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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.

Blackleg, caused by the fungus Leptosphaeria maculans (Desm.) Ces. et de Not. [anamorph = Phoma lingam (Tode: Fr.) Desm.] has become the most important disease affecting canola around the world. A study was conducted to identify sources of resistance to L. maculans in a collection of B. napus plant introduction accessions. Approximately, 5% of accessions showed highly resistance (median severity < 3) reaction to the L. maculans PG-4 under the greenhouse conditions and three of them performed better than commercial hybrids in the field conditions. At the same time, DNA extracted and genome-wide association study (GWAS) was done for 213 and 78 accessions for PG-4 and PG-3. The 0.1 and 0.01 percentile tails of an empirical distribution, obtained from 5,000 bootstraps, was used to determine the cut off P-value to identify significant markers. Finally, 10 and 26 significant single nucleotide polymorphism (SNP) markers associated with resistance to PG-4 and PG-3, respectively. These markers were located across 14 chromosomes (A01, A02, A03, A04, A05, A07, A08, A10, C03, C04, C05, C07, C08 and C09) out of B. napus 19 chromosomes. These markers were validated under field conditions. With exploring flanking region of each significant marker eight candidate genes were identified which involved in plant defense family such as defensing and leucine-rich repeat and serine-threonine protein kinase protein. To infer the presence of R genes in commercial canola hybrids, elite B. napus plant introduction materials, and elite canola breeding lines, they were inoculated with different L. maculans races. The results showed that, resistance gene Rlm9 was present in 18% of the genotypes evaluated; Rlm2 and Rlm3 were each present in 16% of them, while LepR1, Rlm4 and Rlm5 with present in 11, 5, and 5% each, respectively. However, we were not able to infer R gene(s) on 29% of the genotypes evaluated. Approximately 18% of genotypes were susceptible to all the races used. The hybrids with different R genes could use for hybrid rotation.