Plant Molecular Biology

, Volume 85, Issue 3, pp 247–257 | Cite as

Identification of candidate genes for fusarium yellows resistance in Chinese cabbage by differential expression analysis

  • Motoki Shimizu
  • Ryo Fujimoto
  • Hua Ying
  • Zi-jing Pu
  • Yusuke Ebe
  • Takahiro Kawanabe
  • Natsumi Saeki
  • Jennifer M. Taylor
  • Makoto Kaji
  • Elizabeth S. Dennis
  • Keiichi Okazaki


Fusarium yellows caused by Fusarium oxysporum f. sp. conglutinans is an important disease of Brassica worldwide. To identify a resistance (R) gene against Fusarium yellows in Chinese cabbage (Brassica rapa var. pekinensis), we analyzed differential expression at the whole genome level between resistant and susceptible inbred lines using RNA sequencing. Four hundred and eighteen genes were significantly differentially expressed, and these were enriched for genes involved in response to stress or stimulus. Seven dominant DNA markers at putative R-genes were identified. Presence and absence of the sequence of the putative R-genes, Bra012688 and Bra012689, correlated with the resistance of six inbred lines and susceptibility of four inbred lines, respectively. In F2 populations derived from crosses between resistant and susceptible inbred lines, presence of Bra012688 and Bra012689 cosegregated with resistance, suggesting that Bra012688 and Bra012689 are good candidates for fusarium yellows resistance in Chinese cabbage.


Fusarium yellows R-gene RNA-sequence NBS–LRR Chinese cabbage 



This work was supported in part by FY2012 Research Exchange Program between JSPS and AAS, by Grant-in-Aid for Young Scientists (B) (2478002) (JSPS), and Co-operative Research Programme 2012 (OECD) to R. Fujimoto, by Acorn Grant 2010 to R. Fujimoto and H. Ying, by Research Fellowships of JSPS for Young Scientists to M. Shimizu, and by the Programme for Promotion of Basic and Applied Researches for Innovations in Bio-oriented Industry to K. Okazaki.

Supplementary material

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Supplementary material 1 (DOC 53 kb)
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11103_2014_182_MOESM7_ESM.ppt (184 kb)
Figure S1. Schematic diagram of categorization of genes analyzed by RNA-seq. Number of putative disease resistance genes is shown in parentheses. Red letters show the numbers of putative R-genes showing two-fold differential expression level with 95% confidence. Blue letters show the numbers of putative R-genes showing only a two-fold differential expression level without 95% confidence or no expression in either line. (PPT 184 kb)
11103_2014_182_MOESM8_ESM.ppt (228 kb)
Figure S2. Summary of 244 putative R-genes having NBS, LRR, TIR, or CC motifs sub-categorized into 16 categorizes (sited from Brassica database). (PPT 228 kb)
11103_2014_182_MOESM9_ESM.ppt (258 kb)
Figure S3. Deletion of Bra012688 and Bra012689 in fusarium yellows susceptible line. Boxes show exon regions. Red, blue, and green bars show the region tested by PCR using genomic DNAs as templates. The result of PCR is shown in bottom panel. 23, RJKB-T23; 24, RJKB-T24 (PPT 258 kb)


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Copyright information

© Springer Science+Business Media Dordrecht 2014

Authors and Affiliations

  • Motoki Shimizu
    • 1
  • Ryo Fujimoto
    • 1
  • Hua Ying
    • 2
  • Zi-jing Pu
    • 1
  • Yusuke Ebe
    • 1
  • Takahiro Kawanabe
    • 1
    • 3
  • Natsumi Saeki
    • 1
  • Jennifer M. Taylor
    • 2
  • Makoto Kaji
    • 3
  • Elizabeth S. Dennis
    • 2
    • 4
  • Keiichi Okazaki
    • 1
  1. 1.Graduate School of Science and TechnologyNiigata UniversityIkarashi-ninocho, NiigataJapan
  2. 2.CSIRO Plant IndustryCanberraAustralia
  3. 3.Watanabe Seed Co., LtdMachiyashiki, Misato-choJapan
  4. 4.University of Technology, SydneySydneyAustralia

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