数量性状主基因+多基因混合遗传分析R软件包SEA v2.0  

SEA v2.0: an R software package for mixed major genes plus polygenes inheritance analysis of quantitative traits

作　　者：王靖天 张亚雯 杜应雯 任文龙 李宏福 孙文献 葛超 章元明[1] WANG Jing-Tian;ZHANG Ya-Wen;DU Ying-Wen;REN Wen-Long;LI Hong-Fu;SUN Wen-Xian;GE Chao;ZHANG Yuan-Ming(College of Plant Science and Technology,Huazhong Agricultural University,Wuhan 430070,Hubei,China)

机构地区：[1]华中农业大学植物科学技术学院,湖北武汉430070

出　　处：《作物学报》2022年第6期1416-1424,共9页Acta Agronomica Sinica

基　　金：国家自然科学基金项目(32070557)资助。

摘　　要：利用双亲分离群体数量性状表型值可鉴定其主基因+多基因混合遗传模型,为数量性状遗传基础和作物育种提供参考信息。为全面总结数量性状分离分析的研究成果、添加软件包新功能和矫正以前版本的缺陷,在RStudio-1.4.1103平台和R编程语言框架下,开发了具有交互式图形用户界面的R软件包SEA v2.0。该软件可分析14种双亲分离群体类型,每种群体类型均有数据导入、数据分析、后验概率计算和分布曲线绘制4个模块。为节省计算时间,用doParallel包并行计算、data.table包读写数据和MASS包估计分布参数。用KScorrect、kolmim和shiny包简化程序。只要用户上传*.csv格式数据文件并设置相关参数,可快速显示计算结果。通过大豆结荚习性数据分析和MonteCarlo模拟研究,证实了SEAv2.0软件包的有效性。软件包可从https://cran.r-project.org/web/packages/SEA/index.html下载。The phenotypic values for quantitative trait from bi-parental segregation populations can be used to identify its mixed major genes plus polygenes inheritance model, which provides important information for the genetic basis of quantitative traits and crop breeding. To comprehensively summarize the research results of methodological advances, add the new functions of the software and correct its shortcomings in previous versions, an R software package SEA v2.0 with interactive graphical user interface is developed under R studio–1.4.1103 platform and R environment. In this software, there were 14 types of bi-parental segregation populations, and each type included four modules: data input, data analysis, posterior probability calculation, and distribution curve drawing. To save running time, do Parallel was used to conduct parallel computing, data.table was used to quickly read and write datasets, and MASS was used to estimate the parameters in component distributions. KScorrect, kolmim, and shiny packages were used to simplify the programs. As long as users uploaded the data file with *.csv format and set the related parameters, the results could be quickly displayed. The software was validated by real data analysis of soybean podding habit and Monte Carlo simulation studies, and can be downloaded from https://cran.r-project.org/web/packages/SEA/index.html.

关 键 词：双亲分离群体 数量性状 主基因+多基因混合模型 R软件包 SEA 

分 类 号：S330[农业科学—作物遗传育种]