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

  • Ha-Seung Seong
  • Nam-Young Kim
  • Dae Cheol Kim
  • Nam-Hyun Hwang
  • Da-Hye Son
  • Jong Suh Shin
  • Joon-Hee Lee
  • Won-Hyong ChungEmail author
  • Jung-Woo ChoiEmail author
Research Article

Abstract

Background

The Jeju horse is an indigenous horse breed in Korea. However, there is a severe lack of genomic studies on Korean horse breeds.

Objective

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).

Results

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.

Conclusion

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.

Keywords

Jeju horse Przewalski's horse Re-sequencing Single-nucleotide polymorphism 

Notes

Acknowledgements

This study was supported by National Research Foundation of Korea (Project no. NRF-2016R1D1A3B03934278).

Author contributions

J-WC, W-HC, and N-YK designed the whole project. DCK collected the blood samples from Jeju, Jeju crossbred, and Thoroughbred populations. H-SS and W-HC analyzed the data. J-WC, W-HC, H-SS, and N-YK analyzed the data and interpreted the results. N-HH and D-HS carried out statistical analysis for this manuscript. H-SS and N-YK, W-HC, and J-WC wrote the draft of the manuscript. JSS and J-HL revised a part of the paper. All authors contributed to the paper and approved the final manuscript.

Compliance with ethical standards

Conflict of interest

The authors declare that there is no conflict of interest.

Ethical approval

All experiments and all its procedures were carried out in accordance with the regulation approved by National Institute of Animal Science (NIAS, National Institute of Animal Science’s Institutional Animal Care and Use Committee).

Supplementary material

13258_2019_795_MOESM1_ESM.xlsx (4.6 mb)
Supplementary material 1 (XLSX 4728 KB)
13258_2019_795_MOESM2_ESM.xlsx (1.3 mb)
Supplementary material 2 (XLSX 1306 KB)

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Copyright information

© The Genetics Society of Korea 2019

Authors and Affiliations

  • Ha-Seung Seong
    • 1
  • Nam-Young Kim
    • 2
  • Dae Cheol Kim
    • 3
  • Nam-Hyun Hwang
    • 1
  • Da-Hye Son
    • 1
  • Jong Suh Shin
    • 1
  • Joon-Hee Lee
    • 4
  • Won-Hyong Chung
    • 5
    Email author
  • Jung-Woo Choi
    • 1
    Email author
  1. 1.College of Animal Life ScienceKangwon National UniversityChuncheonRepublic of Korea
  2. 2.Subtropical Animal Research Institute, National Institute of Animal ScienceRDAJejuRepublic of Korea
  3. 3.Jeju Special Self-Governing Province Livestock PromotionJejuRepublic of Korea
  4. 4.Institute of Agriculture and Life Science, College of Agriculture and Life SciencesGyeongsang National UniversityJinjuRepublic of Korea
  5. 5.Division of Food Functionality ResearchResearch Group of HealthcareWanju-gunRepublic of Korea

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