中国农业科学2024，Vol.57Issue(21)：4356-4366,11.DOI:10.3864/j.issn.0578-1752.2024.21.014
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
摘要
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.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Key words
yolk ratio/heritability/genetic architecture/genetic correlation/single-step GWAS引用本文复制引用
郭军,李永峰,郭伟,童海兵,曲亮,邵丹,马猛,窦套存,卢建,胡玉萍,王星果,王强..基于一步法全基因组关联分析解析蛋黄比率遗传结构[J].中国农业科学,2024,57(21):4356-4366,11.基金项目
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) （2023ZD04052）
