Integration of Genetics and RNA-Seq Data to Dissect a Durable Blast Resistance in Rice

Gigante Vercelli (GV) and Vialone Nano (VN) are two old temperate japonica Italian rice cultivars with contrasting response to blast (Magnaporthe oryzae) infection. GV displays a durable and broad resistance, whereas VN is highly susceptible. A GV x VN segregating population, used to develop an SSR-based genetic map, led to the identification of two loci, localized to the long arm of chromosomes 1 and 4, responsible for blast resistance in GV. RNA-Seq was then employed to dissect the early molecular processes deployed during the resistance response of GV at 24 h after blast inoculation. Differential gene expression analysis identified 726 and 699 up regulated genes in response to infection in GV and VN, respectively. GV exhibited a dramatic up-regulation of defense genes and genes involved in the early steps of defence perception-signalling (e.g., MAPK cascades and WRKY transcription factors). Sequences carrying the NBS-LRR domain, a distinguish feature of a major class of plant disease resistance genes, and displaying expression patterns consistent with a potential role as GV-specific functional resistance gene(s) were identified and localized on the Nipponbare reference genome. A co-localization of four of them was observed with the two loci responsible for blast resistance in GV. The integration of genetics and transcriptomics studies has therefore provided candidates for the GV durable resistance. The ongoing de-novo assembly of the GV genome will allow a better definition of the positional relationships between the candidates and the blast resistance loci.