Comparison of gene co-networks analysis provide a systems view of rice (Oryza sativa L.) response to Tilletia horrida infection

Abstract

The biotrophic soil-borne fungus Tilletia horrida causes rice kernel smut, an important disease affecting the production of rice male sterile lines in most hybrid rice growing regions of the world. There are no successful ways of controlling this disease and there has been little study of mechanisms of resistance to T. horrida. Based on transcriptional data of different infection time points, we found 23, 782 and 23, 718 differentially expressed genes (fragments per kilobase of transcript sequence per million, FPKM >1) in Jiangcheng 3A (resistant to T. horrida) and 9311A (susceptible to T. horrida), respectively. In order to illuminate the differential responses of the two rice male sterile lines to T. horrida, we identified gene co-expression modules using the method of weighted gene co-expression network analysis (WGCNA) and compared the different biological functions of gene co-expression networks in key modules at different infection time points. The results indicated that gene co-expression networks in the two rice genotypes were different and that genes contained in some modules of the two groups may play important roles in resistance to T. horrida, such as DTH8 and OsHop/Sti1a. Furthermore, these results provide a global view of the responses of two different phenotypes to T. horrida, and assist our understanding of the regulation of expression changes after T. horrida infection.

Comparative secretome analysis of different smut fungi and identification of plant cell death-inducing secreted proteins from Tilletia horrida

“…However, only two genes LOC_Os03g16610 (OsLAC10) and LOC_Os07g42450 (OsRbs5) showed up-regulated expression after T. horrida inoculation according to the transcriptome data from our earlier report (Fig. 10d) [31]. In addition, laccase is associated with lignification and plays an important role in iron metabolism [33–36].…”

“…In plant-pathogen interactions, the effector genes in filamentous pathogens are often transcriptionally induced [30]. To clarify the change in effector gene expression during T. horrida infection, the young panicles of rice male sterile lines Jiangcheng 3A (phenotype resistant to T. horrida ), and 9311A (phenotype susceptible to T. horrida ) were infected with the highly virulent isolate JY-521 [31]. The expression levels of these two secreted protein-encoding genes 8, 12, 24, 48, and 72 h after infection were identified by quantitative real time reverse transcription-polymerase chain reaction (qRT-PCR).…”

“…Two rice cultivars that displayed marked differences in their susceptibility to infection by T. horrida , the resistant rice male sterile line Jiangcheng 3A and the susceptible rice male sterile line 9311A [31], were used in this study. They were provided by the Department of Rice Research Institute of Sichuan Agricultural University.…”

“…The resistant rice male sterile line Jiangcheng 3A and the rice male sterile line 9311A that is highly susceptible to T. horrida were infected with the T. horrida strain JY-521 [31]. The method of T. horrida inoculation according to our former reported [23].…”

Genome-Wide Expression Profiling of Small RNAs in Indian Strain of Rhizoctonia solani AG1-1A Reveals Differential Regulation of milRNAs during Pathogenesis and Crosstalk of Gene Regulation

“…Compared to plants and animals, there are very limited reports on milRNAs of phytopathogenic fungi which are primary agents causing diseases and huge loss to agriculture crops. In the absence of resistance in the rice germplasm against R. solani, it is extremely important to decipher the gene regulatory networks and biology of pathogens to devise effective strategies for controlling the menace of sheath blight disease in rice [31,[33][34][35]. We analyzed the milRNAs of sheath blight disease causing pathogen R. solani AG1 IA by RNAseq of small RNAs.…”