Genome-wide characterisation of gene expression in rice leaf blades at 25 °C and 30 °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 °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.

Figure 1

A scatter plot of gene expression values (per kb per million total reads, RPKM) in log2 scale for the 25°C versus 30°C datasets. Grey dots indicate each gene expressed in the two samples. Coloured dots indicate a specific group of genes. Two diagonal dashed lines indicate twofold changes (increases and decreases).