Genome-Wide Characterisation of Gene Expression in Rice Leaf Blades at 25 degrees C and 30 degrees C

Abstract

Rice growth is greatly affected by temperature. To examine how temperature influences gene expression in rice on a genome-wide basis, we utilised recently compiled next-generation sequencing datasets and characterised a number of RNA-sequence transcriptome samples in rice seedling leaf blades at 25 degrees C and 30 degrees C. Our analysis indicated that 50.4% of all genes in the rice genome (28,296/56,143) were expressed in rice samples grown at 25 degrees C, whereas slightly fewer genes (50.2%; 28,189/56,143) were expressed in rice leaf blades grown at 30 degrees C. Among the genes that were expressed, approximately 3% were highly expressed, whereas approximately 65% had low levels of expression. Further examination demonstrated that 821 genes had a twofold or higher increase in expression and that 553 genes had a twofold or greater decrease in expression at 25 degrees C. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses suggested that the ribosome pathway and multiple metabolic pathways were upregulated at 25 degrees C. Based on these results, we deduced that gene expression at both transcriptional and translational levels was stimulated at 25 degrees C, perhaps in response to a suboptimal temperature condition. Finally, we observed that temperature markedly regulates several super-families of transcription factors, including bZIP, MYB, and WRKY.