Clubroot resistance gene Rcr6 in Brassica nigra resides in a genomic region homologous to chromosome A08 in B. rapa

• Published in: BMC plant biology 2019-05, Vol.19 (1), p.224-224, Article 224
• Main Authors: Chang, Adrian, Lamara, Mebarek, Wei, Yangdou, Hu, Hao, Parkin, Isobel A P, Gossen, Bruce D, Peng, Gary, Yu, Fengqun
• Format: Article
• Language: English
• Subjects: alleles; B7 antigen; Binding sites; Bioinformatics; Brassica; Brassica nigra; Brassica rapa; Bulked segregant RNA-sequencing; Canola; Chromosomes; class; Clubroot; Disease control; dominant genes; Evolution; Gene mapping; Gene sequencing; Genes; genetic resistance; Genomes; Genomics; Homology; Interleukin 1; Interleukins; Leucine; Mapping; Marker-assisted selection; Markers; Nucleotides; Plasmodiophora brassicae; Rape plants; resistance genes; Ribonucleic acid; RNA; Segregation; Single-nucleotide polymorphism; species; Target recognition
• ISSN: 1471-2229; 1471-2229
• DOI: 10.1186/s12870-019-1844-5

Clubroot, caused by Plasmodiophora brassicae Woronin, is a very important disease of Brassica species. Management of clubroot relies heavily on genetic resistance. In a cross of Brassica nigra lines PI 219576 (highly resistant, R) × CR2748 (highly susceptible, S) to clubroot, all F plants were resistant to clubroot. There was a 1:1 ratio of R:S in the BC and 3R:1S in the F , which indicated that a single dominant gene controlled clubroot resistance in PI 219576. This gene was designated Rcr6. Mapping of Rcr6 was performed using genome sequencing information from A-genome of B. rapa and B-genome of B. nigra though bulked segregant RNA sequencing (BSR-Seq) and further mapping with Kompetitive Allele Specific PCR (KASP) analysis. Reads of R and S bulks from BSR-Seq were initially aligned onto B. rapa (A-genome; B. nigra has the B-genome) where Rcr6 was associated with chromosome A08. KASP analysis showed that Rcr6 was flanked by SNP markers homologous to the region of 14.8-15.4 Mb of chromosome A08. There were 190 genes annotated in this region, with five genes (Bra010552, Bra010588, Bra010589, Bra010590 and Bra010663) identified as encoding the toll-interleukin-1 receptor / nucleotide-binding site / leucine-rich-repeat (TIR-NBS-LRR; TNL) class of proteins. The reads from BSR-Seq were then aligned into a draft B-genome of B. nigra, where Rcr6 was mapped on chromosome B3. KASP analysis indicated that Rcr6 was located on chromosome B3 in a 0.5 Mb region from 6.1-6.6 Mb. Only one TNL gene homologous to the B. rapa gene Bra010663 was identified in the target region. This gene is a likely candidate for Rcr6. Subsequent analysis of the Rcr6 equivalent region based on a published B. nigra genome was performed. This gene is located into chromosome B7 of the published B-genome, homologous to BniB015819. Rcr6 was the first gene identified and mapped in the B-genome of Brassica species. It resides in a genomic region homologous to chromosome A08 of A-genome. Based on this finding, it could possibly integrate into A08 of B. napus using marker assisted selection with SNP markers tightly linked to Rcr6 developed in this study.