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

Abstract EN

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°C and 30°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°C, whereas slightly fewer genes (50.2%; 28,189/56,143) were expressed in rice leaf blades grown at 30°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°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°C.

Based on these results, we deduced that gene expression at both transcriptional and translational levels was stimulated at 25°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.