Mapping of a novel clubroot resistance QTL using ddRAD-seq in Chinese cabbage (Brassica rapa L.)

Abstract

BackgroundPlasmodiophora brassicae is a soil-borne plant pathogen that causes clubroot disease, which results in crop yield loss in cultivated Brassica species. Here, we investigated whether a quantitative trait locus (QTL) in B. rapa might confer resistance to a Korean P. brassicae pathotype isolate, Seosan. We crossed resistant and susceptible parental lines and analyzed the segregation pattern in a F2 population of 348 lines. We identified and mapped a novel clubroot resistance QTL using the same mapping population that included susceptible Chinese cabbage and resistant turnip lines. Forty-five resistant and 45 susceptible F2 lines along with their parental lines were used for double digest restriction site-associated DNA sequencing (ddRAD-seq). High resolution melting (HRM)-based validation of SNP positions was conducted to confirm the novel locus.ResultsA 3:1 ratio was observed for resistant: susceptible genotypes, which is in accordance with Mendelian segregation. ddRAD-seq identified a new locus, CRs, on chromosome A08 that was different from the clubroot resistance (CR) locus, Crr1. HRM analysis validated SNP positions and constricted CRs region. Four out of seventeen single nucleotide polymorphisms (SNPs) positions were within a 0.8-Mb region that included three NBS-LRR candidate genes but not Crr1.ConclusionThe newly identified CRs locus is a novel clubroot resistance locus, as the cultivar Akimeki bears the previously known Crr1 locus but remains susceptible to the Seosan isolate. These results could be exploited to develop molecular markers to detect Seosan-resistant genotypes and develop resistant Chinese cabbage cultivars.Electronic supplementary materialThe online version of this article (10.1186/s12870-018-1615-8) contains supplementary material, which is available to authorized users.

Construction of SSR linkage maps and identification of QTL for resistance to root rot in sweetpotato (Ipomoea batatas (L.) Lam.)

“…Shen et al obtained similar QTL mapping results when using transformed and non-transformed nematode resistance data [30]. Non-transformed abnormally distributed data have been used for QTL mapping in various studies [9,23,[31][32][33][34]. Therefore, we used the non-transformed data for QTL analysis in this study and mapped seven stable QTLs, which explained 52.6-57.0% of the phenotypic variation in root rot resistance.…”

Genetics of Clubroot and Fusarium Wilt Disease Resistance in Brassica Vegetables: The Application of Marker Assisted Breeding for Disease Resistance

“…Several CR genes have been identified and mapped in B. rapa , B. oleracea , and other Brassica species [ 33 ]. In B. rapa , 18 major CR loci have been identified ( Figure 2 , Table 1 ); Crr2 mapped on chromosome 1 [ 34 ], CRc and CR QTL, designated as Rcr8 , on chromosome 2 [ 35 , 36 ], Crr3 , CRa , CRb , CRd , CRk , Rcr1 , Rcr2 , and Rcr4 on chromosome 3 [ 35 , 36 , 37 , 38 , 39 , 40 , 41 , 42 , 43 , 44 , 45 , 46 , 47 , 48 , 49 , 50 ], CrrA5 on chromosome 5 [ 51 ], Crr4 on chromosome 6 [ 52 ], Crr1 ( Crr1a , Crr1b ), Rcr9 , and CRs on chromosome 8 [ 36 , 44 , 53 , 54 ]. Most of the CR genes were identified through QTL mapping using a range of resistant sources based on molecular markers, genotyping-by-sequencing (GBS), or bulked segregant RNA sequencing (BSR-seq) strategies.…”

Understanding Host–Pathogen Interactions in Brassica napus in the Omics Era

“…These NGS-based SNP genotyping approaches have been applied widely for the QTL mapping of disease resistance traits and identification of candidate genes through genome-wide association studies (GWAS) in Brassica crops ( Table 2 ). Highlights include the discovery of novel disease resistance QTLs/genes at an unprecedented speed, for example, in Blackleg [ 72 , 73 ], Sclerotinia [ 74 , 75 , 76 ] and Clubroot [ 77 , 78 , 79 ]. The other benefit of the application of NGS-based SNP genotyping is the successful breeding of B. napus varieties containing multiple improved traits.…”