Integrated RNA-seq and ATAC-seq analyses reveal muscle development differences between european meat pigeon and shiqi pigeon during embryonic to post-hatching stages.

Poultry muscle growth and development critically depend on skeletal muscle formation during embryonic and hatching stages. However, early embryonic muscle development differences between pigeon breeds remain unclear. We used European meat pigeons and Shiqi pigeons, which differ in body size, as models. Pectoral muscles from both breeds were subjected to ATAC-seq and RNA-seq at embryonic day 14 (E14) and post-hatching day 1 (P1). At P1, Shiqi pigeons had a significantly greater proportion of myofibers with 1-50 μm diameters, higher myofiber density, and a predominant 50-100 μm distribution across developmental stages compared to European meat pigeons. Integrated ATAC-seq and RNA-seq analyses revealed developmental dynamics driven by muscle contraction, cardiac regulatory pathways, and PI3K-Akt/muscle remodeling signaling, as well as breed differences in chromosomal structure/cell cycle regulation, cancer-related pathways, metabolic homeostasis, and calcium/estrogen signaling. Furthermore, 62 chromatin accessibility-gene expression co-varying DEGs (59 upregulated) were enriched in insulin receptor binding and AMPK/cGMP-PKG pathways; key genes including Sln, MYOM2, Trim63, Fabp3, ATP1A2, KLF15, IRS2, and RYR3 showed RT-qPCR expression highly consistent with RNA-seq (r ≥ 0.8181). This study found that the number of pectoral myofibers in Shiqi pigeons was significantly greater than in European meat pigeons at P1. Chromatin accessibility was higher near the transcription start site than in other regions. Integrating proximal, distal, and transcriptomic data, key candidate genes were screened and validated. Subsequently, genes differentially expressed between breeds were validated by tissue expression profiling, and Sln was selected for functional study. Cellular and quantitative experiments showed that Sln positively regulates pigeon embryonic myoblast proliferation and differentiation by upregulating Myf5 during proliferation and Myog and MyH1 during differentiation. Western blot confirmed higher MyoD and MyHC protein levels in Sln-overexpressing versus knockdown groups. This study revealed significant differences in pectoral myofiber diameter, embryonic chromatin structure, and gene expression between Shiqi and European meat pigeons, providing molecular insights into divergent muscle growth and development. The findings provide a theoretical basis for understanding growth performance differences among pigeon breeds and a foundation for molecular marker-assisted breeding.