Transcriptome Reprogramming During the Early Response to Magnaporthe oryzae in Durable Resistant vs Susceptible Rice Genotypes

Two temperate japonica old Italian rice cultivars presenting contrasting response to blast infection represented by Gigante Vercelli (GV), with durable and wide resistance to blast and Vialone Nano (VN), highly susceptible, were subjected to an RNA-seq experiment using three biological replicates of four tested conditions, namely control leaves and leaves at 24 h after inoculation. About 40 million paired-end reads for each  biological replicate were obtained. Reads were aligned to rice japonica (cv Nipponbare) genome and 1,070 and 1,484 genes were found to be modulated in GV and VN, respectively. GO enrichment analyses revealed a set of GO terms enriched in both varieties including “defence response to fungus, incompatible interaction”. Despite this commonality, however, the gene set contributing to common GO enriched terms were dissimilar. Expression patterns of genes grouped in GV-specific enriched GO terms where examined in detail down to the transcript isoform level. At 24 hours post infection, GV exhibited a dramatic upregulation of diterpene phytoalexin biosynthesis genes and wall associated kinases (WAKs). Further, GV-specific upregulated genes included flavin-containing monooxygenase and discrete members of class I chitinase and glycosyl hydrolase 17 gene families. Furthermore, RNA-Seq procedure allowed the identification of genes critically involved in conferring resistance to GV through acting in the early steps of defence circuitry. These included chitin oligosaccharides sensing, MAPK cascades and WRKY transcription factors. Finally, resistance (R) candidate genes with expression patterns consistent with a potential role for GV-specific functional R gene(s) were identified.
Research supported by Project AGER, grant n° 2010-2369.