基于SNP芯片的荣昌猪全基因组选择信号分析

doi:10.16431/j.cnki.1671-7236.2025.11.001

摘要/Abstract

摘要： 【目的】基于荣昌猪的SNP芯片数据，使用选择信号分析筛选荣昌猪重要经济性状的候选基因，为地方猪遗传解析研究提供参考信息。【方法】本研究利用66K芯片对492头荣昌猪进行基因分型，使用PLINK v 1.90软件对基因型数据进行质控，通过selscan软件的整合单倍型分数(integrated haplotype score，iHS)方法进行全基因组选择信号分析，对显著位点进行基因和数量性状基因座(quantitative trait locus,QTL)注释分析以及GO功能和KEGG通路富集分析，并整合PigGTEx数据库进行表达数量性状基因座(expression quantitative trait locus，eQTL)注释分析。【结果】荣昌猪基因型质控后剩余488个个体和60 301个SNPs位点用于后续分析；群体结构分析显示，试验群体可分为4个亚群，无明显的群体分层，可用于后续分析；iHS共检测到1 693个显著位点；显著位点生物学功能注释结果表明，HNF4A、FOXP1、SLC2A8和GALNT15可能是影响荣昌猪日增重、体尺、繁殖及肉质性状的重要候选基因；QTL注释结果表明，荣昌猪的选择信号主要与肉品质和胴体性状相关；通过整合PigGTEx数据库进行eQTL注释发现，与显著位点rs1245720970(17_36433465)紧密连锁的rs322464023(17_36481691)是调控DNMT3B基因表达的eQTL位点。结合荣昌猪肉质表型发现,携带rs322464023位点AA基因型的个体在屠宰后24 h肉色亮度评分极显著高于AG和GG基因型(P＜0.01)，连锁位点rs1245720970的基因型对屠宰后24 h肉色亮度值的影响与之高度相似。【结论】本研究基于芯片数据检测了荣昌猪的选择信号，筛选出与荣昌猪日增重、体尺、繁殖及肉质性状的重要候选基因，并发现肌肉组织中显著位点rs1245720970与DNMT3B基因的eQTL位点rs322464023高度连锁。

关键词: 荣昌猪; 选择信号; 候选基因; 表达数量性状基因座

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 color L^* 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.

Key words: Rongchang pigs; selection signatures; candidate genes; eQTL

中图分类号:

S813.9

陈信佑, 吴平先, 巫小倩, 张廷焕, 阿超, 吴薛珊, 石锐, 刘澜, 陈力, 郭宗义, 王金勇, 刁淑琪. 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.

CHEN Xinyou, WU Pingxian, WU Xiaoqian, ZHANG Tinghuan, A Chao, WU Xueshan, SHI Rui, LIU Lan, CHEN Li, GUO Zongyi, WANG Jinyong, DIAO Shuqi. Analysis of Selection Signatures for Rongchang Pigs Across the Whole Genome Based on SNP Chip[J]. China Animal Husbandry & Veterinary Medicine, 2025, 52(11): 5021-5029.

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