贝类全基因组遗传育种评估与分析系统的开发  

Development of the Genomic Analysis and Evaluation System for Shellfish Genetic Breeding

作　　者：苏海林[1] 王扬帆[1] 胡晓丽[1] 王师[1] 包振民[1] 

机构地区：[1]中国海洋大学海洋生命学院,山东青岛266003

出　　处：《中国海洋大学学报（自然科学版）》2016年第10期65-72,共8页Periodical of Ocean University of China

基　　金：国家高技术研究发展计划项目(2012AA10A405);现代农业产业技术体系建设专项资金项目(CARS-48)资助~~

摘　　要：为在贝类育种工作中推广应用准确率高于传统系谱资料最佳线性无偏估计方法的全基因组选择育种评估技术,以实现全基因组选择算法的MixP软件为核心,结合国内贝类育种项目研究,本研究设计开发了一套以网站服务形式为基础的基因组选择网络育种平台。该系统在Ubuntu Linux环境下使用MySQL数据库和基于Java编程语言的服务器端动态页面(Java Server Pages,JSP)技术开发完成,主要包括系统公告、综合查询、信息维护、任务管理、育种评估、选种选配等6个功能模块,能够完成数据模拟,性状测量记录的储存和查询,遗传参数估计,分子标记效应估计从而计算基因组估计育种值,以及选种选配方案定制等主要工作。系统在可行性测试中分析了98个栉孔扇贝,包括2个亲本和96个子代的壳长数据和基因型信息,计算出分布于全基因组的单个苷酸多态性(Single Nucleotide Polymorphism,SNP)分子标记效应以及个体的估计育种值,并简单计算出估计育种值与表型值的相关系数为0.703 9。这些结果表明系统运行正常。该系统在贝类育种工作中的推广和应用能够有效提升行业的整体技术水平,推动中国贝类育种工作的发展。Working on shellfish breeding and in order to popularize genomic selection technology which is expected to be able to achieve higher prediction accuracy than the nowadays widely used Best Linear Unbiased Prediction（BLUP）breeding technology,we designed and developed an edge cutting web based breeding platform for the research and application of the genomic selection technology for domestic shellfish breeding programs.The MixP software,which utilized the Pareto principle in prior variance component assumptions and implemented a type of algorithm that performs genomic selection analysis that differs from Genomic Best Linear Unbiased Prediction（GPLUP）and Bayesian Regression based marker effect models,was adopted in this study and used as the computing kernel of the system.This system was built on the most widely used Linux operating system,i.e.the Ubuntu distribution,along with MySQL database system,Java programming language and the Java Server Pages technology,structured by the Apache Struts 2.0frameworks.This system consists of 6functioning modules consisting of the system announcement module,the comprehensive inquiry module,the information maintenance module,the task management module,the breeding evaluation module,and the selection and mating program design module.The system was competent for accomplishing jobs such as data simulation,storage and inquiry of phenotypic trait records and environmental information,genetic parameter estimation,Single Nucleotide Polymorphism（SNP）marker effect estimation and breeding value estimation,mating plan formulation,et al.In addition,a simple analysis was performed on this system using field data to test the system＇s feasibility.The shell length measurement records and the 2b-RAD de novo genotyping technology enhanced genotypic information of 98 Chlamys Farreri individuals,including two parents and their 96 offspring,were inputted into the system and were analyzed using the breeding value estimation module of the system.Results have shown that this system is opera

关 键 词：贝类育种 全基因组选择 网络育种系统 

分 类 号：Q38[生物学—遗传学]