Abstract
BackgroundThe fungal pathogen Leptosphaeria maculans (Lm). causes blackleg disease on canola/rapeseed in many parts of the world. It is important to use resistant cultivars to manage the disease and minimize yield losses. In this study, twenty-two Lm isolates were used to identify resistance genes in a collection of 243 canola/rapeseed (Brassica napus L.) accessions from Canada and China. These Lm isolates carry different compliments of avirulence genes, and the investigation was based on a genome-wide association study (GWAS) and genotype-by-sequencing (GBS).ResultsUsing the CROP-SNP pipeline, a total of 81,471 variants, including 78,632 SNPs and 2839 InDels, were identified. The GWAS was performed using TASSEL 5.0 with GLM + Q model. Thirty-two and 13 SNPs were identified from the Canadian and Chinese accessions, respectively, tightly associated with blackleg resistance with P values < 1 × 10− 4. These SNP loci were distributed on chromosomes A03, A05, A08, A09, C01, C04, C05, and C07, with the majority of them on A08 followed by A09 and A03. The significant SNPs identified on A08 were all located in a 2010-kb region and associated with resistance to 12 of the 22 Lm isolates. Furthermore, 25 resistance gene analogues (RGAs) were identified in these regions, including two nucleotide binding site (NBS) domain proteins, fourteen RLKs, three RLPs and six TM-CCs. These RGAs can be the potential candidate genes for blackleg resistance.ConclusionThis study provides insights into potentially new genomic regions for discovery of additional blackleg resistance genes. The identified regions associated with blackleg resistance in the germplasm collection may also contribute directly to the development of canola varieties with novel resistance genes against blackleg of canola.
Highlights
The fungal pathogen Leptosphaeria maculans (Lm). causes blackleg disease on canola/rapeseed in many parts of the world
In western Canada, a few studies have revealed that the structure of Lm population has been shifting over the past decade; PG2 was classified as the primary pathogenicity group (PG) of Lm collected between 1984 and 2000 [19, 20], but PG3 and PGT emerged from Lm isolates collected between 1998 and 2004
Genetic variation in resistance to L. maculans Total of 22 Lm isolates were employed to assess the resistance of 243 canola accessions at the seedling stage
Summary
The fungal pathogen Leptosphaeria maculans (Lm). causes blackleg disease on canola/rapeseed in many parts of the world. Zhang et al reported thatRlm resistance had been broken down because AvrLm3 was no longer a predominant avirulence effector in western Canada [22] These studies indicate that the Lm population has evolved with the selection pressure from resistant canola varieties which carry a limited number of resistance genes; a single R gene will unlikely provide durable resistance against highly diverse Lm races in western Canada. Continued efforts to identify novel resistance loci from canola or rapeseed germplasm can aid in blackleg resistance breeding by providing new resistance sources for disease management Another type of resistance is quantitative resistance (QR, race non-specific), which is conferred typically by patterntriggered immunity (PTI) mechanisms in conjunction with pathogen associated molecular patterns [23, 24]. Canadian and Chinese canola germplasm has not been used to identify QR or QTL against the diverse Canadian Lm population
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