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

Abstract

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

CLC Number:

S813.3
Q78

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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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

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