Background

Rice (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).

Results

Using 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 (T_w) 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-T_w (D15DN) and SJ under control (CKSJ) vs. SJ under low-T_w 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.

Conclusion

Cold 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-T_w 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.

中文翻译：

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不同水稻品种的转录组测序和iTRAQ研究为粳稻耐寒性响应的分子机制提供了见识。

背景

水稻（Oryza sativa L.）是热带和温带地区最重要的农作物之一。但是，它对冷胁迫具有很高的敏感性，而冷胁迫限制了其氮的吸收和代谢。为了鉴定涉及耐寒性的基因和途径，特别是在氮代谢途径中，我们比较了耐寒品种东农428（DN）和耐寒品种Songjing10（SJ）之间的基因和蛋白质表达差异。

结果

使用等通量标签通过高通量mRNA测序（RNA-seq）技术进行相对或绝对定量（iTRAQ），我们鉴定了5549个基因和DN中的450种蛋白质以及SJ中的6145个基因和790个蛋白质，它们在低水温下差异表达（T _w）治疗。有354转录因子（TF）基因（212下调，上调142）和366个TF基因（220下调，上调146），包括47个基因家族，在控制之下在DN差异表达（CKDN）对DN在低-T_瓦特（D15DN）和受控制的SJ（CKSJ）与低T _w受控制的SJD15SJ。与水稻寒冷相关的生物合成途径相关的基因，特别是丝裂原激活的蛋白激酶（MAPK）信号传导，玉米蛋白合成和植物激素信号转导途径，在两个水稻品种中均显着差异表达。与水稻寒冷相关的生物合成途径特别是谷胱甘肽代谢相关的差异表达蛋白（DEPs）在两个水稻品种中均显着差异表达。氮代谢途径的转录组和蛋白质组分析表明，在低温胁迫下，参与γ-氨基丁酸（GABA）和谷氨酰胺合成的主要基因和蛋白质被下调。

结论

生殖生长期间的冷应激条件导致与冷应激生物合成途径相关的基因和蛋白质在DN和SJ中显着差异表达。本研究证实了已知的冷应激相关基因，并确定了新的假定的冷应答基因。我们还发现冷应激下的翻译调控在耐寒性DN中起重要作用。低T _w处理会影响水稻对氮的吸收和氮代谢，并促进冷敏感SJ中的Glu代谢以及鸟氨酸和脯氨酸的合成。