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

Abstract

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

CLC Number:

S813.9

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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Analysis of Selection Signatures for Rongchang Pigs Across the Whole Genome Based on SNP Chip

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