基于Camoco算法挖掘谷子叶鞘和叶枕颜色相关基因  

Exploring color-related genes of cotyledon sheath and pulvinus of foxtail millet based on Camoco algorithm

作　　者：杨宇琭 罗韶凡 郄倩茹 张雅坤 段明 李亚军 孙蓉 韩渊怀[1] 李旭凯 马芳芳[1] Yang Yulu;Luo Shaofan;Qie Qianru;Zhang Yakun;Duan Ming;Li Yajun;Sun Rong;HanYuanhuai;Li Xukai;Ma Fangfang(College of Agriculture,Shanxi Agricultural Univercity,Taigu 030801,China;College of Life Sciences,Shanxi Agricultural University,Taigu 030801,China;Experimental and Teaching Centre,Shanxi Agricultural University,Taigu 030801,China)

机构地区：[1]山西农业大学农学院,山西太谷030801 [2]山西农业大学生命科学学院,山西太谷030801 [3]山西农业大学实验教学中心,山西太谷030801

出　　处：《山西农业大学学报（自然科学版）》2022年第2期12-20,共9页Journal of Shanxi Agricultural University(Natural Science Edition)

基　　金：山西省应用基础研究面上青年基金项目(201901D211362);山西省重点研发项目(201803D221019-2;201703D211008);山西农业大学科技创新基金(2017YJ27;2013YJ04);山西农谷建设科研专项(SXNGJSKYZX201702);山西农业大学科技创新项目(2017GPY01);山西省研究生教育创新(2020SY208)。

摘　　要：[目的]基于Camoco(Co-analysis of molecular components)挖掘影响谷子叶鞘颜色和叶枕颜色的关键候选基因,为下一步研究候选基因调控谷子颜色相关性状的分子机制及应用潜力奠定基础。[方法]利用Camoco算法,对谷子叶鞘颜色和叶枕颜色进行候选基因预测。使用加权基因共表达网络分析(WGCNA)进一步聚焦候选基因,并初步确定候选基因的功能。[结果]检测到10个调控谷子颜色性状的关键候选基因,其中叶鞘颜色6个和叶枕颜色4个,多数基因直接或间接与叶绿体有关,其中Si4g01380和Si4g01390是双性状共定位到的候选基因。Si4g01380属于GRAS家族,该家族中有多个转录因子参与光敏色素的信号传导,与叶绿素密切相关。此研究为培育高光效谷子,提高谷子产量,发掘谷子形态标记奠定基础。[结论]本研究中使用的Camoco算法结合基因表达量数据,可以将候选基因的数量减少两个数量级,有效的缩小候选基因范围,并筛选出表达模式一致的基因,进一步提高候选基因的有效性,为后续验证功能基因奠定基础。此方法同样适用于对其他动植物功能基因的挖掘与鉴定;另外,本研究将GWAS和共表达数据进行整合分析的思路也可以应用到对其它动植物的功能基因鉴定上。[Objective]Based on Camoco(Co-analysis of molecular components),the key candidate genes affecting the color of leaf sheath and pulvinus of foxtail millet were investigated,and aimed to lay a foundation for further research on molecular mechanism and the application potential of candidate genes regulating color-related traits of foxtail millet.[Methods]Camoco algorithm was used to predict the candidate genes for the color of leaf sheath and pulvinus of foxtail millet.Weighted gene coexpression network analysis(WGCNA)was used to further focus on candidate genes and the function of candidate genes was preliminarily determined.[Results]Ten key candidate genes were detected for the regulation of foxtail grain color,including six for leaf sheath color and four for pulvinus color.Most of the genes were directly or indirectly related to chloroplast;among which Si4g01380 and Si4g01390 were candidate genes co-located with both traits.Si4g01380 was a member of the GRAS family,in which several transcription factors were involved in photochromes signaling and closely related to chlorophyll.This study laid a foundation for cultivating high light efficiency millet,improving millet yield and exploring morphological markers of millet.[Conclusion]The Camoco algorithm used in this study combined with gene expression data can reduce the number of candidate genes by two orders of magnitude,effectively narrow the range of candidate genes,and screen out genes with consistent expression patterns,further improve the effectiveness of candidate genes.This method was also applicable to explore and identify the functional genes of other animals and plants;in addition,the idea of integrating GWAS and co-expression data in this study can also be applied to the identification of functional genes of other animals and plants.

关 键 词：谷子 叶鞘颜色 叶枕颜色 Camoco 

分 类 号：S515[农业科学—作物学]