Transcriptomics profiling in response to cold stress in cultivated rice and weedy rice
Transcriptomics profiling in response to cold stress in cultivated rice and weedy rice
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DOI：
10.1016/j.gene.2018.10.066
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发表时间：
2019-02-15
期刊：
影响因子：
3.5
通讯作者：
Guo, Zhifu
中科院分区：
文献类型：
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作者：
Guan, Shixin;Xu, Quan;Guo, Zhifu
杂草稻是水稻改良的重要种质资源，因为它含有许多非生物胁迫的有用基因，包括耐冷性。对两个杂草水稻品系(WR03-35和WR03-26)和两个栽培稻品系(空育131和9311)的耐冷性和冷敏性进行了鉴定。在这些品系的苗期，我们利用RNA-seq技术检测了杂草稻和栽培稻全基因组转录组在低温处理前后的变化。在耐冷品种(WR03-35、孔玉131)中发现了14,213和14,730个差异表达基因，在WR03-26、9311两个冷敏感品种中分别发现了9219和720个差异表达基因。分别分析了耐冷型和冷敏型中的许多常见基因和特殊基因。一些与冷胁迫相关的典型基因，如碱性螺旋-环-螺旋(BHLH)基因和富含亮氨酸重复序列(LRR)结构域基因等，在耐冷型中的数目多于在冷敏型中发现的数目。基因本体论(GO)丰富分析显示，生物过程、细胞成分和分子功能的术语显著丰富。此外，还发现了与几种植物激素相关的基因，如脱落酸(ABA)、赤霉酸(GA)、生长素和乙烯。为了验证RNA-seq数据，对12个随机选择的DEG进行了半定量RT-PCR和qRT-PCR。RNA-seq在这些基因上的表达模式与半定量RT-PCR和qRT-PCR方法一致。本研究表明杂草水稻与冷害相关的基因资源可能对了解冷害机制和水稻抗冷性育种有一定的参考价值。
Weedy rice is an important germplasm resource for rice improvement because it has useful genes for many abiotic stresses including cold tolerance. We identified the cold tolerance and cold sensitivity of two weedy rice lines (WR 03-35 and WR 03-26) and two cultivated rice lines (Kongyu 131 and 9311). During the seedling stage of these lines, we used RNA-seq to measure changes in weedy rice and cultivated rice whole-genome transcriptome before and after cold treatment. We identified 14,213 and 14,730 differentially expressed genes (DEGs) in cold-tolerant genotypes (WR 03-35, Kongyu 131), and 9219 and 720 DEGs were observed in two cold sensitive genotypes (WR 03-26, 9311). Many common and special DEGs were analyzed in cold-tolerant and cold sensitive genotypes, respectively. Some typical genes related to cold stress such as the basic helix-loop-helix (bHLH) gene and leucine-rich repeat (LRR) domain gene etc. The number of these DEGs in cold-tolerant genotypes is more than those found in cold-sensitive genotypes. The gene ontology (GO) enrichment analyses showed significantly enriched terms for biological processes, cellular components and molecular functions. In addition, some genes related to several plant hormones such as abscisic acid (ABA), gibberellic acid (GA), auxin and ethylene were identified. To confirm the RNA-seq data, semi-quantitative RT-PCR and qRT-PCR were performed on 12 randomly selected DEGs. The expression patterns of RNA-seq on these genes corresponded with the semi-quantitative RT-PCR and qRT-PCR method. This study suggests the gene resources related to cold stress from weedy rice could be valuable for understanding the mechanisms involved in cold stress and rice breeding for improving cold tolerance.