Molecular Breeding

, 39:131 | Cite as

Fine mapping of a clubroot resistance gene from turnip using SNP markers identified from bulked segregant RNA-Seq

  • Z. Huang
  • G. Peng
  • B. D. Gossen
  • F. YuEmail author


Clubroot caused by Plasmodiophora brassicae poses a serious threat to canola production around the world, but sources of clubroot resistance in canola are limited. In this study, turnip cultivar “Purple Top White Globe,” which is highly resistant to pathotype 3 (Williams’ system), was used as the source of resistance. Genetic studies showed that the resistance in this cultivar was controlled by a major gene, Rcr5. Bulked segregant RNA-Seq was used to map the gene. A total of 124.6 M raw reads were generated from the resistant (R) and susceptible (S) pooled samples, and 78 K polymorphic DNA variants between the pooled R and the pooled S samples were identified. The percentage of polymorphic variants (PPV) on A03 was much higher than that on the other chromosomes, which indicated that Rcr5 was located on A03. Rcr5 was further mapped into the 23–31 Mb region of A03 through analysis of PPV in the chromosome. A segregated population consisting of 824 plants was genotyped based on 15 SNP markers in the region using Kompetitive Allele Specific PCR. Rcr5 was finely mapped between SNP_A03_83 and SNP_ A03_100, with 0.2 and 0.3 cM from Rcr5, respectively. The markers were located between 23,339,019 and 23,465,030 bp on A03. Eighteen genes were annotated in the Rcr5 target region, seven genes were expressed, and DNA variants were identified in the genes. The SNP markers developed in this study could be used for marker-assisted selection for resistance to clubroot when the gene is transferred to canola.


Clubroot Plasmodiophora brassicae RNA-Seq SNPs Fine mapping KASP Brassica napus Brassica rapa 



We thank Dr. M. Hecker for providing the MiSeq facility for sequencing, J. Wang and L. McGregor for assistance on phenotyping, Dr. K. Falk for proving line ACDC, and Dr. Q. Chen for assistance on analyzing KASP markers.

Funding information

We thank Agriculture and Agri-Food Canada for providing funding for the study.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Supplementary material

11032_2019_1038_MOESM1_ESM.xlsx (54 kb)
ESM 1 (XLSX 54 kb)
11032_2019_1038_MOESM2_ESM.jpg (527 kb)
Supplemental Figure 1 Distribution of the percentage of polymorphic variants on chromosomes A01, A02 and A04-A10 through BSR-Seq in the BC1 population derived from ACDCx (ACDC x PTWG) (JPG 526 kb)


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Copyright information

© Springer Nature B.V. 2019

Authors and Affiliations

  1. 1.Agriculture and Agri-Food CanadaSaskatoon Research and Development CentreSaskatoonCanada
  2. 2.State Key Laboratory of Crop Stress Biology for Arid Areas/College of AgronomyNorthwest A&F UniversityYanglingChina

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