Genome-wide Association Study Identifies New Loci for Resistance to Leptosphaeria maculans in Canola

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.

GWAS hints at pleiotropic roles forFLOWERING LOCUS Tin flowering time and yield-related traits in canola

“…Of them, seven SNP markers map in the vicinity (0.2 Mb) of SPA3 (A01), PRR5 (A02), MAF4 (A02), ASH1 (A07), POWERDRESS (A10) and ELF6 (C09), genes underlying photoperiod response in canola accessions; of which ANAC029, EFF6, ABF2, FVE , and PAF1 were detected in CE experiments and ANAC029 , and ASH1 , were detected (within 200 kb) under field experiments (S11 Table). Consistent with our previous study (Raman et al 2016a), our results reinforces that while the major players of flowering time appear to be conserved between Arabidopsis and canola, the specific roles of the paralogs might be different depending on the environmental conditions.…”

“…To ensure capturing the relevance of entire genetic architecture of flowering time variation, we considered the SAgS DH mapping population derived from a BC 1 F 1 cross between Australian spring type cultivars; Skipton (less responsive to vernalisation) and Ag-Spectrum (more responsive to vernalisation), which was previously utilised for genetic analyses for range of traits of interest (Luckett et al , 2011; Raman et al , 2016a; Raman et al , 2013; Raman et al , 2016c; Raman et al , 2012; Tollenaere et al , 2012). There were moderate to high genetic correlations for flowering time, early vigour, plant biomass and grain yield across environments (phenotyping years) in the SAgS DH population (Fig.…”

Genetic and physical mapping of loci for resistance to blackleg disease in canola (Brassica napus L.)

“…Other consistent QTL on chromosome A07 for resistance to L. maculans evaluated by ascospore shower test was localized within the marker-intervals for Rlm3 and Rlm4. QTL for field resistance on chromosome A01 was also identified within 1 Mb of previously identified QTL for QR in B. napus populations 5,35 .…”

“…Therefore, identification and deployment of both effective R and QR genes is needed for stable canola production. In previous studies, genetic resistance to L. maculans has been mapped in various Australian populations derived from Ag-Castle, AG-Spectrum, AV-Sapphire, Dunkeld, Maluka, Rainbow, Skipton, Shiralee and Surpass400 [3][4][5][6][8][9][10][39][40][41] . Both parental lines of the RADH population, RP04 and Ag-Outback, have shown good levels of blackleg resistance under field conditions previously.…”

Brassica 2016 – Phenomics to genomics and everything in between

“…The discussion, led by Dr Thierry Rouxel, highlighted the various issues with nomenclature whereby the same gene has been given multiple names by various groups, for example the confusion around the resistance gene(s) in Surpass400 which have been identified as LepR3, RlmS, Rlm1, BLMR1 and BLMR2 (Balesdent et al 2005; Van de Wouw et al 2009, 2014Long et al 2011;Larkan et al 2013). In addition, it was highlighted that we now have the added confusion that the same nomenclature used for major resistance genes, Rlm (resistance to L. maculans), has been used for quantitative or minor gene resistance, with the first locus of this kind identified and named Rlm12 (Raman et al 2016). A consensus amongst the group was that the Rlm nomenclature should be exclusive for the major genes.…”