Omneity® Pellets
All-In-One Vitamin & Mineral Pellet
Comparative Analysis for Genetic Characterization in Korean Native Jeju Horse.
Abstract: The Jeju horse is a native Korean species that has been breeding on Jeju Island since the 13th century. Their shape has a distinct appearance from the representative species, Thoroughbred. Here, we performed a comparison of the Jeju horse and Thoroughbred horse for the identification of genome-wide structure variation by using the next-generation sequencing (NGS) technique. We generated an average of 95.59 Gb of the DNA sequence, resulting in an average of 33.74 X sequence coverage from five Jeju horses. In addition, reads obtained from WGRS data almost covered the horse reference genome (mapped reads 98.4%). Based on our results, we identified 1,244,064 single nucleotide polymorphisms (SNPs), 113,498 genomic insertions, and 114,751 deletions through bioinformatics analysis. Interestingly, the results of the WGRS comparison indicated that the eqCD1a6 gene contains signatures of positive natural selection in Jeju horses. The eqCD1a6 gene is known to be involved in immunity. The eqCD1a6 gene of Jeju horses commonly contained 296 variants (275 SNPs and 21 INDELs) that were compared with its counterpart of two Thoroughbred horses. In addition, we used LOAA, digital PCR, to confirm the possibility of developing a molecular marker for species identification using variant sites. As a result, it was possible to confirm the result of the molecular marker with high accuracy. Nevertheless, eqCD1a6 was shown to be functionally intact. Taken together, we have found significant genomic variation in these two different horse species.
Publication Date: 2021-06-28 PubMed ID: 34203473PubMed Central: PMC8300358DOI: 10.3390/ani11071924Google Scholar: Lookup The Equine Research Bank provides access to a large database of publicly available scientific literature. Inclusion in the Research Bank does not imply endorsement of study methods or findings by Mad Barn.
- Journal Article
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 compared the genetic structures of Korean Jeju horses and Thoroughbreds using advanced genomic sequencing techniques, and identified considerable genetic variations specially in a certain immunity-related gene,eqCD1a6.
Overview
- Scientists conducted a genetic study of the Korean Jeju horse, one that’s native to Jeju Island and different from the standard Thoroughbred horse.
- They used a technique known as next-generation sequencing (NGS) for their comparison, which helped to identify genome-wide structural variations between the two horse breeds.
Methodology
- The researchers obtained a substantial amount of DNA sequence data from five Jeju horses, providing a comprehensive genome coverage.
- The data was then compared with the horse reference genome, with 98.4% of the reads mapping correctly.
Findings
- The results of the research showed over a million single nucleotide polymorphisms (SNPs), which are variations in a single nucleotide that occurs at a specific position in the genome.
- In addition, more than 100,000 genomic insertions and deletions were identified.
- An interesting discovery was the presence of signatures of positive natural selection in a gene known as eqCD1a6 in Jeju horses. This gene plays a crucial role in immunity.
- The eqCD1a6 gene found in Jeju horses contained 296 variants when compared to its counterpart in two Thoroughbred horses.
Confirmation and implications
- To confirm these findings, the researchers utilized digital PCR and a loss of function assay, also known as LOAA.
- These techniques confirmed the potential for creating a molecular marker for species identification using variant sites.
- However, despite the variations, the gene eqCD1a6 was still found to be functionally intact.
- The findings underscore the significant genomic variation between the Korean Jeju horse and the standard Thoroughbred horse. This offers insights into the evolution and breeding history of these species and provides potential markers for future research and species identification.
Cite This Article
APA
Lee W, Mun S, Choi SY, Oh DY, Park YS, Han K.
(2021).
Comparative Analysis for Genetic Characterization in Korean Native Jeju Horse.
Animals (Basel), 11(7), 1924.
https://doi.org/10.3390/ani11071924 Publication
Researcher Affiliations
- Center for Bio-Medical Engineering Core Facility, Dankook University, Cheonan 31116, Korea.
- Center for Bio-Medical Engineering Core Facility, Dankook University, Cheonan 31116, Korea.
- Department of Nanobiomedical Science & BK21 PLUS NBM Global Research Center for Regenerative Medicine, Dankook University, Cheonan 31116, Korea.
- Department of Pathology, Colleage of Medicine, Chungnam National University, Daejeon 34134, Korea.
- Livestock Research Institute, Gyeongsangbuk-Do, Yeongju 36052, Korea.
- Department of Equine Industry, Korea National College of Agriculture and Fisheries, Jeonju 54874, Korea.
- Center for Bio-Medical Engineering Core Facility, Dankook University, Cheonan 31116, Korea.
- Department of Microbiology, College of Science and Technology, Dankook University, Cheonan 31116, Korea.
Conflict of Interest Statement
The authors declare no conflict of interest.
References
This article includes 25 references
- Ludwig A, Pruvost M, Reissmann M, Benecke N, Brockmann GA, Castaños P, Cieslak M, Lippold S, Llorente L, Malaspinas AS, Slatkin M, Hofreiter M. Coat color variation at the beginning of horse domestication.. Science 2009 Apr 24;324(5926):485.
- Outram AK, Stear NA, Bendrey R, Olsen S, Kasparov A, Zaibert V, Thorpe N, Evershed RP. The earliest horse harnessing and milking.. Science 2009 Mar 6;323(5919):1332-5.
- Lippold S, Matzke NJ, Reissmann M, Hofreiter M. Whole mitochondrial genome sequencing of domestic horses reveals incorporation of extensive wild horse diversity during domestication.. BMC Evol Biol 2011 Nov 14;11:328.
- Petersen JL, Mickelson JR, Rendahl AK, Valberg SJ, Andersson LS, Axelsson J, Bailey E, Bannasch D, Binns MM, Borges AS, Brama P, da Câmara Machado A, Capomaccio S, Cappelli K, Cothran EG, Distl O, Fox-Clipsham L, Graves KT, Guérin G, Haase B, Hasegawa T, Hemmann K, Hill EW, Leeb T, Lindgren G, Lohi H, Lopes MS, McGivney BA, Mikko S, Orr N, Penedo MC, Piercy RJ, Raekallio M, Rieder S, Røed KH, Swinburne J, Tozaki T, Vaudin M, Wade CM, McCue ME. Genome-wide analysis reveals selection for important traits in domestic horse breeds.. PLoS Genet 2013;9(1):e1003211.
- Zhou M, Wang Q, Sun J, Li X, Xu L, Yang H, Shi H, Ning S, Chen L, Li Y, He T, Zheng Y. In silico detection and characteristics of novel microRNA genes in the Equus caballus genome using an integrated ab initio and comparative genomic approach.. Genomics 2009 Aug;94(2):125-31.
- Gim JA, Hong CP, Kim DS, Moon JW, Choi Y, Eo J, Kwon YJ, Lee JR, Jung YD, Bae JH, Choi BH, Ko J, Song S, Ahn K, Ha HS, Yang YM, Lee HK, Park KD, Do KT, Han K, Yi JM, Cha HJ, Ayarpadikannan S, Cho BW, Bhak J, Kim HS. Genome-wide analysis of DNA methylation before-and after exercise in the thoroughbred horse with MeDIP-Seq.. Mol Cells 2015 Mar;38(3):210-20.
- Kim NY, Seong HS, Kim DC, Park NG, Yang BC, Son JK, Shin SM, Woo JH, Shin MC, Yoo JH, Choi JW. Genome-wide analyses of the Jeju, Thoroughbred, and Jeju crossbred horse populations using the high density SNP array.. Genes Genomics 2018 Nov;40(11):1249-1258.
- Wade CM, Giulotto E, Sigurdsson S, Zoli M, Gnerre S, Imsland F, Lear TL, Adelson DL, Bailey E, Bellone RR, Blöcker H, Distl O, Edgar RC, Garber M, Leeb T, Mauceli E, MacLeod JN, Penedo MC, Raison JM, Sharpe T, Vogel J, Andersson L, Antczak DF, Biagi T, Binns MM, Chowdhary BP, Coleman SJ, Della Valle G, Fryc S, Guérin G, Hasegawa T, Hill EW, Jurka J, Kiialainen A, Lindgren G, Liu J, Magnani E, Mickelson JR, Murray J, Nergadze SG, Onofrio R, Pedroni S, Piras MF, Raudsepp T, Rocchi M, Røed KH, Ryder OA, Searle S, Skow L, Swinburne JE, Syvänen AC, Tozaki T, Valberg SJ, Vaudin M, White JR, Zody MC, Lander ES, Lindblad-Toh K. Genome sequence, comparative analysis, and population genetics of the domestic horse.. Science 2009 Nov 6;326(5954):865-7.
- Park KD, Park J, Ko J, Kim BC, Kim HS, Ahn K, Do KT, Choi H, Kim HM, Song S, Lee S, Jho S, Kong HS, Yang YM, Jhun BH, Kim C, Kim TH, Hwang S, Bhak J, Lee HK, Cho BW. Whole transcriptome analyses of six thoroughbred horses before and after exercise using RNA-Seq.. BMC Genomics 2012 Sep 12;13:473.
- Yang YH, Kim KI, Cothran EG, Flannery AR. Genetic diversity of Cheju horses (Equus caballus) determined by using mitochondrial DNA D-loop polymorphism.. Biochem Genet 2002 Jun;40(5-6):175-86.
- Zhang C, Ni P, Ahmad HI, Gemingguli M, Baizilaitibei A, Gulibaheti D, Fang Y, Wang H, Asif AR, Xiao C, Chen J, Ma Y, Liu X, Du X, Zhao S. Detecting the Population Structure and Scanning for Signatures of Selection in Horses (Equus caballus) From Whole-Genome Sequencing Data.. Evol Bioinform Online 2018;14:1176934318775106.
- Do KT, Lee JH, Lee HK, Kim J, Park KD. Estimation of effective population size using single-nucleotide polymorphism (SNP) data in Jeju horse.. J Anim Sci Technol 2014;56:28.
- Yoon SH, Kim J, Shin D, Cho S, Kwak W, Lee HK, Park KD, Kim H. Complete mitochondrial genome sequences of Korean native horse from Jeju Island: uncovering the spatio-temporal dynamics.. Mol Biol Rep 2017 Apr;44(2):233-242.
- Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2.. Nat Methods 2012 Mar 4;9(4):357-9.
- McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, Garimella K, Altshuler D, Gabriel S, Daly M, DePristo MA. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data.. Genome Res 2010 Sep;20(9):1297-303.
- Untergasser A, Cutcutache I, Koressaar T, Ye J, Faircloth BC, Remm M, Rozen SG. Primer3--new capabilities and interfaces.. Nucleic Acids Res 2012 Aug;40(15):e115.
- Parmley JL, Hurst LD. How common are intragene windows with KA > KS owing to purifying selection on synonymous mutations?. J Mol Evol 2007 Jun;64(6):646-55.
- Metzger J, Tonda R, Beltran S, Agueda L, Gut M, Distl O. Next generation sequencing gives an insight into the characteristics of highly selected breeds versus non-breed horses in the course of domestication.. BMC Genomics 2014 Jul 4;15(1):562.
- Bindea G, Mlecnik B, Hackl H, Charoentong P, Tosolini M, Kirilovsky A, Fridman WH, Pagès F, Trajanoski Z, Galon J. ClueGO: a Cytoscape plug-in to decipher functionally grouped gene ontology and pathway annotation networks.. Bioinformatics 2009 Apr 15;25(8):1091-3.
- Porcelli SA, Modlin RL. The CD1 system: antigen-presenting molecules for T cell recognition of lipids and glycolipids.. Annu Rev Immunol 1999;17:297-329.
- Rahman MT, Herron LL, Kapur V, Meijer WG, Byrne BA, Ren J, Nicholson VM, Prescott JF. Partial genome sequencing of Rhodococcus equi ATCC 33701.. Vet Microbiol 2003 Jul 1;94(2):143-58.
- Park SH, Bendelac A. CD1-restricted T-cell responses and microbial infection.. Nature 2000 Aug 17;406(6797):788-92.
- Dossa RG, Alperin DC, Hines MT, Hines SA. The equine CD1 gene family is the largest and most diverse yet identified.. Immunogenetics 2014 Jan;66(1):33-42.
- Proutski V, Holmes E. SWAN: sliding window analysis of nucleotide sequence variability.. Bioinformatics 1998 Jun;14(5):467-8.
- Sommer S. The importance of immune gene variability (MHC) in evolutionary ecology and conservation.. Front Zool 2005 Oct 20;2:16.
Citations
This article has been cited 0 times.Use Nutrition Calculator
Check if your horse's diet meets their nutrition requirements with our easy-to-use tool Check your horse's diet with our easy-to-use tool
Talk to a Nutritionist
Discuss your horse's feeding plan with our experts over a free phone consultation Discuss your horse's diet over a phone consultation
Submit Diet Evaluation
Get a customized feeding plan for your horse formulated by our equine nutritionists Get a custom feeding plan formulated by our nutritionists
