Single- and Multi-Trait GWASs Combined with Genetic Parameter Estimation Reveal Candidate Genes for Body Conformation Traits in Sika Deer (Cervus nippon)

Both the productive efficiency and physical health of sika deer are strongly linked to their body conformation phenotypes. Breeding sika deer with excellent growth traits using molecular breeding technologies has become essential. Phenotypic data of 12 body conformation traits were measured for 613 sika deer across three age groups, including body traits and cephalic traits. Genetic typing was performed using the Sika Deer 100K SNP Liquid Chip, and genetic parameters were estimated through animal models to obtain the heritability and genetic correlation of traits within each age group. Single-trait and multi-trait GWASs were conducted, using GEMMA software to identify gene variants significantly associated with sika deer body conformation traits. Most of the 12 body conformation traits exhibited moderate to high heritability. The single-trait GWAS identified 49 SNPs (38 candidate genes), while multi-trait GWAS detected 134 SNPs (80 candidate genes), including 114 novel loci. A total of 163 SNPs and 196 candidate genes were identified, with 17 genes detected by both methods. These genes may be involved in pain perception, cell cycle regulation, immune response, and protein ubiquitination. Two significant KEGG pathways were enriched: steroid hormone biosynthesis and drug metabolism–cytochrome P450. Collectively, these detected loci and genes may serve as potential genetic resources for marker-assisted breeding, contributing to subsequent genetic improvement of body conformation in sika deer.