Analysing the genetic architecture of clubroot resistance variation in Brassica napus by associative transcriptomics

Abstract

Clubroot is a destructive soil-borne pathogen of Brassicaceae that causes significant recurrent reductions in yield of cruciferous crops. Although there is some resistance in oilseed rape (a crop type of the species Brassica napus), the genetic basis of that resistance is poorly understood. In this study, we used an associative transcriptomics approach to elucidate the genetic basis of resistance to clubroot pathotype ECD 17/31/31 across a genetic diversity panel of 245 accessions of B. napus. A single nucleotide polymorphism (SNP) association analysis was performed with 256,397 SNPs distributed across the genome of B. napus and combined with transcript abundance data of 53,889 coding DNA sequence (CDS) gene models. The SNP association analysis identified two major loci (on chromosomes A2 and A3) controlling resistance and seven minor loci. Within these were a total of 86 SNP markers. Altogether, 392 genes were found in these regions. Another 21 genes were implicated as potentially involved in resistance using gene expression marker (GEM) analysis. After GO enrichment analysis and InterPro functional analysis of the identified genes, 82 candidate genes were identified as having roles in clubroot resistance. These results provide useful information for marker-assisted breeding which could lead to acceleration of pyramiding of multiple clubroot resistance genes in new varieties.

Keywords: Association genetics; Brassica napus; Clubroot; Transcriptomics.

Fig. 1

a Disease severity was assessed after 7 weeks from inoculation by using a standard 0–3 scale (0 = no visual symptoms, 1 = clubs only on the lateral roots, 2 = main root clubs, 3 = deformed entire root system). b Histogram of disease index (DI) in 245 accessions including colour coded crop types

Fig. 2

Population structure and trait variation across 245 B. napus accessions. a Relatedness of accessions in the panel based on 355,536 scored SNPs. b Main crop types in the panel, colour-coded: orange for spring oilseed rape, green for semi-winter oilseed rape, light blue for swede, dark blue for kale, black for fodder and red for winter oilseed rape, grey for crop type not assigned. c Population structure for highest likelihood K = 2. d Variation for clubroot resistance by using disease index DI (DI = 0, no visual symptoms; DI = 100, deformed entire root system)

Fig. 3

Transcriptome SNP association analysis for clubroot resistance. The SNP markers are positioned on the x-axis based in the genomic order of the gene models in which the polymorphism was scored, with the significance of the trait association, as –log10P, on the y-axis. A1 to A10 and C1 to C9 are the chromosomes of B. napus, shown in alternating black and blue colours to permit boundaries to be distinguished. Hemi-SNP markers (i.e. polymorphisms involving multiple bases called at the SNP position in one allele of the polymorphism) for which the genome of the polymorphism cannot be assigned are shown as light points, whereas simple SNP markers (i.e. polymorphisms between resolved bases) and hemi-SNPs that have been directly linkage mapped, both of which can be assigned to a genome, are shown as dark points. The broken blue and red horizontal lines mark significance − log10P = 5 and -log10P = 4, respectively

Fig. 4

SNP association analysis for clubroot resistance focus on part of pseudomolecule with the highest associated locus (around 26 million bases from the beginning of the A03 chromosome). The SNP are positioned on the x-axis based on their location (units 10⁵), the positions of the candidate genes for this locus are further indicated on x-axis. On the y-axis are values of the trait association significance (− log10P). The black signs represent simple SNP and hemi-SNP markers assigned to the corresponding genome and grey hemi-SNP markers for which the genome of the polymorphism cannot be assigned. The dashed blue and red lines mark significance − log10P = 5 and − log10P = 4, respectively

Fig. 5

SNP association analysis for clubroot resistance focus on part of pseudomolecule with the second most prominent association peak (around 26 million bases from the beginning of the A02 chromosome). The SNP are positioned on the x-axis based on their location (units 10⁵), the positions of the candidate genes for this locus are further indicated on x-axis. On the y-axis are values of the trait association significance (− log10P). The black signs represent simple SNP and hemi-SNP markers assigned to the corresponding genome and grey hemi-SNP markers for which the genome of the polymorphism cannot be assigned. The dashed blue and red lines mark significance − log10P = 5 and − log10P = 4, respectively