GSE192588
Transcriptomic analysis of resistant (BR2655) and susceptible (HR12) rice cultivars after infection with rice blast fungus M. Oryzae (M036)
Purpose: To study the differential gene expression by comparing resistant and susceptible rice cultivars against the rice blast fungus M. Oryzae. Methods: Rice leaves were collected after M. Oryzae (MO36) infection from resistant and susceptible cultivars, preserved on deep freezer on -80O C frozen on liquid nitrogen, Total RNA from rice plant tissues was extracted using RNeasy Plant Mini Kit (Qiagen) by following manufacturer protocol. RNA libraries were prepared for sequencing using standard Illumina protocols. Results: Around 35 million pairs of filtered 150 base paired reads were obtained for each biological sample. These reads were mapped against RGAP7 using reference assembly tool of CLC Genomics Workbench. The mapped read data was summarised in to a matrix for each sample. count data was compared between the samples to identify the differentially expressed genes. genes were further filtered based on fold change, p value and FDR p value. The count data was further statistically analysed using Kal's Z test integrated into CGWB. Genes exhibiting 3 fold change and FDR p value <0.05 were filtered as either up regulated or down regulated gene. we obtained 7577 and 4290 significant (FDR adjusted p value =0.05) differentially expressed locus id in the resistant and susceptible rice cultivars, respectively . The number of significant DEL with fold change value greater and less than 3 were 3523 upregulated 4054 downregulated and 2190 upregulated & 2100 downregulated in resistance and susceptible cultivars, respectively. 2-way and and 4-way upregulated and downregulated gene comparisions was carried out. To identify the changes in biological process and molecular function the pathway and gene set enrichment analysis was performed in resistant BR2655 and susceptible HR12 rice cultivars. Conclusions: This study represents the first transcriptome analysis of resistant BR2655 and susceptible HR12 upon M.oryzae infection, generated by RNA-seq technology. This transcriptome analysis further helps to understand the differential gene expression analysis response to the M.oryzae. And candidate genes which are involved in triggering defense mechanism in rice plants. Further it helps to understand the mechanism of activating a cascade of defense responses in resistant and susceptible plants. Overall design: Transcriptome profiling of rice resistant BR2655 cultivar and susceptible HR12 cultivar, leaves after mock and M.oryzae infection