Identification of genes with nonsynonymous SNP in Jeju horse by whole-genome resequencing reveals a functional role for immune response.
Abstract: Jeju horse (Natural Monument number 347) is a breed of horse that has experienced long-term isolation and domestication in Jeju Island, South Korea. We evaluated genetic features of this breed, including SNP, by whole-genome resequencing using an Illumina HiSeq 2000. A total of 5,986,852 SNP were identified in 4 Jeju horses and were divided into homozygous and heterozygous SNP (2,357,099 and 3,629,753 SNP, respectively). It revealed that 63.8% of these SNP resided in intergenic regions. Immune response genes with nonsynonymous SNP were overrepresented in Jeju horses as evidenced by Gene Ontology clustering. Among these genes, Toll-like receptors (TLR) are highly enriched. Comparing TLR genes between Jeju horses and the Przewalski's horse, and genes showed "possibly damaging" mutations in several regions by analysis with PolyPhen-2. These results provide a framework for further genetic studies in Jeju horse by domestication. Furthermore, research on functions of SNP-associated genes would aid in understanding the molecular genetic variation of horse breeds.
Publication Date: 2016-04-12 PubMed ID: 27065251DOI: 10.2527/jas.2014-8488Google Scholar: Lookup
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- Journal Article
- Research Support
- Non-U.S. Gov't
Summary
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The researchers conducted a genetic analysis of the Jeju horse breed, found in South Korea’s Jeju Island, by examining nearly 6 million single nucleotide polymorphisms (SNPs, variations in a single DNA building block) and identified that the genes related to immune response with functional differences are more prevalent in this breed.
Whole-Genome Resequencing
- The scientists utilized whole-genome resequencing technology to examine the DNA of the Jeju breed. This type of analysis allows for a comprehensive representation of the entire genetic makeup of the horse, rather than just specific sections or genes.
- For this study, the team used the Illumina HiSeq 2000, an advanced technology device for mapping and sequencing genomes. This can provide in-depth and accurate genetic data for the researchers to scrutinize.
Identification of Single Nucleotide Polymorphisms (SNPs)
- In the DNA of the Jeju horses, nearly six million SNPs were located. These SNPs are essentially variations in a single DNA building block (nucleotide) and are a major source of genetic diversity among individuals.
- The researchers differentiated between homozygous (SNPs with only one type of the same gene) and heterozygous (SNPs that have different types of the same gene). It was found that the majority of these SNPs were in intergenic areas, which are regions not included in genes and typically contain regulatory elements controlling the genetic function.
Immune Response Genes and Toll-Like Receptors
- The findings highlighted that immune response genes with nonsynonymous SNPs were particularly predominant in Jeju horses. Nonsynonymous SNPs represent varying types of changes in the DNA sequence that lead to altering the function or structure of the gene products (proteins).
- Toll-like receptors (TLRs), a type of protein that plays a key role in the immune system, were highly enriched amongst these. However, when compared with Przewalski’s horse, regarded as the closest breed to the wild ancestor of domestic horses, certain regions of the TLR genes were potentially damaging, as suggested by PolyPhen-2 analysis. This particular technique can predict whether an amino acid substitution in a protein can affect its function leading to a disease.
Future Research
- These results provide a foundation for further genetic research on Jeju horse and its domestication process. By studying the functions of the genes associated with the identified SNPs, scientists hope to understand better the genetic variations present among different horse breeds.
Cite This Article
APA
Lee JH, Song KD, Kim JM, Leem HK, Park KD.
(2016).
Identification of genes with nonsynonymous SNP in Jeju horse by whole-genome resequencing reveals a functional role for immune response.
J Anim Sci, 94(3), 895-901.
https://doi.org/10.2527/jas.2014-8488 Publication
Researcher Affiliations
MeSH Terms
- Animals
- Cluster Analysis
- Genome
- Heterozygote
- Homozygote
- Horses / genetics
- Horses / immunology
- Polymorphism, Single Nucleotide / genetics
Citations
This article has been cited 3 times.- Polani S, Dean M, Lichter-Peled A, Hendrickson S, Tsang S, Fang X, Feng Y, Qiao W, Avni G, Kahila Bar-Gal G. Sequence Variant in the TRIM39-RPP21 Gene Readthrough is Shared Across a Cohort of Arabian Foals Diagnosed with Juvenile Idiopathic Epilepsy. J Genet Mutat Disord 2022 Jan;1(1).
- 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. Comprehensive genome and transcriptome analyses reveal genetic relationship, selection signature, and transcriptome landscape of small-sized Korean native Jeju horse. Sci Rep 2019 Nov 13;9(1):16672.
- Khummuang S, Lee HG, Joo SS, Park JW, Choi JY, Oh JH, Kim KH, Youn HH, Kim M, Cho BW. Comparison for immunophysiological responses of Jeju and Thoroughbred horses after exercise. Asian-Australas J Anim Sci 2020 Mar;33(3):424-435.
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