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

Area of Science:

• Genomics
• Animal Breeding

Background:

• Inter-species hybridization in cervids aims to enhance traits via hybrid vigor.
• Genomic underpinnings of cervid hybridization remain underexplored.

Purpose of the Study:

• To perform whole-genome analysis of Hua-Ma hybrid deer (sika deer x Tianshan red deer).
• To investigate genetic diversity and ancestry in hybrid cervids using genomic data.

Main Methods:

• Employed restriction-site-associated DNA sequencing (RAD-seq) for whole-genome analysis.
• Utilized strict filtering to obtain high-quality single nucleotide polymorphisms (SNPs).
• Performed principal component analysis (PCA) on independent SNPs after linkage disequilibrium pruning.

Main Results:

• Generated over 571,000 SNPs, with 427,000 high-quality SNPs from five individuals.
• Observed heterozygosity (Ho=0.2130) was lower than expected (He=0.3560), suggesting preliminary insights into genetic diversity.
• PCA indicated relative genomic clustering, reflecting mixed ancestry rather than definitive assignments.

Conclusions:

• Identified synonymous and nonsynonymous variants, including a potentially functional mutation near the BEND5 gene.
• Results suggest heterozygosity and mixed ancestry in Hua-Ma hybrids.
• Established an initial SNP resource for genomic selection, parentage analysis, and breeding optimization in cervids.