Abstract
Genetic resistance is widely used to manage clubroot (Plasmodiophora brassicae) in brassica crops, but new pathotypes have recently been identified on canola (Brassica napus) on the Canadian prairies. Resistance effective against both the most prevalent pathotype (3H, based on the Canadian Clubroot Differential system) and the new pathotypes is needed. BC1 plants of Brassica rapa from a cross of line 96-6990-2 (clubroot resistance originating from turnip cultivar ‘Waaslander’) and a susceptible doubled-haploid line, ACDC, exhibited a 1:1 segregation for resistance against pathotypes 3H and 5X. A resistance gene designated as Rcr3 was mapped initially based on the percentage of polymorphic variants using bulked segregant RNA sequencing (BSR-Seq) and further mapped using Kompetitive Allele Specific PCR. DNA variants were identified by assembling short reads against a reference genome of B. rapa. Rcr3 was mapped into chromosome A08. It was flanked by single nucleotide polymorphisms (SNP) markers (A90_A08_SNP_M12 and M16) between 10.00 and 10.23 Mb, in an interval of 231.6 Kb. There were 32 genes in the Rcr3 interval. Three genes (Bra020951, Bra020974, and Bra020979) were annotated with disease resistance mechanisms, which are potential candidates for Rcr3. Another resistance gene, designated as Rcr9wa, for resistance to pathotype 5X was mapped, with the flanking markers (A90_A08_SNP_M28 and M79) between 10.85 and 11.17 Mb using the SNP sites identified through BSR-Seq for Rcr3. There were 44 genes in the Rcr9wa interval, three of which (Bra020827, Bra020828, Bra020814) were annotated as immune-system-process related genes, which are potential candidates for Rcr9wa.
Highlights
Clubroot, caused by Plasmodiophora brassicae Woronin, is a soil-borne disease of brassica crops that causes around 15% annual yield loss worldwide [1]
To define the genomic region of Rcr3, a total of 240 plants in the BC1 population were analyzed with three single nucleotide polymorphisms (SNP) sites from the 0–1 Mb and 11 SNP sites from the 8–11 Mb physical intervals of chromosome A08 through Kompetitive Allele Specific PCR (KASP) assay (Figure 3, Supplementary Figure S1)
Bulk-segregant analysis (BSA) and Next-generation sequencing (NGS) have recently been applied to mapping and marker development for Clubroot resistance (CR) genes in Brassica spp. [34,35,46,57,59]
Summary
Clubroot, caused by Plasmodiophora brassicae Woronin, is a soil-borne disease of brassica crops that causes around 15% annual yield loss worldwide [1]. A single dominant gene, Rcr, was identified that provided resistance to pathotypes 3H and 5X in the C genome on chromosome C07, which was homologous to a region on the A03 chromosome [46]. Enhancers and locus control regions are occasionally located away from candidate genes, with the result that communications may occur via histone modification or intra- and inter-chromosomal loops [47]. Such unusual relationships can complicate use of marker-assisted selection for CR genes. RNA-Seq has been used to identify functional variants related to disease resistance [35,56,57]. A similar number of reads were assembled against the top and bottom strands of the reference genome using the pooled sample assembly method [57] (Table 2)
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
