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Blackleg is one of the major fungal diseases in oilseed rape/canola worldwide. Most commercial cultivars carry  R  gene-mediated qualitative resistances that confer a high level of race-specific protection against  Leptosphaeria maculans , the causal fungus of blackleg disease. However, monogenic resistances of this kind can potentially be rapidly overcome by mutations in the pathogen’s avirulence genes. To counteract pathogen adaptation in this evolutionary arms race, there is a tremendous demand for quantitative background resistance to enhance durability and efficacy of blackleg resistance in oilseed rape. In this study, we characterized genomic regions contributing to quantitative  L. maculans  resistance by genome-wide association studies in a multiparental mapping population derived from six parental elite varieties exhibiting quantitative resistance, which were all crossed to one common susceptible parental elite variety. Resistance was screened using a fungal isolate with no corresponding avirulence ( AvrLm ) to major  R  genes present in the parents of the mapping population. Genome-wide association studies revealed eight significantly associated quantitative trait loci (QTL) on chromosomes A07 and A09, with small effects explaining 3–6% of the phenotypic variance. Unexpectedly, the qualitative blackleg resistance gene  Rlm9  was found to be located within a resistance-associated haploblock on chromosome A07. Furthermore, long-range sequence data spanning this haploblock revealed high levels of single-nucleotide and structural variants within the  Rlm9  coding sequence among the parents of the mapping population. The results suggest that novel variants of  Rlm9  could play a previously unknown role in expression of quantitative disease resistance in oilseed rape.

Dissection of Quantitative Blackleg Resistance Reveals Novel Variants of Resistance Gene Rlm9 in Elite Brassica napus