杜洛克猪平均日增重的全基因组关联分析

doi:10.16431/j.cnki.1671-7236.2025.10.027

摘要/Abstract

摘要： 【目的】利用全基因组关联分析(genome-wide association study，GWAS)鉴定杜洛克猪平均日增重(average daily gain，ADG)的候选基因，并结合基因表达调控数据开展共定位分析，深入阐明ADG的遗传调控机制。【方法】基于1 346头杜洛克猪ADG的表型记录和中芯一号50K芯片基因型数据，开展GWAS以识别ADG的数量性状基因座(quantitative trait locus，QTL)和候选基因。采用GO和KEGG富集分析探索候选基因的生物学功能，并结合PigGTEx(pig genotype-tissue expression)项目中34个组织的表达数量性状基因座(expression quantitative trait locus，eQTL)数据进行共定位分析，解析ADG的潜在因果基因和功能组织。【结果】通过GWAS共检测出1 530个显著单核苷酸多态性(single nucleotide polymorphisms，SNPs)(P＜5×10^-5)，定位到50个QTL，分布在第1、3～8、10～13、15～18号染色体上。基于Ensembl数据库对QTL区域进行注释，得到513个候选基因。其中，ALPK2、TULP3和TMOD4基因通过GO和KEGG富集分析在肢体发育、肌肉细胞发育等通路显著富集。共定位分析结果显示，3个潜在因果变异通过调控不同组织中的MVP、PRR14和DDX11基因表达，进而影响ADG性状。【结论】本研究通过GWAS和共定位分析，鉴定了杜洛克猪ADG的关键QTL区域及潜在因果基因，为杜洛克猪ADG性状的遗传改良提供了重要参考信息。

关键词: 杜洛克猪; 全基因组关联分析; 平均日增重; 共定位

Abstract: 【Objective】 Candidate genes associated with average daily gain (ADG) in Duroc pigs were identified using a genome-wide association study (GWAS),and colocalization analysis was performed by integrating gene expression regulatory data to gain deeper insights into the genetic regulatory mechanisms underlying ADG.【Method】 A GWAS was conducted based on ADG phenotypic records from 1 346 Duroc pigs and genotypic data generated using the Zhongxin No.1 50K SNP chip to identify quantitative trait locus (QTL) and associated candidate genes for ADG.GO and KEGG enrichment analyses were employed to explore the biological functions of the candidate genes,and colocalization analysis was performed by integrating expression quantitative trait locus (eQTL) data from 34 tissues provided by the pig genotype-tissue expression (PigGTEx) project,to identify potential causal genes and functionally relevant tissues contributing to the genetic regulation of ADG.【Result】 A total of 1 530 significant single nucleotide polymorphisms (SNPs) (P＜1×10^-5) associated with ADG were identified through GWAS and were mapped to 50 QTL, distributed across chromosomes 1,3-8,10-13,and 15-18.The QTL regions were annotated through the Ensembl database,resulting in the identification of 513 candidate genes.GO and KEGG enrichment analyses revealed that ALPK2,TULP3,and TMOD4 genes were significantly enriched in pathways related to limb development and muscle cell development.Colocalization analysis further revealed that three potential causal variants influence ADG by regulating the expression of MVP,PRR14,and DDX11 genes in different tissues.【Conclusion】 In this study,key QTL regions and potential causal genes associated with ADG in Duroc pigs were identified through the integration of GWAS and colocalization analysis.These findings provided important reference information for the genetic improvement of ADG in Duroc pigs.

Key words: Duroc pigs; genome-wide association studies; average daily gain; colocalization

中图分类号:

S813.3

张长亮, 徐志婷, 郭凯旋, 苏超, 宁文哲, 司景磊, 周隽, 高亚辉, 张哲. 杜洛克猪平均日增重的全基因组关联分析[J]. 中国畜牧兽医, 2025, 52(10): 4822-4829.

ZHANG Changliang, XU Zhiting, GUO Kaixuan, SU Chao, NING Wenzhe, SI Jinglei, ZHOU Jun, GAO Yahui, ZHANG Zhe. Genome-wide Association Study of Average Daily Gain in Duroc Pigs[J]. China Animal Husbandry & Veterinary Medicine, 2025, 52(10): 4822-4829.

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