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Genes & genomics2018; 40(11); 1249-1258; doi: 10.1007/s13258-018-0722-0

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

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 r 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). F 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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Publication Date: 2018-08-11 PubMed ID: 30099720DOI: 10.1007/s13258-018-0722-0Google Scholar: Lookup
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  • Research Support
  • 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.

This research focuses on the genomic characteristics and relationships of the indigenous Korean Jeju horse, the Thoroughbred, and the Jeju-Thoroughbred crossbreed, finding notable genetic similarities and differences in inbreeding and heterozygosity levels, as well as potential genes of interest.

Methodology and Analysis

  • The genomes of the three horse breeds were compared using the Equine SNP70 Beadchip array, a technology that enables high-resolution genetic mapping.
  • From this analysis, short-range Linkage Disequilibrium (a measure of the non-random association of alleles at different loci) was found to be highest in the Thoroughbred, while r values (recombination rates) were lowest in the Jeju horse.
  • The researchers calculated expected heterozygosity, which refers to the genetic diversity within a population. The highest heterozygosity was found in the Jeju-Thoroughbred crossbreed, followed by the Thoroughbred, and then the Jeju horse.

Genetic Characteristics

  • The level of inbreeding was slightly higher in the Thoroughbred than in the Jeju crossbred and Jeju horse breeds. Inbreeding can be an indicator of genetic diversity within a population, with higher levels often associated with reduction of diversity.
  • Using the F value (a measure of genetic distance between populations), the greatest genetic distance was found between the Thoroughbred and the Jeju horse, while the smallest distance was noted between the Thoroughbred and the Jeju-Thoroughbred crossbreed.

Genetic Relationships and Selection Signatures

  • A further analysis of genetic relationships through principal component analysis (PCA) suggested that the Jeju-Thoroughbred crossbreed is more genetically similar to the Thoroughbred than to the Jeju horse breed.
  • The researchers detected potential selection signatures (patterns of genetic variation consistent with a selective sweep) in loci located on LCORL/NCAPG and PROP1 genes, indicating these may influence certain body traits.
  • The identification of selection signatures could provide insights into the evolution and genetic adaptation of these horse breeds, which may be related to specific traits of interest for breeding or racing.

This study offers crucial insights into the genetic characteristics and relationships between these three horse populations. It underscores the importance of genomic research in understanding the genetic diversity and evolutionary adaptability of domestic species.

Cite This Article

APA
Kim NY, Seong HS, Kim DC, Park NG, Yang BC, Son JK, Shin SM, Woo JH, Shin MC, Yoo JH, Choi JW. (2018). Genome-wide analyses of the Jeju, Thoroughbred, and Jeju crossbred horse populations using the high density SNP array. Genes Genomics, 40(11), 1249-1258. https://doi.org/10.1007/s13258-018-0722-0

Publication

Genes & genomics
ISSN: 2092-9293
NlmUniqueID: 101481027
Country: Korea (South)
Language: English
Volume: 40
Issue: 11
Pages: 1249-1258

Researcher Affiliations

Kim, Nam Young
  • Subtropical Animal Research Institute, National Institute of Animal Science, RDA, Jeju, 63242, Republic of Korea.
Seong, Ha-Seung
  • College of Animal Life Science, Kangwon National University, Chuncheon, 24341, Republic of Korea.
Kim, Dae Cheol
  • Jeju Special Self-Governing Province Livestock Promotion Agency, Jeju, 63078, Republic of Korea.
Park, Nam Geon
  • Subtropical Animal Research Institute, National Institute of Animal Science, RDA, Jeju, 63242, Republic of Korea.
Yang, Byoung Chul
  • Subtropical Animal Research Institute, National Institute of Animal Science, RDA, Jeju, 63242, Republic of Korea.
Son, Jun Kyu
  • Subtropical Animal Research Institute, National Institute of Animal Science, RDA, Jeju, 63242, Republic of Korea.
Shin, Sang Min
  • Subtropical Animal Research Institute, National Institute of Animal Science, RDA, Jeju, 63242, Republic of Korea.
Woo, Jae Hoon
  • Subtropical Animal Research Institute, National Institute of Animal Science, RDA, Jeju, 63242, Republic of Korea.
Shin, Moon Cheol
  • Subtropical Animal Research Institute, National Institute of Animal Science, RDA, Jeju, 63242, Republic of Korea.
Yoo, Ji Hyun
  • Subtropical Animal Research Institute, National Institute of Animal Science, RDA, Jeju, 63242, Republic of Korea.
Choi, Jung-Woo
  • College of Animal Life Science, Kangwon National University, Chuncheon, 24341, Republic of Korea. jungwoo.kor@gmail.com.

MeSH Terms

  • Animals
  • Body Size / genetics
  • Crosses, Genetic
  • Genome
  • Genotyping Techniques / standards
  • Heterozygote
  • Horses / genetics
  • Inbreeding
  • Linkage Disequilibrium
  • Oligonucleotide Array Sequence Analysis
  • Polymorphism, Single Nucleotide
  • Principal Component Analysis

Grant Funding

  • PJ01010503 / Rural Development Administration

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Citations

This article has been cited 11 times.
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