Transcriptomic profiling of germinating seeds under cold stress and characterization of the cold-tolerant gene LTG5 in rice
Transcriptomic profiling of germinating seeds under cold stress and characterization of the cold-tolerant gene LTG5 in rice
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DOI：
10.1186/s12870-020-02569-z
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发表时间：
2020-08-06
影响因子：
5.3
通讯作者：
Deng, Guofu
中科院分区：
文献类型：
--
作者：
Pan, Yinghua;Liang, Haifu;Deng, Guofu
研究背景低温是水稻产量和地理分布的限制因子。野生稻（Oryza rufipogonGriff.）是水稻改良的重要种质资源。它对包括冷胁迫在内的许多非生物胁迫具有上级耐受性，但对其抗寒性的机制知之甚少。结果阐明了野生稻耐低温的分子遗传机制。比较分析了冷敏感水稻ce 253和耐冷水稻Y12-4在萌发期低温胁迫下的综合转录组图谱。共获得4244 - 6871万个读数，分别导致基因型253和Y12-4中的29,128和30,131个基因的比对。分析了冷敏感和耐冷基因型中的许多共同基因和差异表达基因。结果表明，在低温胁迫的4个阶段，耐冷基因型比冷敏感基因型的DEG表达量增加。基于细胞过程、代谢过程、响应刺激、膜部分和催化活性的基因本体富集分析表明，在耐冷基因型中上调的基因多于下调的基因，而在冷敏感基因型中上调的基因多于下调的基因。对7个随机选择的DEG进行定量实时聚合酶链反应，以确认RNA测序（RNA-seq）数据。这些基因显示出与RNA-Seq方法相对应的相似表达模式。加权基因共表达网络分析（WGCNA）显示，Y12-4比253在低温胁迫下表达更多的阳性基因。我们还探索了编码UDP-葡萄糖基转移酶的耐冷基因LTG 5（Low Temperature Growth 5）。LTG 5基因的过量表达赋予籼稻耐冷性。结论野生稻中与冷胁迫相关的基因资源对提高作物的耐冷性具有重要价值。
Background Low temperature is a limiting factor of rice productivity and geographical distribution. Wild rice (Oryza rufipogonGriff.) is an important germplasm resource for rice improvement. It has superior tolerance to many abiotic stresses, including cold stress, but little is known about the mechanism underlying its resistance to cold. Results This study elucidated the molecular genetic mechanisms of wild rice in tolerating low temperature. Comprehensive transcriptome profiles of two rice genotypes (cold-sensitive ce 253 and cold-tolerant Y12-4) at the germinating stage under cold stress were comparatively analyzed. A total of 42.44-68.71 million readings were obtained, resulting in the alignment of 29,128 and 30,131 genes in genotypes 253 and Y12-4, respectively. Many common and differentially expressed genes (DEGs) were analyzed in the cold-sensitive and cold-tolerant genotypes. Results showed more upregulated DEGs in the cold-tolerant genotype than in the cold-sensitive genotype at four stages under cold stress. Gene ontology enrichment analyses based on cellular process, metabolic process, response stimulus, membrane part, and catalytic activity indicated more upregulated genes than downregulated ones in the cold-tolerant genotype than in the cold-sensitive genotype. Quantitative real-time polymerase chain reaction was performed on seven randomly selected DEGs to confirm the RNA Sequencing (RNA-seq) data. These genes showed similar expression patterns corresponding with the RNA-Seq method. Weighted gene co-expression network analysis (WGCNA) revealed Y12-4 showed more positive genes than 253 under cold stress. We also explored the cold tolerance geneLTG5(Low Temperature Growth 5) encoding a UDP-glucosyltransferase. The overexpression of theLTG5gene conferred cold tolerance to indica rice. Conclusion Gene resources related to cold stress from wild rice can be valuable for improving the cold tolerance of crops.