Genome-wide expression analysis of the phytohormones signalling pathway in rice seedlings by using RNA-Seq

Rice is highly sensitive to cold stress, low temperature during seedling stage will affect the growth of rice, sometimes even cause death and result in yield loss. In this study, indica rice cultivar Teqing and japonica rice cultivar 02428 were treated under low temperature (10 ℃ for 0, 3 and 24 h) to conduct trancriptome analysis by using RNA-Seq. Our result showed japonica rice 02428 had stronger cold resistance than indica rice Teqing. After cold treatment, we identified many differentially expressed genes in both cultivars. In KEGG (Kyoto Encyclopedia of Genes and Genomes) analysis, “plant hormone signal transduction” pathway was the most significant enriched pathway, which suggested that plant hormones could play important roles in regulating cold tolerance in rice. By analyzing the number and expression level of plant hormone related DEGs, we understanded the expression trend of key genes among the plant hormone signalling pathways. We found ethylene, abscisic acid and jasmonic acid may worked as positive regulators in cold resistance in rice seedlings, while cytokinin and gibberenllin played negative roles. Our result provides direction and basis for further study of cold response mechanism of plant hormones in rice seedlings.