Genome-Wide SNP Discovery and Preliminary Genomic Insights into Hua-Ma Hybrid Deer Using RAD Seq; An Exploratory Study

Background: Inter-species hybridization has been extensively used in breeding cervids to improve productive traits by hybrid vigor, but the genomic processes behind the process are not well studied. Methods: In this study, we investigated restriction-site-associated DNA sequencing (RAD-seq) to conduct a whole-genome analysis of Hua-Ma hybrid individuals (a cross of sika deer and Tianshan red deer). Results: A total of 571,835 SNPs were obtained and 427,121 high-quality SNPs were obtained from five individuals upon strict filtering. An analysis of genetic diversity has shown that the observed heterozygosity (Ho = 0.2130) was lower than expected heterozygosity (He = 0.3560). Although these estimates provide preliminary insights into the genetic diversity of the sampled Hua-Ma hybrids, they should be interpreted cautiously because of the limited sample size. After the pruning of linkage disequilibrium, 189,975 independent SNPs underwent principal component analysis (PCA). The first two principal components (PC1 = 32.6%, PC2 = 26.2%) indicate relative genomic clustering rather than definitive ancestry assignments. These patterns reflect relative genomic clustering rather than definitive ancestry assignments. Conclusions: The high polymorphic loci were functionally annotated and revealed the existence of synonymous and nonsynonymous variants, including a conserved locus adjacent to the BEND5 gene that exhibited a nonsynonymous mutation generating a valine-to-isoleucine amino acid substitution which may have potential functional relevance, although no phenotypic effects were evaluated in this study. On the whole, these results suggest heterozygosity and mixed ancestry in Hua-Ma hybrids. This exploratory study provides an initial SNP resource that may support future genomic selection, parentage analysis, and breeding optimization efforts.