基于WGCNA的谷子苗期冷胁迫应答基因网络构建与核心因子发掘

Identification of Co-expression Genes Related to Cold Stress in Foxtail Millet by WGCNA

研究植物响应低温胁迫的分子基础及选育与种植耐冷作物品种对于保障粮食安全具有重要的现实意义,但目前谷子(Setaria italica)耐冷相关研究比较匮乏。为深入研究谷子苗期响应低温胁迫的分子机制,利用谷子33份不同发育阶段和不同冷处理时间的RNA-Seq数据,筛选获得32017个高表达基因并构建基因表达矩阵。利用R软件的WGCNA包构建共表达网络,进一步将网络划分为44个模块,发现谷子冷胁迫应答基因分布于多个模块中。选取包含冷胁迫基因数目排名前3的模块进一步分析,对预测到的靶基因进行GO富集分析,并对此3个模块进行基因调控网络的构建及核心基因注释,发现大多候选基因与非生物胁迫响应相关。以上结果为谷子抗逆研究提供了新思路,发掘的冷胁迫关键基因为谷子耐冷新品种选育提供了基因资源。

It is of great practical significance to study the molecular basis of plant response to low temperature stress and breed new varieties of cold-tolerant for ensuring food security.However,the study is relatively scarce about cold resistance of foxtail millet(Setaria italica).To further explore the molecular mechanism of millet responsing to low temperature stress at seedling,33 RNA-Seq data of foxtail millet at different development stages and different cold stress times were used.Gene expression matrix was constructed using 32017 highly expressed genes.WGCNA package of R software was used to construct a co-expression network,which was further divided into 44 modules.The genes related to cold stress of foxtail millet were existed in several modules.Here,3 modules with most cold stress genes were selected for GO enrichment analysis to annotate the function of target genes,and it was found that most candidate genes were related to abiotic stress responses.Above results provided new ideas for stress resistance of foxtail millet,and the key genes of cold stress provided effective resources for breeding the new variety of cold tolerance in foxtail millet.