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

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.