Interacting Transcriptomes Revealing Molecular Mechanisms Underlying Xa39 Mediated Broad Spectrum Resistance of Rice to Bacterial Blight

Interaction between rice (Oryza sativa L.) and its bacterial blight (BB) pathogen Xanthomonas oryzae pv. oryzae (Xoo) is the model system between monocot plants and their bacterial pathogens. To understand the genome-wide interactions between Xoo and rice resulting from a broad-spectrum hypersensitive reaction (BSHR) mediated by a new rice resistance (R) gene, Xa39, comparative dynamic transcriptomic profiles in the incompatible and compatible interactions were investigated using three related rice lines and a highly virulent Xoo isolate, PXO99. Large numbers of rice and Xoo differentially expressed genes (DEGs) were identified in comparisons between the incompatible interactions and compatible ones, suggesting the gene network consisted of 27 genes in four groups of distinct functions involving leading to BSHR of rice in the sequential events from the avrXa39 x Xa39 interaction -> signal recognition and transduction -> protein modification -> programmed cell death. Correspondingly, several groups of Xoo genes expressed or upregulated specifically in the incompatible interaction were those for type III secretion system (T3SS) and type III secretion effectors (T3SEs). Combined evidence suggests LOC_Os11g37759, one of a two-member CC-NBS-LRR gene family on rice chromosome 11, as the most likely candidate for Xa39 in rice and two genes, XopN and XopX involved in T3SS of Xoo, as the most likely candidate genes for the corresponding avrXa39 in Xoo. Our transcriptome data and identified rice and Xoo DEGs provided a valuable source of information for future investigations on the Xoo-rice interactions.