Abstract
Clubroot, caused by Plasmodiophora Brassicae, is a serious soil-borne disease in worldwide. In recent years, progression of clubroot is rapid and serious in Shanghai, China. In this study, The inheritance of clubroot resistance (CR) were determined in pakchoi using F2 segregation population that were developed by crossing highly resistant line ‘CR38’ and susceptible line ‘CS22’. Two novel QTLs, qBrCR38-1 and qBrCR38-2, was identified by BSA-seq (Bulked Segregant Sequencing) resistant to P. brassicae physiological race 7. Two significant peak qBrCR38-1 and qBrCR38-2 were observed by three statistical methods between interval of 19.7–20.6 Mb in chromosome A07 and 20.0–20.6 Mb in chromosome A08, respectively. In addition, Polymorphic SNPs identified within target regions were converted to kompetitive allele-specific PCR (KASP) assays. In target regions of qBrCR38-1 and qBrCR38-2, there were twenty SNP sites identified, eleven KASP markers of which are significantly associated to CR (P < 0.05). Seven candidate genes were identified and found to be involved in disease resistance (TIR-NBS-LRR proteins), defense responses of bacterium and fungi and biotic/abiotic stress response in the target regions harboring the two QTLs. Two novel QTLs and candidate genes identified from the present study provide insights into the genetic mechanism of CR in B.rapa, and the associated SNPs can be effectively used for marker-assisted breeding.
Highlights
In Brassica Rapa, genetic analysis and quantitative trait locus (QTL) mapping studies have identified at least eight race-specific clubroot resistance(CR) loci
Kompetitive Allele Specific PCR (KASP) is one of the high-throughput SNP genotyping technologies is a cost-effective, low genotyping error rates and flexible system which is widely used for genetic mapping, trait-specific markers development, germplasm characterization, and quality control (QC) analysis[32,33,34]
The underlying QTLs were mapped by three statistical methods and examined sequence variation in the target region to identify the most probable candidate gene associated with CR
Summary
In Brassica Rapa, genetic analysis and quantitative trait locus (QTL) mapping studies have identified at least eight race-specific clubroot resistance(CR) loci. In B. rapa canola, Rcr[4], Rcr[8], and Rcr[9] breeding line T19 were mapped to chromosomes A03, A02, and A08, respectively through genotyping by sequencing[16]. Clubroot-resistant gene Rcr[2] was mapped on chromosome 3 in chinese cabbage ‘Jazz’. Bulked segregant analysis by sequencing (BSA-seq), is an effective technique used to identify quantitative trait loci (QTLs)[19,20]. BSA-seq was applied to determine the inheritance of clubroot resistance (CR) in Pakchoi inbred line ‘CR38’ and F2 population.
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