Abstract
Key message “We identified both quantitative and quantitative resistance loci to Leptosphaeria maculans, a fungal pathogen, causing blackleg disease in canola. Several genome-wide significant associations were detected at known and new loci for blackleg resistance. We further validated statistically significant associations in four genetic mapping populations, demonstrating that GWAS marker loci are indeed associated with resistance to L. maculans. One of the novel loci identified for the first time, Rlm12, conveys adult plant resistance in canola.” Blackleg, caused by Leptosphaeria maculans, is a significant disease which affects the sustainable production of canola (Brassica napus). This study reports a genome-wide association study based on 18,804 polymorphic SNPs to identify loci associated with qualitative and quantitative resistance to L. maculans. Genomic regions delimited with 694 significant SNP markers, that are associated with resistance evaluated using 12 single spore isolates and pathotypes from four canola stubble were identified. Several significant associations were detected at known disease resistance loci including in the vicinity of recently cloned Rlm2/LepR3 genes, and at new loci on chromosomes A01/C01, A02/C02, A03/C03, A05/C05, A06, A08, and A09. In addition, we validated statistically significant associations on A01, A07, and A10 in four genetic mapping populations, demonstrating that GWAS marker loci are indeed associated with resistance to L. maculans. One of the novel loci identified for the first time, Rlm12, conveys adult plant resistance and mapped within 13.2 kb from Arabidopsis R gene of TIR-NBS class. We showed that resistance loci are located in the vicinity of R genes of Arabidopsis thaliana and Brassica napus on the sequenced genome of B. napus cv. Darmor-bzh. Significantly associated SNP markers provide a valuable tool to enrich germplasm for favorable alleles in order to improve the level of resistance to L. maculans in canola.
Highlights
Blackleg disease, caused by the hemibiotrophic fungal pathogen Leptosphaeria maculans (Desm.) Ces. et de Not. is a major threat to the consistent global supply of canola (Brassica napus L)
Our results showed that resistance expressed at the cotyledon stage and in the crown canker was not always highly correlated; Pearson’s product-moment correlation coefficient ranged from 0.03 to 0.76 (Supplementary Table S2; Figure 1B), suggesting that some lines of the GWAS panel may have loci for adult plant and/or quantitative resistance
Our result showed that the majority of genotypes were susceptible to pathotypes especially present on stubble derived from AV-Garnet, CB-JardeeHT and Monola76TT (Supplementary Table S1; Figure 1C), suggesting that the R genes; Rlm1, Rlm2, Rlm4, Rlm9, and LepR3 were no longer effective in conferring resistance to L. maculans
Summary
Blackleg disease, caused by the hemibiotrophic fungal pathogen Leptosphaeria maculans (Desm.) Ces. et de Not. is a major threat to the consistent global supply of canola (Brassica napus L). Two types of resistance to L. maculans; qualitative and quantitative, have been reported in B. napus (Delourme et al, 2006). Eighteen qualitative (R) genes for ETI have been identified in Brassica species; B. rapa, B. juncea, B. napus, and B. nigra and several of them are deployed in commercial canola varieties (Delourme et al, 2011; Marcroft et al, 2012; Balesdent et al, 2013; Larkan et al, 2013, 2015; Raman et al, 2013b). Intensive cultivation of broad-acre varieties carrying specific R genes results in the emergence of new virulent (avr) races and rapid change in the frequency of existing avirulence (Avr) alleles in natural populations of L. maculans. Some R genes have become ineffective just within 5 years of their commercial release (Brun et al, 2000; Howlett et al, 2001; Li et al, 2003; Rouxel et al, 2003; Sprague et al, 2006; Van de Wouw et al, 2014)
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