基于GWAS及双选系胚胎基因表达差异联合分析鉴定北京黑猪胸椎数主效基因

doi:10.16431/j.cnki.1671-7236.2025.09.017

摘要/Abstract

摘要： 【目的】本研究旨在精准定位并筛选影响北京黑猪胸椎数的候选基因，为深入解析北京黑猪胸椎数基因调控机制提供关键信息。【方法】选取645头北京黑猪，通过增加猪7号染色体(Sus scrofa chromosome 7，SSC7)数量性状基因座(quantitative trait locus，QTL)中基因的单核苷酸多态性(single nucleotide polymorphism，SNP)密度开展全基因组关联研究(genome-wide association study，GWAS)，结合连锁不平衡(linkage disequilibrium，LD)分析，筛选影响北京黑猪胸椎数的候选基因。对北京黑猪胸椎数双选系的5个17胚龄胚胎进行转录组差异表达基因分析，利用DOSE、org.Ss.eg.db、topGO以及clusterProfiler等软件包对差异表达基因展开GO功能和KEGG通路富集分析，并通过多组学联合分析确定影响胸椎数的关键基因。【结果】对SSC7的GWAS结果中最显著的位点进行LD分析，最终将与北京黑猪胸椎数相关区域精确定位到SSC7：97 619 505―97 779 063 bp，该区间内包含VRTN、SYNDIG1L、NPC2、ISCA2和LTBP2共5个候选基因。GO功能富集分析显示，在生物过程、细胞组分和分子功能三大类别中分别显著富集到401、31、50个条目，其中与胸椎发育相关的生物过程包括Wnt信号通路的正调控和骨矿化等条目，分子功能涵盖钙离子结合等条目。KEGG通路富集分析表明，差异表达基因显著富集于41条通路，其中MAPK信号通路和PI3K/Akt信号通路与胸椎发育密切相关。整合分析结果发现，GO条目和KEGG信号通路共包含AKT1、CSF1、HOXA11和LTBP2等82个候选基因。【结论】多组学联合分析共同筛选到LTBP2基因，可作为影响北京黑猪胸椎数的重要候选基因。本研究首次用胸椎数表型差异的胚胎进行转录组表达差异分析来筛选候选基因，为探究影响猪胸椎数的机制提供了新见解。

关键词: 北京黑猪; 胸椎数; 基因组; 转录组; 候选基因

Abstract: 【Objective】 This study was aimed to precisely locate and screen candidate genes that affected the number of thoracic vertebrae in Beijing Black pigs,providing crucial information for in-depth analysis of the gene regulatory mechanism of the number of thoracic vertebrae in Beijing Black pigs. 【Method】 In this study,645 Beijing Black pigs were selected.A genome-wide association study (GWAS) was carried out by increasing the density of single nucleotide polymorphism (SNP) of gene in the quantitative trait loci (QTL) on Sus scrofa chromosome 7(SSC7).Combined with linkage disequilibrium (LD) analysis,the candidate genes that affected the number of thoracic vertebrae in Beijing Black pigs were screened.Meanwhile,transcriptome differentially expressed gene analysis was performed on five 17-day-old embryos from the bi-directional selection lines of Beijing Black pigs with different numbers of thoracic vertebrae.Software packages such as DOSE,org.Ss.eg.db,topGO,and clusterProfiler were used to conduct GO function and KEGG pathway enrichment analysis on the differentially expressed genes.Key genes affecting the number of thoracic vertebrae were identified through multi-omics joint analysis. 【Result】 LD analysis was performed on the most significant loci of the SSC7 GWAS results.Finally,the region related to the number of thoracic vertebrae in Beijing Black pigs was located at SSC7:97 619 505-97 779 063 bp,it contained five genes,namely VRTN,SYNDIG1L,NPC2,ISCA2,and LTBP2.GO function enrichment analysis results showed that there were 401,31,and 50 significantly enriched terms in the three major categories of biological process,cellular component,and molecular function,respectively.Among them,the biological processes related to thoracic vertebrae development included terms such as the positive regulation of Wnt signaling pathway and bone mineralization,and the molecular functions covered terms such as calcium ion binding.In the KEGG pathway enrichment analysis,the differentially expressed genes were significantly enriched in 41 pathways.Among them,MAPK and the PI3K-Akt signaling pathways were closely related to thoracic vertebrae development.By integrating the analysis results,the above-mentioned GO terms and KEGG signaling pathways collectively contained 82 candidate genes,such as AKT1,CSF1,HOXA11,and LTBP2. 【Conclusion】 LTBP2 gene was jointly screened through multi-omics analysis and could be regarded as an important candidate gene affecting the number of thoracic vertebrae in Beijing Black pigs.In addition,for the first time,transcriptome expression difference analysis was performed on embryos with different phenotypes of the number of thoracic vertebrae to screen candidate genes,providing new insights for exploring the mechanism affecting the number of thoracic vertebrae in pigs.

Key words: Beijing Black pigs; number of thoracic vertebrae; genome; transcriptome; candidate genes

中图分类号:

S813.3
Q78

赵润泽, 闵兆玲, 牛乃琪, 宗文成, 闫益波, 张龙超. 基于GWAS及双选系胚胎基因表达差异联合分析鉴定北京黑猪胸椎数主效基因[J]. 中国畜牧兽医, 2025, 52(9): 4182-4194.

ZHAO Runze, MIN Zhaoling, NIU Naiqi, ZONG Wencheng, YAN Yibo, ZHANG Longchao. Identification of Major Genes Affecting the Number of Thoracic Vertebrae in Beijing Black Pigs Based on the Joint Analysis of GWAS and Embryonic Gene Expression Differences in Divergently Selected Lines[J]. China Animal Husbandry & Veterinary Medicine, 2025, 52(9): 4182-4194.

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