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Genes & genomics2019; 41(6); 621-628; doi: 10.1007/s13258-019-00795-w

Whole genome sequencing analysis of horse populations inhabiting the Korean Peninsula and Przewalski’s horse.

Abstract: The Jeju horse is an indigenous horse breed in Korea. However, there is a severe lack of genomic studies on Korean horse breeds. The objective of this study was to report genomic characteristics of domestic horse populations that inhabit South Korea (Jeju, Jeju crossbred, and Thoroughbred) and a wild horse breed (Przewalski's horse). Using the equine reference genome assembly (EquCab 2.0), more than ~ 6.5 billion sequence reads were successfully mapped, which generated an average of 40.87-fold coverage throughout the genome. Using these data, we detected a total of 12.88 million SNPs, of which 73.7% were found to be novel. All the detected SNPs were deeply annotated to retrieve SNPs in gene regions using the RefSeq and Ensemble gene sets. Approximately 27% of the total SNPs were located within genes, whereas the remaining 73% were found in intergenic regions. Using 129,776 coding SNPs, we retrieved a total of 49,171 nonsynonymous SNPs in 12,351 genes. Furthermore, we identified a total of 10,770 deleterious nonsynonymous SNPs which are predicted to affect protein structure or function. We showed numerous genomic variants from domestic and wild horse breeds. These results provide a valuable resource for further studies on functions of SNP-containing genes, and can aid in determining the molecular basis underlying variation in economically important traits of horses.
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Publication Date: 2019-04-02 PubMed ID: 30941726DOI: 10.1007/s13258-019-00795-wGoogle Scholar: Lookup
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  • Non-U.S. Gov't

Summary

This research summary has been generated with artificial intelligence and may contain errors and omissions. Refer to the original study to confirm details provided. Submit correction.

The research article primarily focuses on genomic analysis of certain horse populations in South Korea, particularly the Jeju horse, and a wild horse breed known as Przewalski’s horse. The scientists carefully mapped billions of sequences reads and identified various genetic variants in these horses, providing valuable information for potential further studies on gene functionalities and economically important traits in horses.

Genomic Analysis of Horse Populations:

In an effort to understand the genomic characteristics of certain domestic horse populations in South Korea (including Jeju, Jeju crossbreds, and Thoroughbreds) and a wild horse breed (Przewalski’s horse), the researchers used the equine reference genome assembly.

  • Over 6.5 billion sequence reads were mapped, generating an average coverage of 40.87-fold throughout the genome. This deep sequencing and mapping of the equine genome offered a comprehensive view of the genetic make-up of these Korean horse populations as well as the Przewalski’s horse.

Identification and Annotation of SNPs:

The study detected a total of nearly 13 million Single Nucleotide Polymorphisms (SNPs) in the genomes analyzed. SNPs represent a variation in a single nucleotide and are the most frequent type of genetic variation in the genome.

  • A fraction of 73.7% of the detected SNPs were found to be novel, indicating new genetic variations not previously recorded.
  • Annotations were carried out to determine the specific locations of these SNPs. Approximately 27% of the SNPs were located within genes while the rest were found in the non-coding, intergenic regions of the genome.
  • By identifying SNPs in particular gene regions, further studies can explore the impact of these genetic variations on gene function, potentially shedding light on various biological processes and diseases.

Detection of Nonsynonymous and Deleterious SNPs:

The research further identified nonsynonymous and deleterious SNPs among the detected variations.

  • A total of 49,171 nonsynonymous SNPs in 12,351 genes were found out. These SNPs induce changes in the amino acid sequence of the encoded proteins, potentially affecting protein structure or function.
  • Also identified were 10,770 deleterious nonsynonymous SNPs. These variations are predicted to have a significant impact on the protein structure or function.
  • The identification of these potentially harmful SNPs can highlight potential genes of interest in future studies of genetic diseases or abnormalities in horses.

Potential Implications:

This study provides a plethora of genomic variations from domestic and wild horse breeds, enhancing the understanding of the genetic diversity present among these populations.

  • These results are a valuable resource for further functional studies on SNP-containing genes that can enhance the understanding of biology and disease development in horses.
  • This work will also contribute to determining the molecular basis for variation in essential traits in horses, thereby having potential economic implications.

Cite This Article

APA
Seong HS, Kim NY, Kim DC, Hwang NH, Son DH, Shin JS, Lee JH, Chung WH, Choi JW. (2019). Whole genome sequencing analysis of horse populations inhabiting the Korean Peninsula and Przewalski’s horse. Genes Genomics, 41(6), 621-628. https://doi.org/10.1007/s13258-019-00795-w

Publication

Genes & genomics
ISSN: 2092-9293
NlmUniqueID: 101481027
Country: Korea (South)
Language: English
Volume: 41
Issue: 6
Pages: 621-628

Researcher Affiliations

Seong, Ha-Seung
  • College of Animal Life Science, Kangwon National University, Chuncheon, 24341, Republic of Korea.
Kim, Nam-Young
  • Subtropical Animal Research Institute, National Institute of Animal Science, RDA, Jeju, 690-150, Republic of Korea.
Kim, Dae Cheol
  • Jeju Special Self-Governing Province Livestock Promotion, Jeju, Republic of Korea.
Hwang, Nam-Hyun
  • College of Animal Life Science, Kangwon National University, Chuncheon, 24341, Republic of Korea.
Son, Da-Hye
  • College of Animal Life Science, Kangwon National University, Chuncheon, 24341, Republic of Korea.
Shin, Jong Suh
  • College of Animal Life Science, Kangwon National University, Chuncheon, 24341, Republic of Korea.
Lee, Joon-Hee
  • Institute of Agriculture and Life Science, College of Agriculture and Life Sciences, Gyeongsang National University, Jinju, 52828, Republic of Korea.
Chung, Won-Hyong
  • Division of Food Functionality Research, Research Group of Healthcare, Wanju-gun, 55365, Republic of Korea. whchung@kfri.re.kr.
Choi, Jung-Woo
  • College of Animal Life Science, Kangwon National University, Chuncheon, 24341, Republic of Korea. jungwoo.kor@gmail.com.

MeSH Terms

  • Animals
  • Genome
  • Horses / genetics
  • Polymorphism, Single Nucleotide
  • Whole Genome Sequencing

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Citations

This article has been cited 1 times.
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