利用动态转录组学挖掘大豆百粒重候选基因  

Utilization of dynamic transcriptomics analysis for candidate gene mining of 100-seed weight in soybean

作　　者：曾健 徐先超 徐昱斐 王秀成 于海燕 冯贝贝 邢光南[1] ZENG Jian;XU Xian-Chao;XU Yu-Fei;WANG Xiu-Cheng;YU Hai-Yan;FENG Bei-Bei;XING Guang-Nan(Soybean Research Institute,Nanjing Agricultural University/National Center for Soybean Improvement/Key Laboratory for Biology and Genetic Improvement of Soybean(General),Ministry of Agriculture and Rural Affairs/National Key Laboratory for Crop Genetic and Germplasm Enhance-ment/Jiangsu Collaborative Innovation Center for Modern Crop Production,Nanjing 210095,Jiangsu,China)

机构地区：[1]南京农业大学大豆研究所/国家大豆改良中心/农业农村部大豆生物学与遗传育种重点实验室(综合)/作物遗传与种质创新国家重点实验室/江苏省现代作物生产协同创新中心,江苏南京210095

出　　处：《作物学报》2021年第11期2121-2133,共13页Acta Agronomica Sinica

基　　金：国家重点研发计划项目(2016YFD0100201);国家自然科学基金项目(31571694);中央高校基本科研业务费专项资金(KYT201801);长江学者和创新团队发展计划(PCSIRT_17R55);高等学校学科创新引智基地项目111(B08025);国家现代农业产业技术体系(大豆)建设专项(CARS-04);江苏省优势学科建设工程专项;江苏省JCIC-MCP项目资助

摘　　要：百粒重是影响大豆产量的重要农艺性状,揭示其分子基础发掘关键候选基因对大豆改良具有重要意义。本研究通过对12个大豆品种籽粒发育3个时期共36个样本的转录组数据进行加权基因共表达网络分析(weighted gene co-expression network analysis,WGCNA),得到20个基因共表达模块,与百粒重及4个粒形性状关联后发现green模块与表型最为相关,之后根据Gene Significance(GS)值和Eigengene Connectivity(kME)值筛选出13个green模块内的核心基因(hub gene);然后对2组百粒重存在极显著差异的大豆品种的籽粒发育3个时期分别进行基因差异表达分析发现大豆在籽粒发育前中期可能通过MAPK信号通路调节百粒重大小;之后对其进行SNPs/InDels挖掘并根据Gene Ontology(GO)注释发现green模块内的Glyma.14G043900和Glyma.15G217400由于SNP变异造成同义以及非同义突变,且存在调控基因表达相关的GO Terms以及锌指结构域,表明它们可能通过调控hub基因和差异表达基因调控大豆百粒重及粒形性状。Glyma.15G217400位于已报道的4个百粒重QTL中,而Glyma.14G043900位于已报道的一个籽粒蛋白含量及一个油脂含量QTL中。通过比对大豆公共数据库发现这2个基因的百粒重增效等位变异受到人工选择,其频率从野生大豆到地方品种再到育成品种的过程中逐渐升高。这些结果为进一步发掘大豆百粒重候选基因及其表达调控机制提供了新思路。100-seed weight of soybean is an important agronomic trait that affects yield,and it is of great significance to reveal its molecular basis and discover key candidate genes for soybean improvement breeding.In this study,weighted gene co-expression network analysis(WGCNA)was performed on the transcriptome data of 36 samples from 12 soybean varieties at three stages of seed development,and 20 gene co-expression modules were obtained.After correlating with 100-seed weight and four-seed shape traits,the green module was found to be most correlated with the phenotypes.Then 13 hub genes of green module were screened based on the Gene Significance(GS)and Eigengene Connectivity(kME)value.Gene differential expression of two groups of soybean varieties with extremely significant differences in 100-seed weight showed that the MAPK signaling pathway in the early and mid-term of seed development might regulate the 100-seed weight in soybean.According to SNPs/InDels calling and Gene Ontology(GO)annotation,Glyma.14G043900 and Glyma.15G217400 in the green module caused synonymous and non-synonymous coding mutations due to SNP mutations,and there were GO Terms and zinc finger domains related to gene ex-pression regulation.These results suggested that they might regulate the 100-seed weight and seed shape of soybeans by regulat-ing the hub gene and differentially expressed genes.Furthermore,Glyma.15G217400 was located in four reported QTLs of 100-seed weight,while Glyma.14G043900 was located in a reported seed protein content QTL and an oil content QTL.Compared with soybean public database,the increasing 100-seed weight alleles of the two genes were artificially selected and their fre-quency was gradually increased from wild accessions to landraces,resulting in the improved cultivars.These results provide new ideas for further discovering 100-seed weight candidate gene in soybean and its expression regulation mechanism.

关 键 词：大豆 百粒重 转录组学 WGCNA 候选基因 

分 类 号：S565.1[农业科学—作物学]