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Scientific reports2019; 9(1); 16672; doi: 10.1038/s41598-019-53102-8

Comprehensive genome and transcriptome analyses reveal genetic relationship, selection signature, and transcriptome landscape of small-sized Korean native Jeju horse.

Abstract: The Jeju horse, indigenous to the Jeju Island in Korea may have originated from Mongolian horses. Adaptations to the local harsh environment have conferred Jeju horse with unique traits such as small-sized body, stocky head, and shorter limbs. These characteristics have not been studied previously at the genomic level. Therefore, we sequenced and compared the genome of 41 horses belonging to 6 breeds. We identified numerous breed-specific non-synonymous SNPs and loss-of-function mutants. Demographic and admixture analyses showed that, though Jeju horse is genetically the closest to the Mongolian breeds, its genetic ancestry is independent of that of the Mongolian breeds. Genome wide selection signature analysis revealed that genes such as LCORL, MSTN, HMGA2, ZFAT, LASP1, PDK4, and ACTN2, were positively selected in the Jeju horse. RNAseq analysis showed that several of these genes were also differentially expressed in Jeju horse compared to Thoroughbred horse. Comparative muscle fiber analysis showed that, the type I muscle fibre content was substantially higher in Jeju horse compared to Thoroughbred horse. Our results provide insights about the selection of complex phenotypic traits in the small-sized Jeju horse and the novel SNPs identified will aid in designing high-density SNP chip for studying other native horse breeds.
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Publication Date: 2019-11-13 PubMed ID: 31723199PubMed Central: PMC6853925DOI: 10.1038/s41598-019-53102-8Google Scholar: Lookup
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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 article primarily focuses on the analysis and study of the unique genetic properties of the Jeju horse breed, which is native to Jeju Island in Korea. The Jeju horses are believed to be originally descended from Mongolian breeds; however, they’ve adapted to their local environment and have developed distinct characteristics.

Summary of Research Work

The researchers sequenced and compared the genome of 41 horses from six different breeds. The aim was to understand and identify the distinct genetic components of the Jeju horse breed through in-depth genomic and transcriptome analysis. This was conducted for the first time considering the specific breed.

  • The team discovered numerous breed-specific non-synonymous SNPs (single nucleotide polymorphisms) and loss-of-function mutations specific to the Jeju horse breed.
  • Despite its close genetic proximity to Mongolian breeds, the demographic and admixture analyses suggest that the Jeju horse’s genetic ancestry is independent of Mongolian breeds. It implies that over time, the Jeju horse has developed a unique genetic lineage.
  • The research also looked at genome-wide selection signature analysis, which revealed certain genes (LCORL, MSTN, HMGA2, ZFAT, LASP1, PDK4, and ACTN2) to be positively selected in the Jeju horse. This points towards a genetic bias towards these genes that might be assisting the Jeju horse with its survival and adaptation in its habitat.

RNAseq and Comparative Muscle Fiber Analysis

In addition to the genomic study, the researchers also conducted a RNAseq analysis which further demonstrated the distinct genetic makeup of the Jeju horse breed.

  • This analysis illustrated that several genes which were positively selected (as identified in the genomic analysis) were also differentially expressed when compared to a Thoroughbred horse breed. This suggests that these genes could be responsible for the specific characteristics of the Jeju horse breed.
  • Furthermore, a comparative muscle fiber analysis between the Jeju horse and the Thoroughbred horse revealed a significantly higher type I muscle fiber content in the former. Type I muscle fibers can influence several characteristics related to stamina and endurance, which might be another unique adaptation trait for the Jeju horse.

This comprehensive genetic analysis has offered insights into how complex phenotypic traits like small body size are selected and inherited in the Jeju horse breed. The novel SNPs identified in the research could be pivotal in designing a high-density SNP chip, which could further assist in studying other native horse breeds.

Cite This Article

APA
Srikanth K, Kim NY, Park W, Kim JM, Kim KD, Lee KT, Son JH, Chai HH, Choi JW, Jang GW, Kim H, Ryu YC, Nam JW, Park JE, Kim JM, Lim D. (2019). Comprehensive genome and transcriptome analyses reveal genetic relationship, selection signature, and transcriptome landscape of small-sized Korean native Jeju horse. Sci Rep, 9(1), 16672. https://doi.org/10.1038/s41598-019-53102-8

Publication

Scientific reports
ISSN: 2045-2322
NlmUniqueID: 101563288
Country: England
Language: English
Volume: 9
Issue: 1
Pages: 16672

Researcher Affiliations

Srikanth, Krishnamoorthy
  • Animal Genomics and Bioinformatics Division, National Institute of Animal Science, Rural Development Administration, Wanju, 55365, Republic of Korea.
Kim, Nam-Young
  • Subtropical Livestock Research Institute, National Institute of Animal Science, Rural Development Administration, Jeju-do, 63242, Republic of Korea.
Park, WonCheoul
  • Animal Genomics and Bioinformatics Division, National Institute of Animal Science, Rural Development Administration, Wanju, 55365, Republic of Korea.
Kim, Jae-Min
  • Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA.
Kim, Kwon-Do
  • C&K genomics, Seoul, Republic of Korea.
Lee, Kyung-Tai
  • Animal Breeding and Genetics Division, National Institute of Animal Science, Rural Development Administration, Wanju, 55365, Republic of Korea.
Son, Ju-Hwan
  • Animal Genomics and Bioinformatics Division, National Institute of Animal Science, Rural Development Administration, Wanju, 55365, Republic of Korea.
Chai, Han-Ha
  • Animal Genomics and Bioinformatics Division, National Institute of Animal Science, Rural Development Administration, Wanju, 55365, Republic of Korea.
Choi, Jung-Woo
  • College of Animal Life Science, Kangwon National University, Chuncheon, 24341, Republic of Korea.
Jang, Gul-Won
  • Animal Genomics and Bioinformatics Division, National Institute of Animal Science, Rural Development Administration, Wanju, 55365, Republic of Korea.
Kim, Heebal
  • C&K genomics, Seoul, Republic of Korea.
Ryu, Youn-Chul
  • Division of Biotechnology, Jeju National University, Jeju, 63243, Republic of Korea.
Nam, Jin-Wu
  • Department of Life Science, Hanyang University, Seoul, 133-791, Republic of Korea.
Park, Jong-Eun
  • Animal Genomics and Bioinformatics Division, National Institute of Animal Science, Rural Development Administration, Wanju, 55365, Republic of Korea.
Kim, Jun-Mo
  • Department of Animal Science and Technology, College of Biotechnology and Natural Resources, Chung-Ang University, Ansung-si, 17546, Republic of Korea. junmokim@cau.ac.kr.
Lim, Dajeong
  • Animal Genomics and Bioinformatics Division, National Institute of Animal Science, Rural Development Administration, Wanju, 55365, Republic of Korea. lim.dj@korea.kr.

MeSH Terms

  • Animals
  • Breeding
  • Gene Expression Profiling
  • Genetics, Population
  • Genome
  • Horses / genetics
  • Phenotype
  • Polymorphism, Single Nucleotide
  • Republic of Korea
  • Selection, Genetic
  • Transcriptome

Conflict of Interest Statement

The authors declare no competing interests.

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