, Volume 211, Issue 1, pp 123–137 | Cite as

Transcriptomic dissection of the rice–Fusarium fujikuroi interaction by RNA-Seq

  • Zhijuan Ji
  • Yuxiang Zeng
  • Yan Liang
  • Qian QianEmail author
  • Changdeng YangEmail author


Rice bakanae disease, caused by the pathogen Fusarium fujikuroi, is becoming severely detrimental to rice production worldwide. To understand the interaction between rice and F. fujikuroi, a moderate resistant genotype, 93-11 (Oryza sativa indica), and a susceptible genotype, Nipponbare (Oryza sativa japonica), were used for transcriptome analysis. Several cDNA libraries were constructed using mRNA isolated from the leaves of non-stressed 93-11 and NIPPONBARE plants and from the leaves of both genotypes inoculated with F. fujikuroi. In total, 1152 and 1052 transcripts were differentially expressed between the controls and the treatments for 93-11 and NIPPONBARE, respectively. Comparative transcriptome analysis revealed different expression patterns for the two genotypes. Although some common defense-related enriched GO terms were shared in both genotypes, specific defense-related terms were enriched exclusively in 93-11. A detailed comparison of defense-related differentially expressed genes revealed that certain WRKYs, WAK and MAP3Ks were responsible for the bakanae disease resistance in 93-11. The OsWAK112d gene was up-regulated in the resistant genotype. The POEI gene response to abiotic stress was modulated in Nipponbare. Further analysis suggested that the defense-related genes WRKYs and MARKs on chromosome 1 that are modulated in 93-11 upon infection might play a crucial role in the rice–F. fujikuroi interaction. Further characterization of these resistance genes may provide candidate genes for the development of molecular markers for rice bakanae resistance breeding programs. Transcriptomic dissection of the rice–F. fujikuroi interaction provides valuable information for future studies on the molecular mechanisms of rice bakanae resistance.


Rice Bakanae disease Resistance Fusarium fujikuroi RNA-sequencing 



Rice bakanae disease


Next-generation sequencing




Gibberellin A3


Double haploid


Differentially expressed genes


Gene ontology


Reactive oxygen species




Kyoto encyclopedia of genes and genomes


Quantitative RT-PCR


7 days post-inoculation


Reads per kilobase per million reads


Superoxide dismutase


Reactive oxygen species



We thank Dr. Dawei Xue of Hangzhou Normal University for his advice on the project design and Dr. Qing Liu of China National Rice Research Institute for assistance in the bioinformatics analysis. We also thank the CapitalBio Corporation at Beijing for its assistance in original data processing. This work was supported by a grant from the Science and Technology Program of Zhejiang Province (2015C32056), the Chinese Natural Science Foundation (31521064) and the Agricultural Sciences and Technologies Innovation Program of the Chinese Academy of Agricultural Sciences.

Compliance with ethical standards

Conflict of interest

The authors declare no competing interests.

Ethical approval

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

Supplementary material

10681_2016_1748_MOESM1_ESM.docx (147 kb)
Supplementary material 1 (DOCX 146 kb)
10681_2016_1748_MOESM2_ESM.docx (125 kb)
Supplementary material 2 (DOCX 125 kb)
10681_2016_1748_MOESM3_ESM.docx (17 kb)
Supplementary material 3 (DOCX 17 kb)


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Copyright information

© Springer Science+Business Media Dordrecht 2016

Authors and Affiliations

  1. 1.State Key Lab of Rice BiologyChina National Rice Research InstituteHangzhouChina
  2. 2.College of AgronomyShengyang Agricultural UniversityShenyangChina

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