中国农业科学2025，Vol.58Issue(9)：1845-1855,11.DOI:10.3864/j.issn.0578-1752.2025.09.013
通过加权基因共表达网络分析揭示影响猪脂肪沉积的候选基因
Weighted Gene Co-Expression Network Analysis Reveals Potential Candidate Genes Affecting Fat Deposition in Pigs
摘要
Abstract
[Objective]Fat deposition is the major energy storage tissue in pigs,and its amount not only has a direct impact on the economic benefits of pig production,but also is closely related to the quality of pork.In this study,based on RNA sequencing data and phenotypic data of fat deposition related traits,a gene co-expression network was constructed to mine key candidate genes affecting pig fat deposition and to explore the potential regulatory mechanism of pig fat deposition.[Method]RNA sequencing was performed on the longissimus dorsi samples of 28 Duroc pigs.Phenotypic data of these pigs regarding fat deposition-related traits were measured and calculated,including backfat thickness,fat percentage,intramuscular fat(IMF)content,and body mass index(BMI).Weighted gene co-expression network analysis(WGCNA)was conducted using an R language WGCNA package based on the RNA sequencing data and these phenotypic data to identify critical genes from co-expression modules related to fat deposition.[Result]WGCNA identified a total of 28 co-expression modules,among which Cyan and Purple modules were strongly correlated with at least two fat deposition-related traits based on the criteria of|module-trait relationships|＞0.3 and module gene significance＞0.25.Functional enrichment analysis revealed that genes in Cyan module were significantly enriched in fat deposition-related pathways,such as fatty acids biosynthesis(adjusted P value=3.48E-02)and glycosphingolipid biosynthesis(adjusted P value=4.40E-02).In contrast,those genes in Purple module were not significantly enriched in any fat deposition-related pathways and GO terms(adjusted P value＞0.05).Furthermore,combining the criteria of intra-modular connectivity greater than 0.2,an absolute correlation coefficient of gene expression with module eigengene exceeding 0.8,and the absolute correlation coefficient of gene expression with at least two fat deposition-related traits greater than 0.3,24 hub genes of 92 genes in this fat deposition-related module were identified.Among these hub genes,the correlation coefficients between the expression of four genes,including BET1L,NAGLU,B3GALT4,and TMEM115,and four fat deposition-related traits,backfat thickness,fat percentage,IMF content,and BMI,were all greater than 0.3.Moreover,gene function annotation showed that the biological function of these genes were closely related to fat deposition.These results indicated that the four genes might play essential roles in fat deposition.[Conclusion]In this study,WGCNA was applied to Duroc pigs,resulting in the discovering a co-expression module closely associated with fat deposition-related traits.Within this module,four potential candidate genes affecting fat deposition were identified,namely BET1L,NAGLU,B3GALT4,and TMEM115.These findings not only deepened our understanding of the genetic factors involved in fat deposition,but also provided a solid theoretical reference for further exploration of the underlying mechanisms of fat deposition in pigs.关键词
猪/脂肪沉积/WGCNA/RNA测序Key words
pig/fat deposition/WGCNA/RNA sequencing引用本文复制引用
王继英,李菁璇,王彦平,郭建凤,蔺海朝,赵雪艳..通过加权基因共表达网络分析揭示影响猪脂肪沉积的候选基因[J].中国农业科学,2025,58(9):1845-1855,11.基金项目
山东省农业良种工程项目(2022LZGCQY007)、国家自然科学基金青年科学基金项目(32002152)、山东省自然科学基金面上基金项目(ZR2024MC064)、山东省现代农业产业技术体系生猪创新团队建设项目(SDAIT-08-03) （2022LZGCQY007）
