中国畜牧兽医2025，Vol.52Issue(11)：5021-5029,9.DOI:10.16431/j.cnki.1671-7236.2025.11.001
基于SNP芯片的荣昌猪全基因组选择信号分析
Analysis of Selection Signatures for Rongchang Pigs Across the Whole Genome Based on SNP Chip
摘要
Abstract
[Objective]Based on the SNP chip data of Rongchang pigs,candidate genes associated with key economic traits were identified through selection signature analysis,providing valuable reference information for the genetic analysis of local pigs.[Method]The 66K SNP chip was used for genotyping 492 Rongchang pigs.Genotype quality control was conducted using PLINK v 1.90 software.Then genome-wide selection signatures were detected by the integrated haplotype score(iHS)method implemented in selscan software,followed by gene and quantitative trait locus(QTL)annotation analysis of significant SNPs and GO functional and KEGG pathway enrichment analysis.Additionally,expression quantitative trait locus(eQTL)annotation was performed by integrating data from the PigGTEx database.[Result]After genotype quality control,488 Rongchang pigs and 60 301 SNPs were retained for subsequent analysis.Population structure analysis revealed that Rongchang pig population could be categorized into four subpopulations with no obvious stratification,which could be used for subsequent analysis.The iHS analysis identified 1 693 significant SNPs.Functional annotation of these significant SNPs revealed that HNF4A,FOXP1,SLC2A8,and GALNT15 were key candidate genes influencing traits such as daily weight gain,body size,reproduction,and meat quality in Rongchang pigs.QTL annotation results showed that the selection signatures of Rongchang pigs were mainly related to meat quality and carcass traits.By integrating the PigGTEx database for eQTL annotation,the results demonstrated that rs322464023(17_36481691),which was in strong linkage disequilibrium with the significant locus rs1245720970(17_36433465),functions as an eQTL locus regulating expression of DNMT3B gene.Analysis integrating meat quality phenotypes in Rongchang pigs revealed that,AA genotype at rs322464023 exhibited extremely significantly higher meat colorL* value at 24 h slaughter than that of GG genotype(P＜0.01),and the genotype of linkage locus rs1245720970 had a similar effect on meat color L* value at 24 h slaughter.[Conclusion]This study identified selection signatures in Rongchang pigs based on chip data,revealing important candidate genes associated with daily weight gain,body size,reproduction and meat quality.Additionally,the significant locus rs1245720970 in muscle tissue was highly linked to the eQTL locus rs322464023 of DNMT3B gene.关键词
荣昌猪/选择信号/候选基因/表达数量性状基因座Key words
Rongchang pigs/selection signatures/candidate genes/eQTL分类
农业科技引用本文复制引用
陈信佑,郭宗义,王金勇,刁淑琪,吴平先,巫小倩,张廷焕,阿超,吴薛珊,石锐,刘澜,陈力..基于SNP芯片的荣昌猪全基因组选择信号分析[J].中国畜牧兽医,2025,52(11):5021-5029,9.基金项目
国家重点研发计划项目(2021YFD1301102) （2021YFD1301102）
国家生猪产业技术体系(CARS-35) （CARS-35）
重庆市现代农业产业技术体系(CQMAITS202312) （CQMAITS202312）
