Genome-Wide Characterization of BMP/GDF Genes in Sika Deer: Spatiotemporal Expression During Antler Regeneration and Computational Analysis of the BMP2–BMPR1A Complex

Antler regeneration involves rapid chondrogenesis and ossification, yet the bone morphogenetic protein/growth differentiation factor (BMP/GDF) genes associated with skeletal development remain poorly characterized in sika deer. We identified 16 BMP genes and two GDF genes belonging to seven phylogenetic subfamilies. Synteny analysis identified segmental and putative tandem duplications; two duplicated pairs had K_a/K_s ratios below 1. RNA-seq data showed differences across regenerative stages, with BMP3B and BMP5 expressed during early regeneration, BMP2, BMP4, and BMP6 during rapid growth, and BMP7 and BMP3 during terminal ossification. RT-qPCR supported distinct spatial expression patterns for five genes in rapidly growing antler tips. AlphaFold 3 modeling and molecular dynamics simulations indicated that the predicted BMP2–BMPR1A complex remained stable over the simulated trajectories. Free-energy decomposition and alanine scanning identified candidate interface residues. Sequence comparisons showed that these residues are conserved across the mammalian species examined. The results describe BMP/GDF family organization and expression during antler regeneration and identify candidate contacts for experimental analysis of BMP2–BMPR1A binding.