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Transcriptome analysis and whole genome re-sequencing provide insights on rice kernel smut (Tilletia horrida) pathogenicity

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Abstract

Rice kernel smut is an important disease caused by Tilletia horrida that affects the production of rice male sterile lines in most hybrid rice growing regions of the world. In this study, the pathogenicity of seven different strains of T. horrida isolated from different parts of China is described. Whole-genome re-sequencing of six T. horrida strains and transcriptome analysis of the reference genome T. horrida strain JY-521 were conducted at different times post inoculation (8, 12, 24, 48, and 72 h) early in the infection. The highest number of differentially expressed genes (DEGs) occurred at 8 h post inoculation. Based on Kyoto Encyclopedia of Genes and Genomes pathway analysis of the DEGs, autophagy processes and lipid degradation were key pathways for T. horrida pathogenicity. In three weakly pathogenic strains, CN-4, XJ-3, and SN-2, the single nucleotide polymorphisms and expression patterns of pathogenicity genes, including carbohydrate-active enzyme genes, pathogen-host interaction genes, effector genes, secondary metabolism-related genes, cytochrome P450 genes, ATP-binding cassette superfamily transporter genes, and G protein-coupled receptor genes, were also analyzed at different times during the infection. Thus, a new understanding of T. horrida pathogenicity was gained by exploring the potential mechanisms for weakened virulence in different strains of rice kernel smut, and a new foundation was provide for further studies on the infection mechanism and future control of this important rice disease.

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Data availability

Sequencing data of Tilletia horrida were deposited at the National Center for Biotechnology (NCBI) Sequence Read Archive (SRA) under bioproject PRJNA494098 (for RNA-Seq) and bioproject PRJNA494149 (for genome sequencing).

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Acknowledgements

We thank the scientific and technological research program of the Chongqing Municipal Education Commission (KJ15012017) and the National Natural Science Foundation (31400130) for supporting this research.

Funding

This study was funded by the scientific and technological research program of the Chongqing Municipal Education Commission (KJ15012017) and the National Natural Science Foundation (31400130).

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Author notes

  1. Aijun Wang and Xinyue Shu contributed equally to this work.

Authors and Affiliations

  1. Rice Research Institute of Sichuan Agricultural University, Chengdu, Sichuan, China

    Aijun Wang, Xinyue Shu, Xianyu Niu, Xiaoqun Yi & Aiping Zheng

  2. Key laboratory of Sichuan Crop Major Disease, Sichuan Agricultural University, Chengdu, Sichuan, China

    Aijun Wang, Xinyue Shu, Xianyu Niu & Aiping Zheng

  3. Key Laboratory of Southwest Crop Gene Resource and Genetic Improvement of Ministry of Education, Sichuan Agricultural University, Ya’an, Sichuan, China

    Aijun Wang, Xinyue Shu, Xianyu Niu & Aiping Zheng

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  1. Aijun Wang
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Correspondence to Aiping Zheng.

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Wang, A., Shu, X., Niu, X. et al. Transcriptome analysis and whole genome re-sequencing provide insights on rice kernel smut (Tilletia horrida) pathogenicity. J Plant Pathol 102, 155–167 (2020). https://doi.org/10.1007/s42161-019-00401-8

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