整合GWAS和WGCNA分析挖掘甘蓝型油菜黄籽微效作用位点

Mining Yellow-seeded Micro Effect Loci in B. napus by Integrated GWAS and WGCNA Analysis

甘蓝型油菜是世界上最重要的油料作物之一,黄籽是提高品质的重要育种目标。本研究以520份具有代表性的甘蓝型油菜品种(系)为材料,结合种子发育过程中8个时期的转录组数据,采取整合全基因组关联分析(GWAS)和权重基因共表达网络分析(WGCNA)的策略,挖掘油菜黄籽性状微效作用位点,2年共检测到199个SNP位点,在SNP位点附近共挖掘出1826个名义候选基因。利用R语言中的WGCNA软件包构建了8个共表达模块,基因功能富集分析显示,turquoise模块和blue模块与黄籽表型相关。苯丙烷代谢途径、类黄酮途径的关键基因BnATCAD4、BnF3H以及BnANS为turquoise模块的枢纽基因(hub gene)。通过已知的黄籽相关基因,挖掘出了一部分黄籽微效作用基因,这些基因多参与苯丙烷、类黄酮以及原花青素代谢途径。本研究挖掘的这些位点和候选基因可作为影响油菜黄籽形成的重要候选区域和基因,有助于探究甘蓝型油菜黄籽基因资源信息、揭示油菜黄籽性状的遗传基础和分子机制、丰富分子育种理论以及提高油菜品质。

Brassica napus is one of the most important oil crops in the world, and developing yellowseeded B. napus with improvedqualities is a major breeding goal. The yellow-seeded minor genes were mined by genome-wide association study （GWAS）and weighted gene co-expression network analysis （WGCNA） with 520 representative varieties （or lines） and the transcriptional data at eight time points during the seed development. The 199 SNPs and 1826 nominally significant GWAS candidate genes weredetected. Weighted gene co-expression network analysis was performed using the WGCNA R package to construct the resultingnetwork composing eight distinct gene modules. Among them, the turquoise module and the blue module were related to the seedcoat color based on gene function enrichment analysis. BnATCAD4, BnF3H, and BnANS, the key enzymes genes of phenylpropanemetabolic pathway and flavonoid metabolic pathway were found in turquoise module. Through the characterization of module content and topology, we mined a number of micro effect genes based on known yellow-seed related genes mainly involvedin the phenylpropanoid metabolic process, flavonoid metabolic process and proanthocyanidin iosynthetic process. Thisinformation of minor loci and candidate genes should be useful in the breeding for yellow-seeded B. napus.