Fatty acid composition and gene regulatory network analysis of pectoral muscle in pigeons across developmental stages

Fatty acid composition is crucial for determining meat quality. Pigeon meat, renowned for its tender texture, high protein content, and abundant polyunsaturated fatty acid (PUFAs), yet the developmental dynamics and molecular mechanisms of intramuscular fatty acid deposition remain unclear. Previous studies suggest that lipid metabolism is often governed by coordinated gene expression programs. Therefore, we hypothesized that fatty acid profiles in pigeon muscle are regulated by gene co-expression modules identifiable via weighted gene co-expression network analysis (WGCNA). To test this, we analyzed pectoral muscles from pigeons at five developmental stages (28 days to 48 months) using gas chromatography–mass spectrometry (GC–MS) and transcriptomic sequencing. A total of 39 fatty acids were identified, with key PUFAs such as DHA increasing and EPA decreasing over time, while overall MUFAs declined and PUFAs peaked at 6 months, revealing distinct stage-dependent patterns in fatty acid composition. WGCNA revealed that three gene modules (green, yellow, turquoise) were significantly associated with fatty acid traits. GO Enrichment analysis indicated their involvement in ribosome activity, mitochondrial pathways, and unsaturated fatty acid biosynthesis, while KEGG pathway highlighted oxidative phosphorylation and phosphatidylinositol signaling. Protein-protein interaction (PPI) analysis pinpointed hub genes, including RPS16, NDUFS6, RHOJ, and NUDT12 as key regulators of fatty acid metabolism. This study provides the first co-expression network linking fatty acid composition with transcriptional regulation in pigeons, broadening WGCNA application in avian lipid metabolism. The findings offer new insights into gene networks underlying lipid deposition and suggest targets for improving meat quality through molecular breeding.