作物学报2018，Vol.44Issue(5)：629-641,13.DOI:10.3724/SP.J.1006.2018.00629
用全基因组关联作图和共表达网络分析鉴定油菜种子硫苷含量的候选基因
Identification of Candidate Genes for Seed Glucosinolate Content of Rapeseed by Using Genome-wide Association Mapping and Co-expression Networks Analysis
摘要
Abstract
Seed meal of rapeseed(Brassica napus L.)is a valuable protein source for livestock raising.However,high seed glu-cosinolates (GSL) content is harmful and toxic to livestock. Therefore, identifying candidate genes of seed GSL content is impor-tant in rapeseed breeding for low seed GSL. In this study, a genome-wide association study (GWAS) for seed GSL content was conducted using 157 rapeseed lines grown in four consecutive years. Meanwhile, a weighted gene co-expression network analysis(WGCNA) was carried out in early seed development stage of 15 low and 15 high seed GSL content lines for detecting candidate genes. In total, 45 SNPs found by GWAS significantly associated with seed GSL contents, explaining 13.5%-23.3% of the phe-notypic variance per SNP. These SNPs were mainly detected from three intervals on chromosomes A09, C02, and C09, covering five known GSL metabolism genes. A total of 2275 differentially expressed genes (DEGs) were identified by RNA-Seq between rapeseed lines with low and high seed GSL contents. These DEGs were clustered into 12 modules by WGCNA, of which one module (contains 163 DEGs) was mainly enriched in the GSL biosynthetic process. By using a weighted analysis for this module, 13 hub-genes were detected including nine known GSL metabolic genes. Among the 18 candidate genes identified by GWAS and WGCNA, 14 genes showed significant correlation between their expressions and the seed GSL contents (r = 0.376-0.638, P <0.05). Furthermore, one gene, BnaC02g41790D (MAM1), was detected by both GWAS and WGCNA. Five haplotypes were formed by five SNPs that significantly linked with BnaC02g41790D,and 63% of the rapeseed population(99/157)were found to carry Hap 5 with significant lower seed GSL contents (an average of 50.79 μmol g-1) compared with those carrying the other four haplotypes (95.04-110.28 μmol g-1). By GWAS and WGCNA, our study not only identified the candidate genes for seed GSL content of rapeseed, but also provided a guidance for digging candidate genes for other complex traits.关键词
甘蓝型油菜/全基因组关联分析/权重基因共表达网络分析/重测序/转录组测序/种子硫苷含量Key words
Brassica napus/GWAS/WGCNA/Re-sequencing/RNA-seq/Seed GSL content引用本文复制引用
魏大勇,崔艺馨,熊清,汤青林,梅家琴,李加纳,钱伟..用全基因组关联作图和共表达网络分析鉴定油菜种子硫苷含量的候选基因[J].作物学报,2018,44(5):629-641,13.基金项目
本研究由国家自然科学基金项目(31601333),国家重点基础研究发展计划(973计划)项目(2015CB150201)和中央高校基本科研业务专项(XDJK2017B036)资助.This study was supported by National Natural Science Foundation of China(31601333),the National Basic Research Program of China(973 Program)(2015CB150201),and the Fundamental Research Funds for the Central Universities(XDJK2017B036). （31601333）
