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The tandem repeated organization of NB-LRR genes in the clubroot-resistant CRb locus in Brassica rapa L.

Molecular Genetics and Genomics volume 292, pages 397–405 (2017)Cite this article

Abstract

To facilitate prevention of clubroot disease, a major threat to the successful cultivation of Chinese cabbage (Brassica rapa L.), we bred clubroot-resistant (CR) cultivars by introducing resistance genes from CR turnips via conventional breeding. Among 11 CR loci found in B. rapa, we identified CRb in Chinese cabbage cultivar ‘CR Shinki’ as a single dominant gene for resistance against Plasmodiophora brassicae pathotype group 3, against which the stacking of Crr1 and Crr2 loci was not effective. However, the precise location and pathotype specificity of CRb have been controversial, because CRa and Rcr1 also map near this locus. Previously, our fine-mapping study revealed that CRb is located in a 140-kb genomic region on chromosome A03. Here, we determined the nucleotide sequence of an approximately 64-kb candidate region in the resistant line; this region contains six open reading frames (ORFs) similar to NB-LRR encoding genes that are predicted to occur in tandem with the same orientation. Among the six ORFs present, only four on the genome of the resistant line showed a strong DNA sequence identity with each other, and only one of those four could confer resistance to P. brassicae isolate No. 14 of the pathotype group 3. These results suggest that these genes evolved through recent gene duplication and uneven crossover events that could lead to the acquisition of clubroot resistance. The DNA sequence of the functional ORF was identical to that of the previously cloned CRa gene; thus, we showed that the independently identified CRb and CRa are one and the same clubroot-resistance gene.

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Acknowledgements

The authors thank S. Negoro, T. Yamakawa, and Y. Higashi, Institute of Vegetable and Floriculture Science, National Agriculture and Food Research Organization, for their technical assistance.

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  1. Satoru Matsumoto

    Present address: Tohoku Agricultural Research Center, NARO, 4 Akahira, Shimo-kuriyagawa, Morioka, Iwate, 020-0198, Japan

Affiliations

  1. Institute of Vegetable and Floriculture Science, NARO, 360 Kusawa, Ano, Tsu, Mie, 514-2392, Japan

    Katsunori Hatakeyama, Tomohisa Niwa, Takeyuki Kato, Takayoshi Ohara, Tomohiro Kakizaki & Satoru Matsumoto

  2. Nippon Norin Seed Co., Ltd., 6-6-5 Takinogawa, Kita-ku, Tokyo, 114-0023, Japan

    Takeyuki Kato

  3. Faculty of Agriculture, Iwate University, 3-18-8 Ueda, Morioka, Iwate, 020-8550, Japan

    Katsunori Hatakeyama

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  1. Katsunori Hatakeyama
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Correspondence to Katsunori Hatakeyama.

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Funding

This work was supported by the Ministry of Agriculture, Forestry and Fisheries of Japan (Genomics for Agricultural Innovation, Grant number HOR1002).

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The authors declare that they have no conflict of interest.

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This article does not contain any studies with human participants or animals performed by any of the authors.

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Communicated by S. Hohmann.

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438_2016_1281_MOESM1_ESM.pptx

Fig. S1 Root phenotype of the T1 plants derived from the three representative T0 lines of the transgenic B. rapa carrying the CRb_α transgene. The presence (+)/absence (—) of the transgene and disease index (DI) of each plant are indicated under the picture. (PPTX 3339 kb)

438_2016_1281_MOESM2_ESM.pptx

Fig. S2 Alignment of the sequences of the fosmid clone P005H06 and CRa genomic DNA (accession no. AB751516). Identical nucleotide sequences are shown in gray. The start and stop codons are boxed. Exon–intron junctions are indicated under the sequences. (PPTX 21183 kb)

438_2016_1281_MOESM3_ESM.pptx

Fig. S3 Alignment of TIR (a), NB (b), and LRR (c) domains between the predicted Crr1a and CRa proteins. The identical amino acid residues are shown in gray. (PPTX 311 kb)

Supplementary material 4 (DOCX 89 kb)

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Hatakeyama, K., Niwa, T., Kato, T. et al. The tandem repeated organization of NB-LRR genes in the clubroot-resistant CRb locus in Brassica rapa L.. Mol Genet Genomics 292, 397–405 (2017). https://doi.org/10.1007/s00438-016-1281-1

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  • DOI: https://doi.org/10.1007/s00438-016-1281-1

Keywords

  • Brassica rapa
  • Plasmodiophora brassicae
  • Clubroot
  • NB-LRR
  • Resistant gene
  • Duplication