转录组分析栽培稻和野生稻响应冷胁迫的反应。

Transcriptomics profiling in response to cold stress in cultivated rice and weedy rice.

机构信息

Rice Research Institute, College of Agronomy, Shenyang Agricultural University, Shenyang 110866, China; Key Laboratory of Agricultural Biotechnology of Liaoning Province, College of Biosciences and Biotechnology, Shenyang Agricultural University, Shenyang, Liaoning 110866, China.

Rice Research Institute, College of Agronomy, Shenyang Agricultural University, Shenyang 110866, China.

出版信息

Gene. 2019 Feb 15;685:96-105. doi: 10.1016/j.gene.2018.10.066. Epub 2018 Oct 30.

DOI:10.1016/j.gene.2018.10.066

PMID:30389557

Abstract

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.

摘要

杂草稻是一种重要的水稻改良种质资源，因为它具有许多非生物胁迫的有用基因，包括耐冷性。我们鉴定了两个杂草稻品系（WR03-35 和 WR03-26）和两个栽培稻品系（空育 131 和 9311）的耐冷性和冷敏感性。在这些品系的幼苗期，我们使用 RNA-seq 技术在冷处理前后测量了杂草稻和栽培稻全基因组转录组的变化。我们在耐冷基因型（WR03-35、空育 131）中鉴定出 14213 个和 14730 个差异表达基因（DEGs），在两个冷敏感基因型（WR03-26、9311）中观察到 9219 个和 720 个 DEGs。在耐冷和冷敏感基因型中分别分析了许多常见和特殊的 DEGs。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（LRR）结构域基因等。在耐冷基因型中，这些 DEGs 的数量多于在冷敏感基因型中发现的数量。基因本体（GO）富集分析显示，生物过程、细胞成分和分子功能的显著富集项。此外，还鉴定出一些与几种植物激素相关的基因，如脱落酸（ABA）、赤霉素（GA）、生长素和乙烯。为了验证 RNA-seq 数据，我们对 12 个随机选择的 DEGs 进行了半定量 RT-PCR 和 qRT-PCR 分析。这些基因的 RNA-seq 表达模式与半定量 RT-PCR 和 qRT-PCR 方法相对应。本研究表明，杂草稻中与冷胁迫相关的基因资源对于理解冷胁迫机制和水稻耐冷性改良育种具有重要价值。