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Transcriptome analysis of different rice cultivars provides novel insights into the rice response to bacterial leaf streak infection

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Abstract

Bacterial leaf streak (BLS) is now the fourth-most devastating disease in rice. Dular and H359 are two indica rice varieties with contrasting responses to BLS. Dular displays high resistance, while H359 is susceptible. In this study, RNA-seq was used to examine the early molecular processes deployed during the resistance response of Dular and H359 at different times after inoculation. Differentially expressed gene (DEG) analysis identified 3031 genes in Dular and 7161 in H359 that were modulated in response to infection after 12 and 24 h. There were significantly more DEGs in H359 than in Dular, and there were significantly more downregulated genes than upregulated genes. Gene ontology (GO) and KEGG enrichment analyses revealed a similar set of GO terms and KEGG pathways enriched in both varieties. However, KEGG analysis of upregulated DEGs revealed that some phenylpropane metabolism-related pathways were specially enriched in Dular. Further comparison and analysis showed that the numbers of resistance-related DEGs in the two varieties were significantly reduced at 24 h compared with 12 h after BLS infection and genes critically involved in conferring resistance during the early stage mainly included WRKY transcription factors, receptor kinases and disease, exocyst, MAPK signalling pathway and hormones related genes. Our study suggests that resistance-related genes may play an important role at an early stage of infection and phenylpropane metabolism related genes may partly response for BLS resistance of Dular, thus providing valuable information for future studies on the molecular mechanisms of BLS resistance in rice.

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Funding

This work was supported in part by the National Key R&D Programme of China (2017YFD0100100), Fujian Provincial Natural Science Foundation, China (2017 J01438; 2019 J01424), Youth Technology Innovation Team of the Fujian Academy of Agricultural Sciences (No. STIT2017-3-3), Regional Development Project of Fujian, China (2018N3011), and General Project of the Fujian Academy of Agricultural Sciences (No. A2017-13).

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  1. Ling Lu and Dewei Yang contributed equally to this work.

Authors and Affiliations

  1. Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education and Plant Immunity Centre, Fujian Agriculture and Forestry University, Fuzhou, 350002, China

    Ling Lu, Dewei Yang, Dingzhong Tang, Shengping Li & Zhiwei Chen

  2. Rice Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, 350019, China

    Dewei Yang

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  1. Ling Lu
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  2. Dewei Yang
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Contributions

Zhiwei Chen, Shengping Li and Dingzhong Tang conceived and designed the research. Lin Lu and Dewei Yang carried out most experiments. Lin Lu, Shengping Li and Dewei Yang wrote the manuscript. Lin Lu, Shengping Li and Dewei Yang analysed the data. All authors read and approved the final manuscript.

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Correspondence to Shengping Li or Zhiwei Chen.

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Lu, L., Yang, D., Tang, D. et al. Transcriptome analysis of different rice cultivars provides novel insights into the rice response to bacterial leaf streak infection. Funct Integr Genomics 20, 681–693 (2020). https://doi.org/10.1007/s10142-020-00744-x

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