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

doi:10.3864/j.issn.0578-1752.2025.09.013

Abstract

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

WANG JiYing, LI JingXuan, WANG YanPing, GUO JianFeng, LIN HaiChao, ZHAO XueYan. Weighted Gene Co-Expression Network Analysis Reveals Potential Candidate Genes Affecting Fat Deposition in Pigs[J].Scientia Agricultura Sinica, 2025, 58(9): 1845-1855.

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Figures/Tables 6

Table 1

Fig. 1

Fig. 2

Fig. 3

Table 2

Hub genes affecting fat deposition in the Cyan module"

基因名称 Gene name	\|模块归属\| \|Module membership\|	连接性 Intra-modular connectivity	\|基因显著性值\| \|Gene significance\|, \|GS\|				基因功能 Gene function
基因名称 Gene name	\|模块归属\| \|Module membership\|	连接性 Intra-modular connectivity	背膘 Backfat thickness	肥肉率 Fat percentage	肌内脂肪 Intramuscular fat (IMF)	身体质量指数 Body mass index (BMI)	基因功能 Gene function
BET1L	0.91	5.61	0.34	0.46	0.32	0.34	促进高尔基囊泡膜的运输过程，具有可溶性N-乙基马来酰亚胺敏感因子附着蛋白受体（SNARE）活性 Promoting the transport of Golgi vesicles. Having a soluble N- ethylmaleimide-sensitive factor attachment protein receptor (SNARE) activity
NAGLU	0.84	4.14	0.47	0.44	0.30	0.35	参与硫酸乙酰肝素的代谢 Involved in the degradation of heparan sulfate
B3GALT4	0.84	3.94	0.45	0.48	0.34	0.38	参与GM1/GD1B/GA1神经节苷脂生物合成 Involved in GM1/GD1B/GA1 ganglioside biosynthesis
TMEM115	0.87	2.58	0.55	0.55	0.32	0.53	参与蛋白质从高尔基体向内质网的逆行运输 Involved in retrograde transport of proteins from the Golgi to the endoplasmic reticulum
SLC35A2	0.83	12.20	0.34	0.39	0.11	0.32	编码一种多通道膜蛋白，将半乳糖从胞浆中转运到高尔基体囊泡中，作为糖基供体用于生成糖基 This gene encodes a multi-pass membrane protein that transports UDP-galactose from the cytosol into Golgi vesicles, where it serves as a glycosyl donor for the generation of glycans
ENSSSCG00000038852	0.94	7.08	0.48	0.57	0.16	0.40
FRMD8	0.88	5.10	0.45	0.43	0.20	0.33	参与正向调节肿瘤坏死因子的产生 Involved in positive regulation of tumor necrosis factor production
SPPL2B	0.89	4.80	0.49	0.54	0.21	0.35	天冬氨酸蛋白酶GXGD家族的一个成员，触发固有和适应性免疫途径中细胞因子的表达 This gene encodes a member of the GXGD family of aspartic proteases, which triggers cytokine expression in the innate and adaptive immunity pathways
EXOSC6	0.93	3.74	0.43	0.42	0.17	0.44	编码外泌体复合物中一个亚基，参与多种细胞RNA加工和降解事件 This gene product constitutes one of the subunits of exosome. It is involved in a multitude of cellular RNA processing and degradation events
INTS5	0.85	3.47	0.30	0.41	0.54	0.26	编码整合因子复合体的亚基，参与mRNA合成调控和snRNA加工 This gene encodes a subunit of the Integrator complex. It is involved in the regulation of mRNA synthesis and snRNA processing
SURF6	0.81	3.40	0.32	0.38	0.16	0.33	编码具有核酸结合特性的一种核酸基质蛋白 This gene encodes a protein which may function as a nucleolar- matrix protein with nucleic acid-binding properties
MCM7	0.83	3.23	0.29	0.33	0.42	0.36	编码一种小染色体维持蛋白，对启动真核生物基因组复制至关重要 The protein encoded by this gene is a mini-chromosome maintenance protein (MCM) that is essential for the initiation of eukaryotic genome replication
RIOX1	0.82	2.51	0.39	0.39	0.10	0.37	编码一种加氧酶，可作为组蛋白赖氨酸去甲基化酶和核糖体组氨酸羟化酶 This gene encodes one kind of oxygenase, which can act as both a histone lysine demethylase and a ribosomal histidine hydroxylase
ENSSSCG00000034092	0.90	2.29	0.51	0.50	0.17	0.47
GPATCH3	0.80	2.14	0.28	0.39	0.35	0.37	参与转录调控 Involved in transcriptional regulation
FBXL12	0.84	3.65	0.42	0.53	0.23	0.26	F-box蛋白家族成员，作为蛋白质泛素连接酶 This gene encodes a member of the F-box protein family, which acts as a protein-ubiquitin ligase
COG8	0.82	3.41	0.22	0.34	0.15	0.34	高尔基寡聚体复合物 This gene encodes a protein that is a component of the conserved oligomeric Golgi (COG) complex
ENSSSCG00000040236	0.84	2.26	0.41	0.48	0.06	0.26

Table 2

Fig. 4

References 43

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	背膘厚 Backfat thickness (mm)	肥肉率 Fat percentage (%)	肌内脂肪含量 Intramuscular fat (IMF) content (%)	身体质量指数 Body mass index (BMI)
平均值 Mean	16.26	15.61	2.36	84.96
标准差 Standard deviation	4.49	3.11	0.71	6.00
变异系数 Coefficient of variation (%)	27.71	20.13	29.75	6.42
最大值 Maximum	24.30	22.80	4.23	95.43
最小值 Minimum	7.60	10.60	1.17	74.49

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

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