Identification and characterization of responsive genes in rice during compatible interactions with pathogenic pathovars of Xanthomonas oryzae

Rice is a staple food for one-half of the world’s population. However, pathogenic pathovars of Xanthomonas oryzae can reduce rice yield up to 60%. To explore the molecular features of rice response to two pathogenic pathovars of X. oryzae pv. oryzae (Xoo) and X. oryzae pv. oryzicola (Xoc), the differentially expressed genes (DEGs) were studied in four independent microarray experiments on infected versus non-infected leaves in rice 24 h after inoculation. The gene ontology (GO) analysis on DEGs demonstrated that while stress related genes were upregulated, the genes encoding photosynthesis components were down regulated in bacterial-infected rice. Moreover, some discrepancy of the genes function was depicted between the two pathovars of X. oryzae, including apoptosis specific to Xoo. Further analysis on cis-regulatory elements (CREs) on the promoter of responsive transcription factors (TFs) revealed the critical role of some hormones such as methyl jasmonate (MeJA) and abscisic acid (ABA) as well as light in the control of genes expression against the bacterial infection. We used a systematic approach to build a network among the responsive TFs that led to discovery of the OsWRKY53 and ERF2 effects on interaction between these pathovars and rice. We also detected miRNA target sites in some of the downregulated genes. These results provided an insight into the genes regulation against bacterial infection and introduced important candidate genes for further investigations in rice.