[1]陈元军,马娟娟,史睿,等.整合关联分析和共表达网络分析挖掘甘蓝型油菜籽粒质量候选基因[J].江苏农业学报,2023,(04):913-930.[doi:doi:10.3969/j.issn.1000-4440.2023.04.001]
　CHEN Yuan-jun,MA Juan-juan,SHI Rui,et al.Integrating genome-wide association study and weighted gene co-expression network analysis to explore candidate genes of seed weight in rapeseed (Brassica napus L.)[J].,2023,(04):913-930.[doi:doi:10.3969/j.issn.1000-4440.2023.04.001]
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整合关联分析和共表达网络分析挖掘甘蓝型油菜籽粒质量候选基因()
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江苏农业学报[ISSN:1006-6977/CN:61-1281/TN]

卷:
期数:
2023年04期
页码:
913-930
栏目:
遗传育种·生理生化
出版日期:
2023-08-30

文章信息/Info

Title:
Integrating genome-wide association study and weighted gene co-expression network analysis to explore candidate genes of seed weight in rapeseed (Brassica napus L.)
作者:
陈元军1; 2; 马娟娟2; 3; 史睿2; 3; 李伟龙1; 2; 王婷2; 4; 彭琦2; 张维2; 陈锋2
（1.福建农林大学农学院，福建福州350002；2.江苏省农业科学院经济作物研究所/农业农村部长江下游棉花与油菜重点实验室/江苏省农业生物学重点实验室/江苏省现代作物生产协同创新中心，江苏南京210014；3.南京农业大学作物遗传与种质创新国家重点实验室，江苏南京210095；4.江苏大学生命科学研究院,江苏镇江212023）
Author(s):
CHEN Yuan-jun1; 2; MA Juan-juan2; 3; SHI Rui2; 3; LI Wei-long1; 2; WANG Ting2; 4; PENG Qi2; ZHANG Wei2; CHEN Feng2
（1.College of Agriculture, Fujian Agriculture and Forestry University， Fuzhou 350002, China;2.Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences/Key Laboratory of Cotton and Rapeseed (Nanjing), Ministry of Agriculture and Rural Affairs/Key Laboratory of Jiangsu Province for Agrobiology/Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing 210014, China;3.Nanjing Agricultural University， State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing 210095， China;4.School of Life Sciences, Jiangsu University, Zhenjiang 212023, China）
关键词:
甘蓝型油菜; 籽粒质量; 产量; 全基因组关联分析; 共表达网络分析
Keywords:
Brassica napus L.; seed weight; yield; genome-wide association study （GWAS）; weighted gene co-expression network analysis （WGCNA）
分类号:
S634.3
DOI:
doi:10.3969/j.issn.1000-4440.2023.04.001
文献标志码:
A
摘要:
甘蓝型油菜是中国重要的油料作物，籽粒质量是油菜产量构成的重要因素。本研究利用A-D Test模型对496份油菜的籽粒质量进行全基因组关联分析，共检测到19个显著位点，联合解释341%的表型变异。整合A-D Test及前期混合线性模型和一般线性模型结果后得到71个位点，联合解释50.1%的表型变异。在22个位点置信区间内找到ARF2、NPC6、TTG2和WRI1等已被报道的拟南芥中的籽粒质量基因的同源基因。同时，利用大粒品种中双11和中小粒品种中油821的籽粒和角果皮转录组数据进行加权基因共表达网络分析，构建了13个共表达模块，其中紫色（purple）和洋红色（magenta）模块与籽粒质量表型显著相关。GO富集分析结果表明，2个模块在L-苯丙氨酸氨基转移酶活性、硫双加氧酶活性、焦磷酸酶活性和RNA解旋酶活性等显著富集。2个模块中的枢纽基因BnaA06g00850D、BnaA01g00990D、BnaC06g10000D和BnaC02g44260D等的同源基因为ETHE1、DAR1、GLN1;1和SMG7等拟南芥籽粒质量已知基因。整合全基因组关联分析和加权基因共表达网络分析的分析结果，在42个显著位点的置信区间内找到90个属于purple和magenta模块的基因，其中BnaA01g06210D、BnaA07g14990D和BnaA07g03030D等拟南芥同源基因已被报道参与种子发育进程调控。本研究整合GWAS与WGCNA 2种分析方法，挖掘甘蓝型油菜的籽粒质量候选基因，为研究籽粒质量的调控机制、指导籽粒质量的遗传改良提供参考。
Abstract:
Brassica napus L. is one of the most important oil crops in China, and seed weight is one of the essential components of seed yield. In this study, we performed a genome-wide association study (GWAS) of seed weight in a collection of 496 rapeseed materials, and detected 19 significant loci via A-D Test model, which accounted for 341% of the phenotypic variance on the whole. Combining the common loci of A-D Test an d previous mixed linear model (MLM) and general linear model (GLM), 71 loci were obtained and accounted for 501% of the phenotypic variance. Genes named ARF2, NPC6, TTG2 and WRI1 were found to be orthologous with reported Arabidopsis seed weight genes in confidence interval of 22 loci. Meanwhile, a total of 13 co-expression modules were constructed through weighted gene co-expression network analysis (WGCNA) based on transcriptome data of seed and silique husk from big seed variety Zhongshuang11 and middle-small seed variety Zhongyou821. The purple and magenta modules were significantly correlated with the seed weight phenotype. Results of GO enrichment analysis showed that, the above two modules were enriched significantly at terms like L-phenylalanine aminotransferase activity, sulfur dioxygenase activity, pyrophosphatase activity and RNA helicase activity, etc. Hub genes from the purple and magenta modules like BnaA06g00850D, BnaA01g00990D, BnaC06g10000D and BnaC02g44260D were orthologous with the reported genes of seed weight in Arabidopsis, such as ETHE1, DAR1, GLN1;1 and SMG7. By combing the results of GWAS and WGCNA, we identified 90 genes of purple module or magenta module in the confidence intervals of 42 significant loci, and the orthologous genes in Arabidopsis like BnaA01g06210D, BnaA07g14990D and BnaA07g03030D were reported to participate in seed development regulation. In this study, we integrated the analytical methods of GWAS and WGCNA to identify the candidate genes of seed weight in rapeseed, so as to lay a foundation for studying the regulation mechanism and guiding the genetic improvement of seed weight.

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备注/Memo

备注/Memo:
收稿日期：2022-08-27 基金项目：国家自然科学基金项目(32001581)；江苏省基础研究计划(自然科学基金)项目(BK20190260)；江苏省区域现代农业与环境保护协同创新中心专项（HSXT3015）;江苏省种业振兴揭榜挂帅项目[JBGS(2021)061] 作者简介：陈元军（1996-），男，海南万宁人，硕士研究生，主要从事油菜遗传育种研究。（E-mail）953825642@qq.com 通讯作者：孙程明, （E-mail）suncm8331537@gmail.com; 季彪俊, （E-mail）307853347@qq.com; 胡茂龙, （E-mail）humolon@163.com
更新日期/Last Update: 2023-09-12