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SNP markers for clubroot resistance gene CR01 based on RNA sequencing.

Yu, F., Zhang, X., Huang, Z., Song, T., Chu, M., Falk, K.C., Gossen, B.D., Deora, A., McDonald, M.R., and Peng, G. 2016. SNP markers for clubroot resistance gene CR01 based on RNA sequencing. Can. J. Plant Pathol. 38: 133.

Abstract

A clubroot resistance gene CR01, resistant to pathotype 3 of Plasmodiophora brassicae Wor., was previously mapped to chromosome A03 of Brassica rapa L. in pak choy cv. ‘Flower Nabana’ (FN). Differentially expressed genes associated with this gene were identified using RNA sequencing. In the current study, genetic mapping demonstrated that resistance to pathotypes 2, 5 and 6 co-segregate with CR01, indicating that the CR01 locus may confer broad resistance against P. brassicae. About 350 M short sequences were identified from resistant (FNR) bulks and and 320 M from susceptible (FNS) bulks. The sequences were assembled, and SNP (85% of total) and Indel (15%) variants were identified. About 80% of variants were homozygous. Unique FNR, unique FNS and heterozygous variants were below 10%, 9% and 4%, respectively. The frequency of homozygous variants in chromosome A03 was only 66%. Four closely linked genes on A03 that carried the highest numbers of variants, including unique FNR in the CR01 region, were used to confirm the presence of SNPs. Seven SNP markers identified in these genes co-segregated with 12 recombinants obtained from a segregating population consisting of 1600 plants, indicating these gene-specific SNP markers are completely linked to CR01. These markers are polymorphic between the resistant donor and three B. napus canola lines, indicating they can be used for marker-assisted selection during the introgression of CR01 into canola.

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