Intramuscular fat (IMF) is an important indicator for determining meat quality, and IMF deposition during muscle development is regulated by a complex molecular network involving multiple genes. The N⁶-methyladenosine (m⁶A) modification of mRNA plays an important regulatory role in muscle adipogenesis. However, the distribution of m⁶A and its role in IMF metabolism in poultry has not been reported. In the present study, a transcriptome-wide m⁶A profile was constructed using methylated RNA immunoprecipitation sequence (MeRIP-seq) and RNA sequence (RNA-seq) to explore the potential mechanism of regulating IMF deposition in the breast muscle based on the comparative analysis of IMF differences in the breast muscles of 42 (group G), 126 (group S), and 180-days old (group M) Jingyuan chickens. The findings revealed that the IMF content in the breast muscle increased significantly with the increase in the growth days of the Jingyuan chickens (P < 0.05). The m⁶A peak in the breast muscles of the 3 groups was highly enriched in the coding sequence (CDS) and 3' untranslated regions (3' UTR), which corresponded to the consensus motif RRACH. Moreover, we identified 129, 103, and 162 differentially methylated genes (DMGs) in the breast muscle samples of the G, S, and M groups, respectively. Functional enrichment analyses revealed that DMGs are involved in many physiological activities of muscle fat anabolism. The m⁶A-induced ferroptosis pathway was identified in breast muscle tissue as a new target for regulating IMF metabolism. In addition, association analysis demonstrated that LMOD2 and its multiple m⁶A negatively regulated DMGs are potential regulators of IMF differential deposition in muscle. The findings of the present study provide a solid foundation for further investigation into the potential role of m⁶A modification in regulating chicken fat metabolism.

The inosine monophosphate (IMP) content in chicken meat is closely related to muscle quality and is an important factor affecting meat flavor. However, the molecular regulatory mechanisms underlying the IMP-specific deposition in muscle remain unclear. This study performed transcriptome analysis of muscle tissues from different parts, feeding methods, sexes, and breeds of 180-day-old Jingyuan chickens, combined with differential expression and weighted gene co-expression network analysis (WGCNA), to identify the functional genes that regulate IMP deposition. Out of the four comparison groups, 1,775, 409, 102, and 60 differentially expressed genes (DEGs) were identified, of which PDHA2, ACSS2, PGAM1, GAPDH, PGM1, GPI, and TPI1 may be involved in the anabolic process of muscle IMP in the form of energy metabolism or amino acid metabolism. WGCNA identified 11 biofunctional modules associated with IMP deposition. The brown, midnight blue, red, and yellow modules were strongly correlated with IMP and cooking loss (p < 0.05). Functional enrichment analysis showed that glycolysis/gluconeogenesis, arginine and proline metabolism, and pyruvate metabolism, regulated by PYCR1, SMOX, and ACSS2, were necessary for muscle IMP-specific deposition. In addition, combined analyses of DEGs and four WGCNA modules identified TGIF1 and THBS1 as potential candidate genes affecting IMP deposition in muscle. This study explored the functional genes that regulate muscle development and IMP synthesis from multiple perspectives, providing an important theoretical basis for improving the meat quality and molecular breeding of Jingyuan chickens.

Intramuscular fat (IMF) has a pivotal influence on meat quality, with its deposition being a multifaceted physiological interaction of several regulatory factors. N6-methyladenosine (m⁶A), the preeminent epigenetic alteration among eukaryotic RNA modifications, holds a crucial role in moderating post-transcriptional gene expression. However, there is a dearth of comprehensive understanding regarding the functional machinery of m⁶A modification in the context of IMF deposition in poultry. Our current study entails an analysis of the disparities in IMF within the breast and leg of 180-day-old Jingyuan chickens. We implemented methylated RNA immunoprecipitation sequencing (MeRIP-seq) and RNA sequencing (RNA-seq) to delve into the distribution of m⁶A and its putative regulatory frameworks on IMF deposition in chickens. The findings demonstrated a markedly higher IMF content in leg relative to breast (P < 0.01). Furthermore, the expression of METTL14, WTAP, FTO, and ALKBH5 was significantly diminished in comparison to that of breast (P < 0.01). The m6A peaks in the breast and leg primarily populated 3'untranslated regions (3'UTR) and coding sequence (CDS) regions. The leg, when juxtaposed with the breast, manifested 176 differentially methylated genes (DMGs), including 151 hyper-methylated DMGs and 25 hypo-methylated DMGs. The Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed a pronounced enrichment of DMGs in the biosynthesis of amino acids, peroxisome, Fatty acid biosynthesis, fatty acid elongation, and cell adhesion molecules (CAMs) pathways. Key DMGs, namely ECH1, BCAT1, and CYP1B1 were implicated in the regulation of muscle lipid anabolism. Our study offers substantial insight and forms a robust foundation for further exploration of the functional mechanisms of m⁶A modification in modulating IMF deposition. This holds profound theoretical importance for improving and leveraging meat quality in indigenous chicken breeds.

Jingyuan chickens are known for their unique meat flavor, but the molecular mechanisms underlying the dynamic changes in meat quality at different developmental stages remain unclear. In this study, we systematically measured the meat quality indicators of 42-, 126- and 180-day-old Jingyuan chickens, and integrated transcriptomic and metabolomic data using weighted gene co-expression network analysis (WGCNA) to identify key regulators of meat quality. The results showed that the growth and slaughter performance of 126- and 180-day-old chickens were significantly better than those of 42-day-old chickens (P < 0.05), but the slaughter rate and half-eviscerated rate of 42-day-old chickens were higher. With increasing age, the crude protein, drip loss, and crude ash content of the breast muscle increased significantly, while the water content decreased significantly (P < 0.05). WGCNA analysis revealed that in the 42- and 126-day-old groups, the greenyellow and blue modules were significantly positively correlated with meat quality indicators (P < 0.01), and their hub genes were significantly enriched in the PI3K - Akt signaling pathway, glycolysis/gluconeogenesis, fatty acid metabolism, and biosynthesis of amino acids. In the 42- and 180-day-old groups, the pink and brown modules were positively correlated with meat quality indicators(P < 0.01), and the hub genes were enriched in the MAPK signaling pathway, AMPK signaling pathway, and FoxO signaling pathway. In the 126- and 180-day-old groups, the magenta module was positively correlated with meat quality indicators (P < 0.01), and the hub genes were enriched in the MAPK signaling pathway, Wnt signaling pathway, glutathione metabolism, and GnRH signaling pathway. Metabolome data analysis showed that in the 42 - and 126 - day - old groups, the darkgrey, steelblue, sienna3, and blue modules were significantly positively correlated with meat quality indicators (P < 0.05), and their characteristic metabolites were significantly enriched in histidine metabolism, primary bile acid biosynthesis, and bile secretion. In the 42 - and 180 - day - old groups, the magenta and cyan modules were highly positively correlated with meat quality indicators (P < 0.05), and their metabolites were enriched in sphingolipid metabolism, vitamin B6 metabolism, thermogenesis, and purine metabolism. In the 126 - and 180 - day - old groups, the cyan module was highly significantly positively correlated with meat quality indicators (P < 0.05), with characteristic metabolites enriched in oxidative phosphorylation, nicotinate and nicotinamide metabolism, vitamin digestion and absorption, and the AMPK signaling pathway. Finally, eight key genes closely related to meat quality (SNORD14, IL7, HACD4, BFSP1, BCL6, FAM13A, ANKRD2, and AGXT2) and five key metabolites (p - Cresol sulfate, 2 - Piperidinone, 4 - Hydroxyquinoline, Succinic acid, and Dihydroxyacetone phosphate) were screened and identified. This study uncovers the age-dependent mechanisms regulating Jingyuan chicken meat quality. This study provides valuable insights into the genetic regulation of meat quality in Jingyuan chickens, which may inform breeding programs aiming to improve poultry meat quality.