Breeding ornamental white sika deer is a new notion that can be used to broaden the sika deer industry However, it is very rare for other coat phenotypes to occur, especially white (apart from albinism), due to the genetic stability and homogeneity of its coat color phenotype, making it difficult to breed white sika deer between species. We found a white sika deer and sequenced its whole genome. Then, the clean data obtained were analyzed on the basis of gene frequency, and a cluster of coat color candidate genes containing 92 coat color genes, one SV (structure variation), and five nonsynonymous SNPs (single nucleotide polymorphisms) was located. We also discovered a lack of melanocytes in the skin tissue of the white sika deer through histological examination, initially proving that the white phenotype of sika deer is caused by a 10.099 kb fragment deletion of the SCF gene(stem cell factor). By designing SCF-specific primers to detect genotypes of family members of the white sika deer, and then combining them with their phenotypes, we found that the genotype of the white sika deer is SCF⁷⁸⁹/SCF⁷⁸⁹, whereas that of individuals with white patches on their faces is SCF⁷⁸⁹/SCF^1–9. All these results showed that the SCF gene plays an important role in the development of melanocytes in sika deer and is responsible for the appearance of the white coat color. This study reveals the genetic mechanism of the white coat color in sika deer and supplies data as a reference for breeding white ornamental sika deer.

Although Cervus elaphus (Linnaeus, 1758) has been well studied, the subspecific taxonomy of Cervus canadensis populations in Qinghai and Gansu, China, is still controversial, and the mitochondrial characteristics of Cervus elaphus (Linnaeus, 1758) remain incompletely understood. We assembled 89 mitogenomes of C. canadensis from five geographical populations across Qinghai and Gansu. Phylogenetic analysis confirmed that the 89 individuals are taxonomically classified as C. c. kansuensis. Nucleotide compositions showed a higher abundance of adenine and cytosine compared to guanine and thymine in both complete mitogenomes and mitochondrial PCGs. Codon usage analysis revealed a strong preference towards A-ending codons (68.04% of over-represented codons, RSCU > 1.6) in mitochondrial PCGs, with systemic avoidance of G-ending codons (53.30% of unused codons, RSCU = 0). The CAMs of 13 PCGs are reported for the first time. Furthermore, the ENC plot showed that the codon usage of all PCGs was biased except for gene ATP8. The PR2 bias plot showed that gene ND6 exhibited bias towards T3 and G3, whereas the other genes preferred A3 and C3. Both the ENC-plot and PR2 bias plot suggested that natural selection played an important role in the forces driving codon usage bias in mitochondrial PCGs. Our results demonstrate the subspecific status of C. canadensis distributed in Qinghai and Gansu as C. c. kansuensis, and provide insights into the mitochondrial characteristics of C. c. kansuensis. The mitogenome sequences assembled in this study provide valuable data for further understanding of the Cervus elaphus (Linnaeus, 1758) mitogenome.

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.