基于一步法全基因组关联分析解析蛋黄比率遗传结构  

Dissecting the Genetic Architecture of Yolk Ratio with Single-Step Genome-Wide Association Study

作　　者：郭军[1] 曲亮[1] 邵丹[1] 马猛[1] 窦套存[1] 卢建[1] 胡玉萍[1] 王星果[1] 王强[1] 李永峰 郭伟 童海兵[1] GUO Jun;QU Liang;SHAO Dan;MA Meng;DOU TaoCun;LU Jian;HU YuPing;WANG XingGuo;WANG Qiang;LI YongFeng;GUO Wei;TONG HaiBing(Jiangsu Institute of Poultry Science,Yangzhou 225125,Jiangsu)

机构地区：[1]江苏省家禽科学研究所,江苏扬州225125

出　　处：《中国农业科学》2024年第21期4356-4366,共11页Scientia Agricultura Sinica

基　　金：科技创新2030—重大项目(2023ZD04052);江苏现代农业产业技术体系建设专项资金(JATS[2023]361);国家现代农业产业技术体系建设专项资金(CARS-40-K01,CARS-40-S23);江苏省种业振兴揭榜挂帅项目(JBGS[2021]104)。

摘　　要：【目的】利用全基因组关联分析(genome-wide association study,GWAS)解析60周龄蛋鸡蛋黄比率遗传结构,旨在挖掘地方鸡种优异基因资源,进而为培育适应市场需求的特色蛋鸡品种奠定基础。【方法】数据采集自江苏省家禽科学研究所蛋鸡资源群体。依据F_(2)设计构建试验群体,分别以东乡绿壳蛋鸡、白来航鸡为亲本,经正反交获得F_(1)、F_(2)代。表型数据组包括开产日龄、胫长、体重、蛋重、哈氏单位以及蛋黄比率。收集F_(2)代产蛋鸡血液样本,以600K基因芯片对1534只试验鸡进行基因型分型。对SNPs数据进行质量控制、基因型数据填充。表型数据经去除离群值等清洗步骤后,以单因素方差分析检验影响性状表型值的因素,确定列入固定效应的因子。以系谱数据构建遗传关系矩阵,以多性状动物模型分析资源群体方差组分及遗传参数;作为对比,以系谱数据加基因型分型数据构建杂交遗传关系矩阵,用单性状动物模型计算遗传力,用双性状动物模型计算遗传相关系数。利用BLUPF90软件获得SNP效应值,以postGSf90获得SNP对应的P值以及权重,从而获得蛋黄比率关联的基因组显著水平SNP。针对蛋黄比率性状,计算染色体遗传力和单倍型片段长度。【结果】东乡绿壳蛋鸡蛋黄比率高于白来航鸡蛋黄比率,品种-批次效应对表型值影响显著,将其列入统计模型固定效应。应用杂交遗传关系矩阵分析,蛋黄比率、蛋重遗传力分别为0.348±0.041、0.500±0.038,蛋黄比率与蛋重、哈氏单位遗传相关系数分别为-0.463±0.075、-0.165±0.111;应用系谱遗传关系矩阵分析,蛋黄比率、蛋重遗传力分别为0.387±0.052、0.465±0.052,蛋黄比率与蛋重、哈氏单位遗传相关系数分别为-0.405±0.091、-0.166±0.121。蛋黄比率关联分析的膨胀系数为1.007,表明蛋鸡资源群体未检测到层化结构。鸡22号染色体存在与蛋黄比率显著关联的遗【Objective】Genome-wide association study(GWAS)was used to dissect the genetic architecture of yolk ratio in the 60-week-old hens,with the aim of discovery and utilization of the excellent genetic resources of local chickens and establishing the foundation for the breeding layer to meet market demand.【Method】The phenotypic data was collected from the resource population of Jiangsu Institute of Poultry Science.The F_(2) population was used in this study,Dongxiang green-shelled chickens and White Leghorn were used as parents respectively,and the F_(1) and F_(2) generations were obtained through reciprocal crosses.The data set included age at the first egg,shank length,body weight,egg size,Haugh unit,and yolk ratio.Blood samples in F_(2) generation were collected,and 1534 hens were genotyped using 600K gene microarray.SNPs data was quality controlled.Missing data was imputed by Beagle software.After data cleaning steps such as removing outliers from the phenotypic data,one-way analysis of variance was used to test the factors that affected the phenotypic value,and these factors enrolled in the fixed effects.The genetic parameters and variance components were determined with multivariate animal model by using pedigree relationship matrix.On the other hand,the genetic relationship matrix was set up with the pedigree and genomic data.Heritabilities were calculated with univariate animal model,and genetic correlation coefficients were determined with bivariate animal model.The BLUPF90 software was used to obtain the SNP effect value,and postGSf90 was used to obtain the P-value and weight corresponding to the SNP.Therefore,the significant SNPs related to the yolk ratio was obtained with GWAS method.Chromosome heritability and haplotype block size were calculated for the yolk ratio.【Result】The yolk ratio of Dongxiang blue shelled chicken was significantly higher than that of White Leghorn.Fixed effects included the combination of laying batch-generation-breed level.Using the hybrid genetic relationship matrix,t

关 键 词：蛋黄比率 遗传力 遗传结构 遗传相关 一步法全基因组关联分析 

分 类 号：S831.2[农业科学—畜牧学]