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

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.

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.

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.

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.

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.