大规模群体解析猪日增重及达百千克体重日龄的潜在因果基因  

Large-scale Population Analysis of Potential Causal Genes for Daily Weight Gain and Age at 100 kg in Pigs

作　　者：黄雅妮 唐熹 李井泉 魏嘉诚 吴珍芳[2] 李新云[3] 肖石军[1] 张志燕[1] HUANG Yani;TANG Xi;LI Jingquan;WEI Jiacheng;WU Zhenfang;LI Xinyun;XIAO Shijun;ZHANG Zhiyan(National Key Laboratory for Swine Genetic Improvement and Germplasm Innovation,Jiangxi Agricultural University,Nanchang 330045,China;College of Animal Science,South China Agricultural University,Guangzhou 510642,China;School of Animal Science and Technology,Huazhong Agricultural University,Wuhan 430070,China)

机构地区：[1]江西农业大学猪遗传改良与种质创新全国重点实验室,南昌330045 [2]华南农业大学动物科学学院,州510642 [3]华中农业大学动物科学技术学院,武汉430070

出　　处：《畜牧兽医学报》2025年第3期1100-1109,共10页ACTA VETERINARIA ET ZOOTECHNICA SINICA

基　　金：国家重点研发项目资金(2021YFD1200801)。

摘　　要：旨在探究影响猪达100 kg体重日龄(age at 100 kg,AGE)和达100 kg体重平均日增重(average daily gain at 100 kg,ADG)的候选基因。本研究采集了来自大白、长白和杜洛克3个品种的共计4593头健康成年猪的耳组织作为试验材料,其中公猪2563头,母猪2030头。通过记录猪只的日龄和体重,计算校正AGE和ADG。通过酚氯仿法提取样品DNA,利用“中芯一号”50K SNP芯片对样本进行基因分型,并对质控后的SNPs进行基因型填充,将SNPs位点数从4万填充至800万。随后,利用GEMMA混合线性模型对AGE和ADG性状进行填充前后的全基因组关联分析,使用BEDTools在显著位点上、下游1 Mb范围查找候选基因。同时,结合PigGTEx中的34个组织的表达量数量性状位点数据,使用R软件进行共定位分析,挖掘与GWAS信号共享同一因果变异的基因,通过GWAS和共定位分析,确定AGE和ADG性状的候选基因。GWAS分析结果显示,AGE与ADG性状的显著SNP为1号染色体上的1_270827213。在该位点上、下游1 Mb范围内,共鉴定到32个基因。共定位分析结果显示,对于AGE性状,有10个基因的eQTL信号与GWAS信号共定位。对于ADG性状,有11个基因的eQTL信号与GWAS信号共定位。最终,确定了CRAT、GPR 107和USP 20这3个基因作为AGE的候选基因,确定了CRAT、GPR107、USP20、FNBP1、PTGES和HMCN 2这6个基因作为ADG的候选基因。本研究为猪品种改良提供了分子标记,对猪生长相关性状功能基因挖掘奠定基础。The aim of this study was to explore candidate genes influencing age at 100 kg(AGE)and average daily weight gain at 100 kg(ADG)in pigs.Ear tissue samples were collected from 4593 healthy adult pigs,including 2563 boars and 2030 sows,representing three breeds:Large White,Landrace,and Duroc.The age and body weight of the pigs were recorded,and the corrected AGE and ADG were calculated accordingly.The DNA from the samples was extracted using the phenol-chloroform method.Genotyping was performed using the"CC-1"50K SNP chip,and SNP markers were imputed from 40000 to 8 million after quality control.Subsequently,genome-wide association study was performed using the GEMMA mixed linear model on AGE and ADG traits.Candidate genes were identified by searching within a 1 Mb window upstream and downstream of significant SNP loci using BEDTools.Additionally,the study integrated expression quantitative trait locus data from 34 tissues in the PigGTEx,and colocalization analysis was conducted using R software to identify genes that shared causal variants with the GWAS signals.Through GWAS and colocalization analysis,candidate genes for AGE and ADG traits were identified.The significant SNP associated with both AGE and ADG traits is 1_270827213 on chromosome 1.Within a 1 Mb region upstream and downstream of this SNP,32 candidate genes were identified.Colocalization analysis showed that,there were 10 genes had eQTL signals that colocalized with the GWAS signal for AGE,while 11 genes had eQTL signals colocalizing with the GWAS signal for ADG.Ultimately,the genes CRAT,GPR 107 and USP 20 were identified as candidate genes for AGE,and CRAT,GPR107,USP20,FNBP1,PTGES and HMCN 2 were identified as candidate genes for ADG.This study provides molecular markers for pig breed improvement and lays the foundation for the functional gene discovery related to growth traits in pigs.

关 键 词：猪 AGE ADG 全基因组关联分析 候选基因 

分 类 号：S828.2[农业科学—畜牧学]