Transcriptomic dissection of the rice–Fusarium fujikuroi interaction by RNA-Seq

Rice bakanae disease, caused by the pathogen Fusarium fujikuroi, is becoming severely detrimental to rice production worldwide. To understand the interaction between rice and F. fujikuroi, a moderate resistant genotype, 93-11 (Oryza sativa indica), and a susceptible genotype, Nipponbare (Oryza sativa japonica), were used for transcriptome analysis. Several cDNA libraries were constructed using mRNA isolated from the leaves of non-stressed 93-11 and NIPPONBARE plants and from the leaves of both genotypes inoculated with F. fujikuroi. In total, 1152 and 1052 transcripts were differentially expressed between the controls and the treatments for 93-11 and NIPPONBARE, respectively. Comparative transcriptome analysis revealed different expression patterns for the two genotypes. Although some common defense-related enriched GO terms were shared in both genotypes, specific defense-related terms were enriched exclusively in 93-11. A detailed comparison of defense-related differentially expressed genes revealed that certain WRKYs, WAK and MAP3Ks were responsible for the bakanae disease resistance in 93-11. The OsWAK112d gene was up-regulated in the resistant genotype. The POEI gene response to abiotic stress was modulated in Nipponbare. Further analysis suggested that the defense-related genes WRKYs and MARKs on chromosome 1 that are modulated in 93-11 upon infection might play a crucial role in the rice–F. fujikuroi interaction. Further characterization of these resistance genes may provide candidate genes for the development of molecular markers for rice bakanae resistance breeding programs. Transcriptomic dissection of the rice–F. fujikuroi interaction provides valuable information for future studies on the molecular mechanisms of rice bakanae resistance.