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Genome-wide analyses of the Jeju, Thoroughbred, and Jeju crossbred horse populations using the high density SNP array

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Abstract

The Jeju horse is an indigenous Korean horse breed that is currently registered with the Food and Agriculture Organization of the United Nations. However, there is severe lack of genomic studies on Jeju horse. This study was conducted to investigate genetic characteristics of horses including Jeju horse, Thoroughbred and Jeju crossbred (Jeju × Thoroughbred) populations. We compared the genomes of three horse populations using the Equine SNP70 Beadchip array. Short-range Linkage disequilibrium was the highest in Thoroughbred, whereas r2 values were lowest in Jeju horse. Expected heterozygosity was the highest in Jeju crossbred (0.351), followed by the Thoroughbred (0.337) and Jeju horse (0.311). The level of inbreeding was slightly higher in Thoroughbred (− 0.009) than in Jeju crossbred (− 0.035) and Jeju horse (− 0.038). FST value was the highest between Jeju horse and Thoroughbred (0.113), whereas Jeju crossbred and Thoroughbred showed the lowest value (0.031). The genetic relationship was further assessed by principal component analysis, suggesting that Jeju crossbred is more genetically similar to Thoroughbred than Jeju horse population. Additionally, we detected potential selection signatures, for example, in loci located on LCORL/NCAPG and PROP1 genes that are known to influence body. Genome-wide analyses of the three horse populations showed that all the breeds had somewhat a low level of inbreeding within each population. In the population structure analysis, we found that Jeju crossbred was genetically closer to Thoroughbred than Jeju horse. Furthermore, we identified several signatures of selection which might be associated with traits of interest. To our current knowledge, this study is the first genomic research, analyzing genetic relationships of Jeju horse, Thoroughbred and Jeju crossbred.

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Acknowledgements

This work was carried out with the support of “Cooperative Research Program for Agriculture Science & Technology Development (Project title: Study on the development of basic population for the use of Jeju horses, Project No. PJ01010503)” Rural Development Administration, Republic of Korea.

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Author notes

  1. Nam Young Kim and Ha-Seung Seong contributed equally to this work.

Authors and Affiliations

  1. Subtropical Animal Research Institute, National Institute of Animal Science, RDA, Jeju, 63242, Republic of Korea

    Nam Young Kim, Nam Geon Park, Byoung Chul Yang, Jun Kyu Son, Sang Min Shin, Jae Hoon Woo, Moon Cheol Shin & Ji Hyun Yoo

  2. College of Animal Life Science, Kangwon National University, Chuncheon, 24341, Republic of Korea

    Ha-Seung Seong & Jung-Woo Choi

  3. Jeju Special Self-Governing Province Livestock Promotion Agency, Jeju, 63078, Republic of Korea

    Dae Cheol Kim

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  1. Nam Young Kim
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Correspondence to Jung-Woo Choi.

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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: 2014-067).

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Kim, N.Y., Seong, HS., Kim, D.C. et al. Genome-wide analyses of the Jeju, Thoroughbred, and Jeju crossbred horse populations using the high density SNP array. Genes Genom 40, 1249–1258 (2018). https://doi.org/10.1007/s13258-018-0722-0

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