. Population structure analysis indicated that the 177 accessions belong to two major populations. SNPs were associated with resistance to each pathotype using MLMM. In total, 23 significant SNP loci were identified, with 14 SNPs mapped to the A-genome and 9 to the C-genome. The SNPs were associated with resistance to pathotypes 5X (4 SNPs), 2B (9), 3A (5) and 3D (5). A blast search of 2 Mb upstream and downstream identified 61 disease resistance genes, of which 24 belonged to TIR-NBS-LRR proteins and 20 belonged to CC-NBS-LRR proteins. The distance between a SNP locus and the nearest resistance genes ranged from 0.11–1.66 Mb. This indicated that NBS-LRR gene family might have an important role in clubroot resistance in B. napus . Conclusion The resistant B. napus lines and the SNP markers identified in this study can be used for breeding for resistance to clubroot and contribute to understanding the genetic mechanism of resistance to clubroot.