Identification of a genomic region containing genes involved in resistance to four pathotypes of Plasmodiophora brassicae in Brassica rapa turnip ECD02.

Clubroot, caused by Plasmodiophora brassicae, is an important disease of brassica crops worldwide. Vegetable turnip (Brassica rapa L.) have proven to be a source of clubroot resistance genes effective against many pathotypes of P. brassicae. The F progeny from the cross B. rapa canola ACDC (susceptible, S) × B. rapa turnip ECD02 (resistant, R) were backcrossed with ACDC, then self-pollinated to produce BC S lines. All the F plants were resistant to four pathotypes (3A, 3D, 3H, and 5X) of P. brassicae. Segregation for R and S in BC to each pathotype was 1:1 and resistance reactions were highly correlated. From whole genome sequencing, 192.1 M sequences with 96% template coverage from ECD02, and 478.9 M sequences with 92% coverage from ACDC, were aligned with the reference genome of B. rapa. Genotyping-by-sequencing was performed on the BC population. The number of aligned short reads per plant in the BC ranged from 1.4 to 8.5 M sequences with 4-8% template coverage. We obtained 1,344 high-quality single-nucleotide polymorphism (SNP) loci with a mean missing rate at 0.27% and distributed them on 10 chromosomes. A single co-localized quantitative trait loci (QTL), designated as Rcr9 on chromosome A08, conferred resistance to the four pathotypes. The QTL explained 68.9-74.4% of phenotypic variation with the logarithm of the odds values of 24.3 to 31.1. Bulked segregant analysis was performed, and 14 SNP markers linked to the gene were developed using the Kompetitive Allele Specific PCR. Rcr9 was mapped into an interval of 2.2 cM, flanked by CF_A08_10664692 and CF_A08_12230973, which spanned 1.51 Mb on the chromosome and included 219 B. rapa genes. Four of these genes (BraA08g012910.3C, BraA08g012920.3C, BraA08g013130.3C, and BraA08g013630.3C) encoded disease resistance proteins.