Transcriptional profiles of skeletal muscles from 11 different anatomical locations in broiler chickens

Chickens ( Gallus gallus domesticus ), one of the most abundant domesticated animals worldwide, are a major source of high-quality protein from their skeletal muscle. The growth and development of skeletal muscle directly determine the meat quality and yield in poultry. Although skeletal muscle exhibit distinct functional specialization across anatomical locations, the transcriptional mechanisms underlying this diversity, especially the postnatal stages of muscle homeostasis maintenance, remain largely unexplored in broilers. Here, to characterize transcriptional regulatory diversity of chicken skeletal muscles, we performed transcriptomic profiling on 55 skeletal muscle samples from 11 anatomical sites of white feather broiler chickens at two specific growth points 61-week-old and 80-week-old of age. Our finding revealed that the expression patterns of HOX gene family were strongly associated with anatomical regions (head, trunk, limbs), confirming region-specific developmental regulation, although the expression profiles of global PCG was mostly indistinguishable among different skeletal muscles. MYH1E and MYH7B were identified as candidate marker for fast-twitch and slow-twitch muscle in chicken, respectively. The MYH1E -correlated genes were enriched in glycolytic pathways, while the MYH7B -correlated genes were involved in oxidative metabolism. Additionally, TPM3 , TNNT1 , TNNI1 , TNNC1 , MYL3 , and MYL10 may serve as potential indicators of slow-twitch muscle in chicken. Collectively, our findings provided a transcriptional atlas of chicken skeletal muscle that substantially supplementing current knowledge of its molecular diversity across anatomical locations and age stages, offering direct insights into muscle specialization and age-related regulation for poultry breeding and meat production. • The transcriptional profiling of chicken skeletal muscles showed greater similarity within anatomical sites than between growth time points. • Distinct pathway enrichment in different anatomical muscles suggested site-specific regulatory mechanisms. • MYH1E as a candidate marker for fast-twitch muscles, and MYH7B , TPM3 , TNNT1 , TNNI1 , TNNC1 , MYL3 , and MYL10 as potential indicators for slow-twitch muscles in chickens.