An association between the nitrogen metabolism pathway and cold tolerance in rice was identified using comparative transcriptome and proteome profiling

AbstractBackgroundRice (Oryza sativaL.), one of the most important crops cultivated in both tropical and temperate regions, has a high sensitivity to cold stress. Chilling stress limits the N uptake and nitrogen metabolism in rice. To identify the genes and pathways involved in cold tolerance, and specifically associations with the nitrogen metabolism pathway, we have compared the gene and protein expression changes between a cold-tolerant cultivar, Dongnong428 (DN), and a cold-sensitive cultivar, Songjing10(SJ).ResultsUsing absolute quantification (iTRAQ) with high-throughput mRNA sequencing (RNA-seq) techniques, we identified 5,549 genes and 450 proteins in DN and 6,145 genes and 790 proteins in SJ, that were differentially expressed during low- water temperature (Tw) treatment. There were 354 transcription factor (TF) genes (212down, 142 up), 366 TF genes (220 down, 146 up), including 47 gene families, differentially expressed in the DN under control (CKDN) vs. DN under low-Tw(D15DN) and CKSJ vs. D15SJ, respectively. These results indicated that TF genes play a major role in post-translational regulations. Genes related to rice cold-related biosynthesis pathways, particularly the MAPK signaling pathway, zeatin biosynthesis, and plant hormone signal transduction pathways, were significantly differentially expressed in both rice cultivars. Differentially expressed proteins (DEPs) related to rice cold-related biosynthesis pathways and particularly glutathione metabolism were significantly differentially expressed in both rice cultivars. Transcriptome and proteome analysis of the nitrogen metabolism pathways showed that major genes and proteins were down-regulated that participated in γ-aminobutyric acid (GABA) and glutamine synthesis.ConclusionUnder cold stress conditions during reproductive growth, genes and proteins related to the biosynthesis pathways of cold stress, were significantly differentially expressed in the DN and SJ. The present study confirmed the known cold stress-associated genes and identified a number of putative new cold-responsive genes. It has also revealed that translational regulation under cold stress plays an important role in cold-tolerant DN. Low-Twtreatments affect the N uptake and N metabolism in rice, and promote Glu metabolism, and the synthesis of ornithine and proline in cold-sensitive SJ.