Transcriptome and co-expression network analysis identified candidate genes for intramuscular fat deposition in chickens.

1. The following study investigated the regulation of Intramuscular fat (IMF) deposition at different developmental stages in Jingyuan chickens. Pectoral muscles from hens at 42, 126 and 180 days of age were analysed using transcriptome sequencing and weighted gene co‑expression network analysis (WGCNA).2. A total of 1187, 1377 and 617 differentially expressed genes (DEGs) were identified in the three pairwise comparisons, respectively. Among these, MAPK8, ACSL4 and ACACB are known to be involved in IMF synthesis and metabolism through energy and amino acid metabolic pathways.3. The WGCNA data identified three modules (MEyellow, MEbrown, MEdarkred) that were significantly correlated with IMF content and age (p < 0.05). Functional analysis indicated that FOXO6, PTEN and EGFR were enriched in both FoxO and GnRH signalling pathways. This suggested potential roles in IMF deposition. Further investigation of DEG and the three modules revealed AGXT2 and LAMB1 as candidate genes that could influence IMF deposition in muscle.4. The data represents a transcriptomic resource for IMF deposition in Jingyuan chicken breast muscle. The results identified candidate genes for future molecular breeding aimed at improving meat quality.