Comparative Analysis for Genetic Characterization in Korean Native Jeju Horse.
Abstract: The Jeju horse is a native Korean species that has been breeding on Jeju Island since the 13th century. Their shape has a distinct appearance from the representative species, Thoroughbred. Here, we performed a comparison of the Jeju horse and Thoroughbred horse for the identification of genome-wide structure variation by using the next-generation sequencing (NGS) technique. We generated an average of 95.59 Gb of the DNA sequence, resulting in an average of 33.74 X sequence coverage from five Jeju horses. In addition, reads obtained from WGRS data almost covered the horse reference genome (mapped reads 98.4%). Based on our results, we identified 1,244,064 single nucleotide polymorphisms (SNPs), 113,498 genomic insertions, and 114,751 deletions through bioinformatics analysis. Interestingly, the results of the WGRS comparison indicated that the eqCD1a6 gene contains signatures of positive natural selection in Jeju horses. The eqCD1a6 gene is known to be involved in immunity. The eqCD1a6 gene of Jeju horses commonly contained 296 variants (275 SNPs and 21 INDELs) that were compared with its counterpart of two Thoroughbred horses. In addition, we used LOAA, digital PCR, to confirm the possibility of developing a molecular marker for species identification using variant sites. As a result, it was possible to confirm the result of the molecular marker with high accuracy. Nevertheless, eqCD1a6 was shown to be functionally intact. Taken together, we have found significant genomic variation in these two different horse species.
Publication Date: 2021-06-28 PubMed ID: 34203473PubMed Central: PMC8300358DOI: 10.3390/ani11071924Google Scholar: Lookup
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Summary
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This research compared the genetic structures of Korean Jeju horses and Thoroughbreds using advanced genomic sequencing techniques, and identified considerable genetic variations specially in a certain immunity-related gene,eqCD1a6.
Overview
- Scientists conducted a genetic study of the Korean Jeju horse, one that’s native to Jeju Island and different from the standard Thoroughbred horse.
- They used a technique known as next-generation sequencing (NGS) for their comparison, which helped to identify genome-wide structural variations between the two horse breeds.
Methodology
- The researchers obtained a substantial amount of DNA sequence data from five Jeju horses, providing a comprehensive genome coverage.
- The data was then compared with the horse reference genome, with 98.4% of the reads mapping correctly.
Findings
- The results of the research showed over a million single nucleotide polymorphisms (SNPs), which are variations in a single nucleotide that occurs at a specific position in the genome.
- In addition, more than 100,000 genomic insertions and deletions were identified.
- An interesting discovery was the presence of signatures of positive natural selection in a gene known as eqCD1a6 in Jeju horses. This gene plays a crucial role in immunity.
- The eqCD1a6 gene found in Jeju horses contained 296 variants when compared to its counterpart in two Thoroughbred horses.
Confirmation and implications
- To confirm these findings, the researchers utilized digital PCR and a loss of function assay, also known as LOAA.
- These techniques confirmed the potential for creating a molecular marker for species identification using variant sites.
- However, despite the variations, the gene eqCD1a6 was still found to be functionally intact.
- The findings underscore the significant genomic variation between the Korean Jeju horse and the standard Thoroughbred horse. This offers insights into the evolution and breeding history of these species and provides potential markers for future research and species identification.
Cite This Article
APA
Lee W, Mun S, Choi SY, Oh DY, Park YS, Han K.
(2021).
Comparative Analysis for Genetic Characterization in Korean Native Jeju Horse.
Animals (Basel), 11(7), 1924.
https://doi.org/10.3390/ani11071924 Publication
Researcher Affiliations
- Center for Bio-Medical Engineering Core Facility, Dankook University, Cheonan 31116, Korea.
- Center for Bio-Medical Engineering Core Facility, Dankook University, Cheonan 31116, Korea.
- Department of Nanobiomedical Science & BK21 PLUS NBM Global Research Center for Regenerative Medicine, Dankook University, Cheonan 31116, Korea.
- Department of Pathology, Colleage of Medicine, Chungnam National University, Daejeon 34134, Korea.
- Livestock Research Institute, Gyeongsangbuk-Do, Yeongju 36052, Korea.
- Department of Equine Industry, Korea National College of Agriculture and Fisheries, Jeonju 54874, Korea.
- Center for Bio-Medical Engineering Core Facility, Dankook University, Cheonan 31116, Korea.
- Department of Microbiology, College of Science and Technology, Dankook University, Cheonan 31116, Korea.
Conflict of Interest Statement
The authors declare no conflict of interest.
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