Abstract
BackgroundRice (Oryza sativa L.) is one of the most important crops cultivated in both tropical and temperate regions. However, it has a high sensitivity to cold stress and chilling stress limits its nitrogen uptake and metabolism. To identify the genes and pathways involved in cold tolerance, specifically within nitrogen metabolism pathways, we compared gene and protein expression differences between a cold-tolerant cultivar, Dongnong428 (DN), and a cold-sensitive cultivar, Songjing10 (SJ).ResultsUsing isobaric tags for relative or absolute quantification (iTRAQ) with high-throughput mRNA sequencing (RNA-seq) techniques, we identified 5549 genes and 450 proteins in DN and 6145 genes and 790 proteins in SJ, which were differentially expressed during low water temperature (Tw) treatments. There were 354 transcription factor (TF) genes (212 downregulated, 142 upregulated) and 366 TF genes (220 downregulated, 146 upregulated), including 47 gene families, differentially expressed in DN under control (CKDN) vs. DN under low-Tw (D15DN) and SJ under control (CKSJ) vs. SJ under low-Tw D15SJ, respectively. Genes associated with rice cold-related biosynthesis pathways, particularly the mitogen-activated protein kinase (MAPK) signaling, zeatin biosynthesis, and plant hormone signal transduction pathways, were significantly differentially expressed in both rice cultivars. Differentially expressed proteins (DEPs) associated with 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 that participated in γ-aminobutyric acid (GABA) and glutamine synthesis were downregulated under cold stress.ConclusionCold stress conditions during reproductive growth, resulted in genes and proteins related to cold stress biosynthesis pathways being significantly differentially expressed in DN and SJ. The present study confirmed the known cold stress-associated genes and identified new putative cold-responsive genes. We also found that translational regulation under cold stress plays an important role in cold-tolerant DN. Low-Tw treatments affected N uptake and N metabolism in rice, as well as promoted Glu metabolism and the synthesis of ornithine and proline in cold-sensitive SJ.
Highlights
Rice (Oryza sativa L.) is one of the most important crops cultivated in both tropical and temperate regions
GABA and Pro were found to reduce the oxidative damage to crops in abiotic stress conditions (Stitt and Hurry 2002; Bouche and Fromm 2004; Fait et al 2008). These results indicate that GABA and Pro may have the potential to enhance the cold tolerance of plants
We explored the molecular mechanisms involved in rice cold tolerance, using high-throughput mRNA sequencing (RNA-seq) and isobaric tags for relative and absolute quantification, to analyze the transcriptome and proteome, respectively
Summary
Rice (Oryza sativa L.) is one of the most important crops cultivated in both tropical and temperate regions. It has a high sensitivity to cold stress and chilling stress limits its nitrogen uptake and metabolism. Rice (Oryza sativa L.) is one of the most important crops cultivated in both tropical and temperate regions but it has a high sensitivity to cold stress. It is known to negatively influence the yield and quality of important food crops, such as rice (Shimono et al 2002; Suzuki et al 2008; Thakur et al 2010; Wang et al 2013; Zhao et al 2013). Low root zone temperatures are known to inhibit the occurrence and elongation of functional roots, and this affects rice growth (Ahamed et al 2012; Kramer and Boyer 1995). There is still no clear understanding of the response mechanisms of rice roots to low temperature stress during the reproductive stage
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