Comparative Analysis for Genetic Characterization in Korean Native Jeju Horse.
Authors: Lee Wooseok, Mun Seyoung, Choi Song-Yi, Oh Dong-Yep, Park Yong-Soo, Han Kyudong
Journal: Animals : an open access journal from MDPI
Summary
# Editorial Summary: Genetic Characterization of Jeju Horses Researchers performed whole-genome resequencing on five Jeju horses—a native Korean breed maintained on Jeju Island since the 13th century—and compared their genetic structure to Thoroughbreds using next-generation sequencing, achieving 33.74× coverage depth and mapping 98.4% of reads to the equine reference genome. The analysis identified over 1.2 million single nucleotide polymorphisms, alongside 113,498 insertions and 114,751 deletions, revealing substantial genomic divergence between the two breeds. Notably, the eqCD1a6 gene—which governs immune function—showed signatures of positive natural selection in Jeju horses and harboured 296 variants (275 SNPs and 21 indels) not present in Thoroughbreds, though the gene remained functionally intact. The researchers validated these findings using digital PCR and confirmed the potential to develop breed-specific molecular markers for accurate species identification based on variant sites. These results establish a foundational genomic profile for Jeju horses and suggest practical applications in breed verification and understanding adaptation-related genetic differences, which may prove particularly relevant for practitioners involved in breeding programmes, parentage verification, or managing this genetically distinct population.
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Practical Takeaways
- •Genomic markers for Jeju horse breed identification are now available and validated, enabling accurate genetic authentication of this native Korean breed
- •The eqCD1a6 gene's role in immunity and positive selection history may inform breeding decisions for disease resistance traits in Jeju horses
- •This genetic characterization provides a foundation for understanding breed-specific traits and potential performance or health differences between Jeju and Thoroughbred horses
Key Findings
- •Whole genome sequencing of 5 Jeju horses identified 1,244,064 SNPs, 113,498 insertions, and 114,751 deletions compared to Thoroughbreds
- •The eqCD1a6 gene showed signatures of positive natural selection in Jeju horses and contains 296 variants (275 SNPs and 21 INDELs) relative to Thoroughbreds
- •eqCD1a6 gene is involved in immunity and remains functionally intact despite carrying multiple variants
- •Digital PCR validation confirmed the potential for developing molecular markers for horse breed identification using identified variant sites