Genome-Wide Identification of Candidate Genes Associated with Antler Weight in Tahe Red Deer

The Tahe red deer is derived from the wild Tarim red deer, an endemic subspecies native to the Tarim Basin in Xinjiang, China. It has recently received official approval as a locally bred deer variety, developed through artificial breeding programs. This breed retains several advantageous traits from its wild ancestors, including tolerance to coarse forage, drought resistance, and a high yield of velvet antlers. To investigate the genetic mechanisms underlying velvet antler production, phenotypic data for antler weight and blood samples were collected from 73 adult Tahe red deer. Whole-genome sequencing and genome-wide association analysis were performed to identify genetic variants associated with antler weight. Population genetic analysis revealed that the observed heterozygosity (Ho) and expected heterozygosity (He) were 0.31291 and 0.32832, respectively, while the nucleotide diversity (π) was 2.17 × 10^-3, indicating relatively high genetic diversity within the Tahe red deer population. Using a mixed linear model (MLM), a total of 189 candidate genes and 1387 significant SNP loci associated with antler weight were identified (p < 1.0 × 10^-5). Gene Ontology (GO) enrichment analysis revealed that these candidate genes are primarily involved in intracellular calcium ion homeostasis, peptide and protein biosynthesis, extracellular matrix organization, the regulation of glycolysis, and cytoskeleton-related processes, including actin filaments and microfibrils. These biological functions are closely related to cell proliferation, differentiation, energy metabolism, and tissue remodeling. The Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis further indicated that the candidate genes are significantly enriched in several pathways, including the Notch signaling pathway, the cGMP-PKG signaling pathway, the regulation of the actin cytoskeleton, ribosome biogenesis, and mucin type O-glycan biosynthesis. These results suggest that these genes may participate in velvet antler growth and development by regulating cell proliferation and differentiation, cytoskeletal remodeling, and protein synthesis. Overall, this study identifies SNP loci and candidate genes significantly associated with antler weight in Tahe red deer, providing a theoretical basis for genetic improvement and marker-assisted selection for velvet antler production in this breed.