中国农业科学 ›› 2025, Vol. 58 ›› Issue (9): 1845-1855.doi: 10.3864/j.issn.0578-1752.2025.09.013

• 畜牧·兽医 • 上一篇    下一篇

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

王继英(), 李菁璇, 王彦平, 郭建凤, 蔺海朝, 赵雪艳()   

  1. 山东省农业科学院畜牧兽医研究所/山东省主要畜禽育种重点实验室,济南 250100
  • 收稿日期:2025-02-14 接受日期:2025-03-25 出版日期:2025-05-01 发布日期:2025-05-08
  • 通信作者:
    赵雪艳,E-mail:
  • 联系方式: 王继英,E-mail:jnwangjiying@163.com。
  • 基金资助:
    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)

Weighted Gene Co-Expression Network Analysis Reveals Potential Candidate Genes Affecting Fat Deposition in Pigs

WANG JiYing(), LI JingXuan, WANG YanPing, GUO JianFeng, LIN HaiChao, ZHAO XueYan()   

  1. Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences/Shandong Provincial Key Laboratory of Livestock and Poultry Breeding, Jinan 250100
  • Received:2025-02-14 Accepted:2025-03-25 Published:2025-05-01 Online:2025-05-08

摘要:

【目的】 脂肪作为猪体内的主要储能组织,其沉积量不仅对养殖经济效益有着直接影响,还与猪肉品质密切相关。通过基于RNA测序数据和脂肪沉积相关性状的表型数据构建基因共表达网络,从而挖掘影响猪脂肪沉积的关键候选基因,探讨猪脂肪沉积的潜在调控机制。【方法】 对28头杜洛克猪的背最长肌样本进行RNA测序,同时测定并计算了背膘厚、肥肉率、肌内脂肪(intramuscular fat, IMF)含量、身体质量指数(body mass index, BMI)等多项与脂肪沉积密切相关性状的表型数据;在此基础上,利用R语言WGCNA软件包开展加权基因共表达网络分析(weighted gene co-expression network analysis, WGCNA),从与脂肪沉积相关的共表达模块中筛选影响脂肪沉积的关键基因。【结果】 通过WGCNA分析,共鉴别到28个基因共表达模块,其中Cyan模块和Purple模块与至少2个脂肪沉积相关性状呈显著相关(|相关系数|>0.3,显著性值>0.25)。这2个模块内基因功能富集分析结果显示,Cyan模块内的基因显著富集在脂肪酸生物合成(矫正后P = 3.48×10-2)、鞘糖脂生物合成(矫正后P = 4.40×10-2)等与脂肪沉积相关的通路中;但Purple模块基因未显著富集在任何与脂肪沉积相关的通路和GO项中(矫正后P >0.05)。另外,基于模块内连接性大于2、基因表达量与模块特征值的相关系数绝对值大于0.8、基因表达量与至少两个脂肪沉积相关表型的相关系数绝对值大于0.3的筛选标准,在与脂肪沉积相关模块内的92个基因中共鉴别到24个核心基因;其中,核心基因BET1LNAGLUB3GALT4TMEM115的表达量与背膘厚、肥肉率、IMF含量和BMI等的相关系数均大于0.3,且基因功能注释结果发现这些基因的功能与脂肪沉积密切相关,表明这些基因可能在脂肪形成过程中发挥着重要作用。【结论】 本研究在杜洛克猪中通过WGCNA鉴别到1个与脂肪沉积相关的关键模块,并在该模块中筛选出BET1LNAGLUB3GALT4TMEM115等影响脂肪沉积的潜在候选基因。这些发现不仅加深了对猪脂肪沉积遗传因素的认识,也为进一步探讨猪脂肪沉积的潜在调控机制奠定了坚实的理论基础。

关键词: 猪, 脂肪沉积, WGCNA, RNA测序

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.

Key words: pig, fat deposition, WGCNA, RNA sequencing