Identification of genomic regions associated with resistance to blackleg (Leptosphaeria maculans) in canola using genome wide association study

Blackleg, caused by Leptosphaeria maculans, is a serious threat to canola (B. napus) production in North Dakota state that is its largest producer in the United States. Genome-wide association study (GWAS) was conducted on a set of 213 B. napus accessions inoculated with a mixture of five L. maculans isolates from pathogenicity group-four (PG-4) to identify genetic regions associated with resistance to this disease. Phenotypic data was obtained at the seedling stage using a 1–9 severity scale. This data was used to generate two binary (binary_3 and binary_5), and two polynomial (polynomial_median and polynomial_3) subsets. Using the median_severity phenotypic dataset (original) three significant markers were identified. By using the other four subsets five additional markers were detected. These eight significant markers (P < 0.00036) were distributed among chromosomes A1, A3, A6, A8, A9, C3, and C5. Two sets of three markers identified using the median_severity (original) and the polynomial_ median datasets, had the highest cumulative R2 values; they explained 36% and 34% of the phenotypic variation, respectively. A BLAST search within ±100 kb of these markers identified five genetic regions involved in the plant defense system. Information presented in this paper shows the benefit of using multiple arrangements of the same phenotypic dataset in GWAS. Furthermore, the markers and their allelic combinations identified in this study are valuable resources that could facilitate marker assisted selection to transfer blackleg resistance into modern breeding lines.