基于加权基因共表达网络分析挖掘影响静原鸡肉品质相关候选基因

doi:10.3864/j.issn.0578-1752.2026.13.017

Abstract

Abstract:

【Background】The Jingyuan chicken, a local chicken breed in Ningxia, boasts advantages such as delicious meat quality and unique flavor. However, it faces challenges including slow growth rates and uneven intramuscular fat deposition. Previous studies have shown that adding 0.6% fresh corn extract (FCE) to the diet could significantly improve the meat quality of Jingyuan chickens, but the key candidate genes through which FCE affected meat quality remained unclear. 【Objective】This research aimed to delve deeper into the key candidate genes influenced by FCE affecting meat quality in Jingyuan chickens, thereby providing a scientific basis for improving meat quality and optimizing meat chicken feeding strategies.【Method】 In earlier studies, 120 Jingyuan chickens at 135 days old (1.5±0.2 kg), raised under the same conditions, were divided into four groups. The control group was fed a basic diet, while the experimental groups received diets supplemented with 0.3%, 0.6%, and 0.9% FCE, respectively. After 45 days of feeding, the chickens reached 180 days old, at which point breast muscle was collected to assess meat quality, determining that the optimal addition amount was 0.6% FCE. Based on the outcomes of previous research, serum and breast muscle lipid factors were measured for the control and 0.6% FCE groups. Weighted Gene Co-expression Network Analysis (WGCNA) was utilized to conduct an in-depth analysis of the transcriptome sequencing data of breast muscle, uncovering key candidate genes significantly associated with meat quality.【Result】 The serum levels of triglycerides (TG) and very-low-density lipoproteins (VLDL) in the 0.6% FCE group were significantly higher than those in the control group (P<0.05). The TG, total cholesterol (TC), and high-density lipoproteins (HDL) in the breast muscle tissue of the 0.6% FCE group were also found to be significantly elevated (P<0.05). Through WGCNA analysis, a total of 19 co-expression modules were identified, with six target modules significantly associated with meat quality being selected: purple, midnight blue, light green, cyan, grey60, and salmon (|R²| ≥ 0.5, P<0.5). KEGG pathway enrichment analysis and Gene Ontology (GO) functional enrichment analysis of the hub genes within these modules revealed significant enrichment of the hub genes in the purple module in pathways, such as insulin signaling and mitochondrial autophagy; the midnight blue module hub genes were enriched in pyrimidine and purine metabolism; the light green module hub genes were associated with protein processing in the endoplasmic reticulum and MAPK signaling pathway; the cyan module hub genes mainly enriched pathways related to cell adhesion molecules and phagosome processes; the grey60 module hub genes were linked to vascular smooth muscle contraction and actin cytoskeleton regulation; and the salmon module hub genes enriched in MAPK signaling and p53 signaling pathways. Through comparative analyses of hub genes and differently expressed genes (DEGs), ten overlapping genes were identified. Protein interaction and functional enrichment analyses identified CLDN18, NKX2-1, and TRIB1 as key candidate genes influencing meat quality. 【Conclusion】 This study ultimately identified key candidate genes affecting meat quality, namely CLDN18, NKX2-1, and TRIB1. The findings provided a reference for understanding the molecular mechanisms by which FCE regulates meat quality and offered a new perspective for the improvement of meat quality in local chicken breeds.

Key words: Jingyuan chicken, fresh corn extract, meat quality, weighted gene co-expression network analysis, transcriptome

ZHAO Wei, TIAN JinLi, CHEN SiYu, YANG LiJuan, MA LiNa, ZHANG GuoJun, ZHANG Hu, HU WeiLong, YU HaiRong, ZHANG HaiBo, ZHANG Juan. Exploration of Candidate Genes Affecting Meat Quality of Jingyuan Chicken Based on Weighted Gene Co-expression Network Analysis[J].Scientia Agricultura Sinica, 2026, 59(13): 2975-2992.

Figures/Tables 9

Table 1

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Table 2

Pathway and functional analysis of key candidate genes"

基因名称 Gene name	类型 Type	KEGG通路 KEGG pathway	GO功能 GO function
AVR2	下调Down	—	胞外区域Extracellular region；生物素结合Biotin binding；生物素转运Biotin transport
NKX2-1	上调 Up	—	RNA聚合酶II对转录的负调控Negative regulation of transcription by RNA polymerase II；转录顺式调控区结合Transcription cis-regulatory region binding； RNA聚合酶II转录调控区序列特异性DNA结合RNA polymerase II transcription regulatory region sequence-specific DNA binding；RNA聚合酶II顺式调控区序列特异性DNA结合RNA polymerase II cis-regulatory region sequence-specific DNA binding；DNA结合转录因子活性DNA-binding transcription factor activity；RNA聚合酶II特异性RNA polymerase II-specific；内含子转录调控区序列特异性DNA结合Intronic transcription regulatory region sequence-specific DNA binding；神经元迁移Neuron migration；DNA结合DNA binding；DNA结合转录因子活性DNA-binding transcription factor activity；细胞核Nucleus；转录调控复合体Transcription regulator complex；DNA模板转录调控Regulation of DNA-templated transcription；RNA聚合酶II介导的转录调控Regulation of transcription by RNA polymerase II；磷脂代谢过程Phospholipid metabolic process；模式决定过程Pattern specification process；轴突引导Axon guidance；脑发育Brain development；内胚层发育Endoderm development；运动行为Locomotory behavior；激素反应Response to hormone；动物器官形态发生Animal organ morphogenesis；基因表达Gene expression；基因表达的正调控Positive regulation of gene expression；上皮-间质转化的负调控Negative regulation of epithelial to mesenchymal transition；酶结合Enzyme binding；大脑发育Telencephalon development；苍白球发育Globus pallidus development；海马体发育Hippocampus development；大脑皮质细胞迁移Cerebral cortex cell migration；前脑背腹模式形成Forebrain dorsal/ventral pattern formation；下丘脑发育Hypothalamus development；前脑神经元命运决定Forebrain neuron fate commitment；前脑神经元分化Forebrain neuron differentiation；大脑皮质γ-氨基丁酸能中间神经元分化Cerebral cortex GABAergic interneuron differentiation；大脑皮质神经元分化Cerebral cortex neuron differentiation；垂体发育Pituitary gland development；大脑皮质细胞迁移Telencephalon cell migration；肺发育Lung development；细胞迁移的负调控Negative regulation of cell migration；转化生长因子β受体信号通路的负调控Negative regulation of transforming growth factor beta receptor signaling pathway；甲状腺发育Thyroid gland development；前脑发育Forebrain development；发育诱导Developmental induction；睾丸间质干细胞分化Leydig cell differentiation；昼夜节律的正调控Positive regulation of circadian rhythm；序列特异性DNA结合Sequence-specific DNA binding；DNA模板转录的负调控Negative regulation of DNA-templated transcription；DNA模板转录的正调控Positive regulation of DNA-templated transcription；RNA聚合酶II介导的转录正调控Positive regulation of transcription by RNA polymerase II；参与形态发生过程的解剖结构形成Anatomical structure formation involved in morphogenesis；神经元命运决定Neuron fate commitment；少突胶质细胞分化Oligodendrocyte differentiation；肺囊泡发育Lung saccule development；上皮管分支在肺形态发生中的作用Epithelial tube branching involved in lung morphogenesis；支气管上皮细胞分化Club cell differentiation；Ⅱ型肺泡细胞分化Type II pneumocyte differentiation；RNA聚合酶Ⅱ特异性DNA结合转录因子结合RNA polymerase II-specific DNA-binding transcription factor binding；γ-氨基丁酸能神经元分化GABAergic neuron differentiation；中间神经元迁移Interneuron migration
CLDN18	上调 Up	细胞黏附分子Cell adhesion molecules；紧密连接Tight junction	蛋白质定位至细胞核Protein localization to nucleus；骨吸收的负调节Negative regulation of bone resorption；消化道发育Digestive tract development；TNFSF11介导的信号传导通路TNFSF11-mediated signaling pathway；蛋白质定位至细胞核的负调节Negative regulation of protein localization to nucleus；破骨细胞发育的负调节Negative regulation of osteoclast development
基因名称 Gene name	类型 Type	KEGG通路 KEGG pathway	GO功能 GO function
NKX2-8	上调Up	—	—
TRIB1	上调 Up	—	蛋白激酶活性Protein kinase activity；蛋白激酶抑制剂活性Protein kinase inhibitor activity；ATP结合ATP binding；细胞核Nucleus；细胞质Cytoplasm；蛋白质磷酸化Protein phosphorylation；蛋白激酶活性的负调控Negative regulation of protein kinase activity；JNK级联反应JNK cascade；平滑肌细胞迁移的负调控Negative regulation of smooth muscle cell migration；丝裂原活化蛋白激酶激酶结合Mitogen-activated protein kinase kinase binding；泛素蛋白连接酶结合Ubiquitin protein ligase binding；脂多糖介导信号通路的负调控Negative regulation of lipopolysaccharide- mediated signaling pathway；蛋白酶体泛素依赖性蛋白分解过程的正向调控Positive regulation of proteasomal ubiquitin-dependent protein catabolic process；脂多糖应答Response to lipopolysaccharide；MAP激酶活性的调控Regulation of MAP kinase activity；DNA结合转录因子活性的负向调控Negative regulation of DNA-binding transcription factor activity；嗜酸性粒细胞分化的正向调控Positive regulation of eosinophil differentiation；巨噬细胞分化的正向调控Positive regulation of macrophage differentiation；中性粒细胞分化的负向调控Negative regulation of neutrophil differentiation；平滑肌细胞增殖的负向调控Negative regulation of smooth muscle cell proliferation；泛素-蛋白转移酶调节活性Ubiquitin-protein transferase regulator activity；RNA聚合酶II特异性DNA结合转录因子结合RNA polymerase II-specific DNA-binding transcription factor binding
ENSGALG00010008091	上调up	—	—
MED13	上调Up	—	转录共调节因子活性Transcription coregulator activity；细胞核Nucleus；核质Nucleoplasm；介导复合物Mediator complex；胆固醇稳态Cholesterol homeostasis；DNA结合转录因子活性的负调控Negative regulation of DNA-binding transcription factor activity；DNA模板转录的正调控Positive regulation of DNA-templated transcription；RNA聚合酶II介导的转录正调控Positive regulation of transcription by RNA polymerase II；核内甲状腺激素受体结合Nuclear thyroid hormone receptor binding；甘油三酯稳态Triglyceride homeostasis
ABAT	上调Up	丙氨酸、天冬氨酸和谷氨酸代谢Alanine, aspartate and glutamate metabolism；缬氨酸、亮氨酸和异亮氨酸降解Valine, leucine and isoleucine degradation； β-丙氨酸代谢Beta-Alanine metabolism；丙酸代谢Propanoate metabolism；丁酸代谢Butanoate metabolism	催化活性Catalytic activity；4-氨基丁酸转氨酶活性4-aminobutyrate transaminase activity；线粒体Mitochondrion；转氨酶活性Transaminase activity；γ-氨基丁酸代谢过程Gamma-aminobutyric acid metabolic process；转移酶活性Transferase activity；吡哆醛磷酸结合Pyridoxal phosphate binding；4-氨基丁酸转氨酶复合物4-aminobutyrate transaminase complex；4-氨基丁酸：2-酮戊二酸转氨酶活性4-aminobutyrate:2-oxoglutarate transaminase activity；神经递质分解代谢过程Neurotransmitter catabolic process；同源蛋白结合Identical protein binding；(S)-3-氨基-2-甲基丙酸转氨酶活性(S)-3-amino-2-methylpropionate transaminase activity；对可卡因的行为反应Behavioral response to cocaine; behavioral response to cocaine
SYNM	上调Up	—	细胞骨架的结构组成部分Structural constituent of cytoskeleton；中间纤维Intermediate filament；肌肉的结构组成部分Structural constituent of muscle；膜Membrane；粘着蛋白结合Vinculin binding；中间纤维结合Intermediate filament binding；快缩型骨骼肌纤维收缩Fast-twitch skeletal muscle fiber contraction；肌膜Sarcolemma；肌膜骨膜复合体Costamere；中间纤维细胞骨架Intermediate filament cytoskeleton
ENSGALG00010026583	上调Up	—	—

Table 2

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日粮组成 Ration composition	含量 Content (%)	日粮组成 Ration composition	含量 Content (%)
配料 Ingredients		营养成分含量Nutritional levels
玉米 Corn	52.00	水分水分Moisture	13.00
豆粕 Soybean meal	26.00	粗蛋白crude protein (CP)	17.00
豆油Soybean oil	4.85	粗纤维Crude fibre (CF)	8.00
玉米蛋白粉Corn protein powder	6.00	粗灰分Crude Ash (Ash)	16.00
石粉Stone powder	8.00	总磷Total Phosphorus (TP)	0.50
磷酸氢钙 Calcium hydrogen phosphate (CaHPO₄)	1.30	钙Calcium (Ca)	3.00
食用盐Edible salt (NaCl)	0.65	食用盐Edible salt (NaCl)	0.65
赖氨酸Lysine (Lys)	0.84	赖氨酸Lysine (Lys)	0.84
蛋氨酸Methionine (Met)	0.36	蛋氨酸Methionine (Met)	0.36
总计Total	100.00

Exploration of Candidate Genes Affecting Meat Quality of Jingyuan Chicken Based on Weighted Gene Co-expression Network Analysis

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