中国农业科学 ›› 2024, Vol. 57 ›› Issue (21): 4356-4366.doi: 10.3864/j.issn.0578-1752.2024.21.014

• 畜牧·兽医 • 上一篇    下一篇

基于一步法全基因组关联分析解析蛋黄比率遗传结构

郭军(), 曲亮, 邵丹, 马猛, 窦套存, 卢建, 胡玉萍, 王星果, 王强, 李永峰, 郭伟, 童海兵()   

  1. 江苏省家禽科学研究所,江苏扬州 225125
  • 收稿日期:2024-04-19 接受日期:2024-06-07 出版日期:2024-11-01 发布日期:2024-11-10
  • 通信作者:
    童海兵,E-mail:
  • 联系方式: 郭军,Tel:0514-85599012;E-mail:guojun.yz@gmail.com。
  • 基金资助:
    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); 国家现代农业产业技术体系建设专项资金(CARS-40-S23); 江苏省种业振兴揭榜挂帅项目(JBGS[2021]104)

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

GUO Jun(), QU Liang, SHAO Dan, MA Meng, DOU TaoCun, LU Jian, HU YuPing, WANG XingGuo, WANG Qiang, LI YongFeng, GUO Wei, TONG HaiBing()   

  1. Jiangsu Institute of Poultry Science, Yangzhou 225125, Jiangsu
  • Received:2024-04-19 Accepted:2024-06-07 Published:2024-11-01 Online:2024-11-10

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F2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F1、F2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F2代产蛋鸡血液样本,以600K基因芯片对1 534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传座位,在显著性SNP之下有8个支持位点超过基因组潜在水平线。显著性以及潜在水平SNP可解释2.18%的表型方差,单倍型片段长度达到71 kb。此外,鸡2号染色体也检测到基因组潜在水平SNP。染色体遗传力分析表明,蛋黄比率受微效多基因控制,染色体遗传力与该染色体容纳的基因数呈正比例。【结论】应用加权一步法GWAS解析了蛋黄比率遗传结构,筛选得到ADAM9基因与60周龄蛋黄比率密切相关;相比于系谱遗传关系矩阵,杂交遗传关系矩阵减少孟德尔抽样误差,获得的遗传参数更准确。

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

Abstract:

【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 F2 population was used in this study, Dongxiang green-shelled chickens and White Leghorn were used as parents respectively, and the F1 and F2 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 F2 generation were collected, and 1 534 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, the heritability on the yolk ratio and egg size were 0.348±0.041 and 0.500±0.038, respectively. The genetic correlation coefficients between yolk ratio and egg size and Haugh unit were -0.463±0.075 and -0.165±0.111, respectively. Using the pedigree genetic relationship matrix, heritability on yolk ratio and egg size were 0.387±0.052 and 0.465±0.052, respectively. The genetic correlation coefficients between yolk ratio and egg size and Haugh unit were -0.405±0.091 and -0.166±0.121, respectively. The inflation factor on the yolk ratio association analysis was 1.007, indicating that no stratified structure was detected in the resource population. There was a locus on chicken chromosome 22 that was significantly associated with the yolk ratio, which was supported by additional SNPs. This QTL explained 2.18% of the phenotypic variance, and the haplotype block size reached 71 kb. In addition, the potential SNP was also detected on chromosome 2. Chromosome heritability analysis showed that the yolk ratio was controlled by small-effect polygenes, and the heritability was directly proportional to the number of genes harbored by the chromosome. 【Conclusion】The weighted single-step GWAS method was used to analyze the genetic architecture of yolk ratio at 60 weeks of age, and the ADAM9 gene was identified to associate with the yolk ratio. Compared with the pedigree genetic relationship matrix, the hybrid genetic relationship matrix reduced Mendelian sampling errors and obtained more accurate genetic parameters.

Key words: yolk ratio, heritability, genetic architecture, genetic correlation, single-step GWAS