Previous investigations of phylogeny in Cervus recovered many clades without whole genomic support. In this study, the genetic diversity and phylogeny of 5 species (21 subspecies/populations from C. unicolor, C. albirostris, C. nippon, C. elaphus and C. eldii) in the genus Cervus were analyzed using reduced-representation genome sequencing. A total of 197,543 SNPs were identified with an average sequencing depth of 16 x. A total of 21 SNP matrices for each subspecies/population and 1 matrix for individual analysis were constructed, respectively. Nucleotide diversity and heterozygosity analysis showed that all 21 subspecies/populations had different degrees of genetic diversity. C. eldii, C. unicolor and C. albirostris showed relatively high expected and observed heterozygosity, while observed heterozygosity in C. nippon was the lowest, indicating there was a certain degree of inbreeding rate in these subspecies/populations. Phylogenetic ML tree of all Cervus based on the 21 SNP matrices showed 5 robustly supported clades that clearly separate C. eldii, C. unicolor, C. albirostris, C. elaphus and C. nippon. Within C. elaphus clade, 4 subclades were well differentiated and statistically highly supported: C. elaphus (New Zealand), C. e. yarkandensis, C. c. canadensis and the other grouping the rest of C. canadensis from China. In the C. nippon clade, 2 well-distinct subclades corresponding to C. n. aplodontus and other C. nippon populations were separated. Phylogenetic reconstruction indicated that the first evolutionary event of the genus Cervus occurred approximately 7.4 millions of years ago. The split between C. elaphus and C. nippon could be estimated at around 3.6 millions of years ago. Phylogenetic ML tree of all samples based on individual SNP matrices, together with geographic distribution, have shown that there were 3 major subclades of C. elaphus and C. canadensis in China, namely C. e. yarkandensis (distributed in Tarim Basin), C. c. macneilli/C. c. kansuensis/C. c. alashanicus (distributed in middle west of China), and C. c. songaricus/C. c. sibiricus (distributed in northwest of China). Among them, C. e. yarkandensis was molecularly the most primitive subclade, with a differentiation dating back to 0.8–2.2 Myr ago. D statistical analysis showed that there was high probability of interspecific gene exchange between C. albirostris and C. eldii, C. albirostris and C. unicolor, C. nippon and C. unicolor, and there might be 2 migration events among 5 species in the genus Cervus. Our results provided new insight to the genetic diversity and phylogeny of Cervus deer. In view of the current status of these populations, their conservation category will need to be reassessed.

Background: Ussuri raccoon dog is an important economic animal, which brings considerable economic benefits to Hebei, China. The high fertility rate of Ussuri raccoon dog is vital for its breeding industry. However, the molecular mechanism of prolificacy traits in raccoon dog remains unclear. Therefore, it is of great importance to identify the related genes and analyze the genetic mechanism of its high reproductive traits. Methods: In our study, RNA-seq was performed using ovarian tissues from six Ussuri raccoon dogs during estrus. The samples were divided into two groups based on the litter size over the last three consecutive years. We performed a standard transcriptomic analysis procedure to dig for differentially expressed genes (DEGs) and analyze gene function in detail. Result: Statistical analysis revealed a total of 612 DEGs between the low-fecundity and high-fecundity group including 277 upregulated and 335 downregulated DEGs, respectively. KEGG pathway analysis shows the DEGs enriched in several reproductive related pathways, such as the Circadian entrainment pathway. A total of 8 DEGs were identified with differential alternative splicing (DAS) events and recognized as DAS-DE genes. Among the up-regulated DAS-DE genes, ABCA6 and GPAM were found to be the most important genes regulating the prolificacy trait of Ussuri raccoon dog. The DEGs and DAS-DE genes identified in this study provide a probable genetic mechanism for improving prolificacy of Ussuri raccoon dog breeding.

Sika deer (Cervus nippon), a species mainly distributed in the northeast of Asia, hold significant economic value in China due to their contributions to traditional Chinese medicine. A systematic investigation of their genetic structure is needed for population management. In this study, mitochondrial genome and AMELY, DBY, USP9Y, and SRY gene fragments on Y chromosome were used to elucidate the genetic structure of 303 individuals across 8 distinct populations. The mitosome analysis identified 72 haplotypes, with a haplotype diversity (Hd) of 0.917 and nucleotide diversity (π) of 0.0143, respectively. Meanwhile, 13 haplotypes were defined by Y chromosome genes with a Hd of 0.791. Analysis of the mitochondrial control region (CR) revealed subspecies-specific patterns of tandem repeat unit organization between continental and Japanese groups. Y chromosome analyses demonstrated a homogeneous paternal lineage across Japanese populations.

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.