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Lee S, Lee EB, Park KW, Jeong H, Shin KY, Kweon YP, Seo JP. Computed tomographic features of the temporomandibular joint in 10 Jeju horses. J Vet Sci 2022; 23:e44. [PMID: 35466600 PMCID: PMC9149492 DOI: 10.4142/jvs.21318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 02/10/2022] [Accepted: 02/28/2022] [Indexed: 11/20/2022] Open
Abstract
Background Objectives Methods Results Conclusions
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Affiliation(s)
- Seyoung Lee
- Department of Veterinary, College of Veterinary Medicine and Veterinary Medical Research Institute, Jeju National University, Jeju 63243, Korea
| | - Eun-Bee Lee
- Department of Veterinary, College of Veterinary Medicine and Veterinary Medical Research Institute, Jeju National University, Jeju 63243, Korea
| | - Kyung-Won Park
- Department of Veterinary, College of Veterinary Medicine and Veterinary Medical Research Institute, Jeju National University, Jeju 63243, Korea
| | - Hyohoon Jeong
- Department of Veterinary, College of Veterinary Medicine and Veterinary Medical Research Institute, Jeju National University, Jeju 63243, Korea
| | - Kwang-Yun Shin
- Institute for Livestock Promotion, Jeju-Special Self-Governing Province, Jeju 63078, Korea
| | - Young-Park Kweon
- Institute for Livestock Promotion, Jeju-Special Self-Governing Province, Jeju 63078, Korea
| | - Jong-Pil Seo
- Department of Veterinary, College of Veterinary Medicine and Veterinary Medical Research Institute, Jeju National University, Jeju 63243, Korea
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Lee W, Mun S, Choi SY, Oh DY, Park YS, Han K. Comparative Analysis for Genetic Characterization in Korean Native Jeju Horse. Animals (Basel) 2021; 11:ani11071924. [PMID: 34203473 PMCID: PMC8300358 DOI: 10.3390/ani11071924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 06/18/2021] [Accepted: 06/22/2021] [Indexed: 11/17/2022] Open
Abstract
Simple Summary In modern times, horse breeds, mostly in horse racing, are the Thoroughbred varieties obtained by breeding three Godolphin Arabians with British mares in England. Especially in Jeju Island, Korea, Jeju horses have been introduced from Mongolia since the 13th century. They have contributed a lot to the agricultural community, but their population has been rapidly decreasing due to rapid agricultural industrialization. Therefore, we sympathize with Jeju horse-specific genetic variation and compare and analyze evolutionary correlations by utilizing Whole Genome Sequencing analysis to evaluate the genetic diversity of Jeju horses and preserve genetic information. We explored Jeju horse-specific genetic differences through a comparative analysis of large-capacity genomic data between the public database and a Thoroughbred variety. In order to adapt to the barren external environment, it is predicted that Jeju horses have experienced strong positive selection in the direction of accumulating many genetic variations, enough to cause functional differences in the eqCD1a6 gene to have an efficient immune function. In addition, we further validate the Jeju horse-specific single nucleotide polymorphisms in the aqCD1a6 gene by employing the digital PCR method, a diagnostic technique for genetic variations. 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.
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Affiliation(s)
- Wooseok Lee
- Center for Bio-Medical Engineering Core Facility, Dankook University, Cheonan 31116, Korea; (W.L.); (S.M.)
| | - Seyoung Mun
- Center for Bio-Medical Engineering Core Facility, Dankook University, Cheonan 31116, Korea; (W.L.); (S.M.)
- Department of Nanobiomedical Science & BK21 PLUS NBM Global Research Center for Regenerative Medicine, Dankook University, Cheonan 31116, Korea
| | - Song-Yi Choi
- Department of Pathology, Colleage of Medicine, Chungnam National University, Daejeon 34134, Korea;
| | - Dong-Yep Oh
- Livestock Research Institute, Gyeongsangbuk-Do, Yeongju 36052, Korea;
| | - Yong-Soo Park
- Department of Equine Industry, Korea National College of Agriculture and Fisheries, Jeonju 54874, Korea
- Correspondence: (Y.-S.P.); (K.H.); Tel.: +82-41-550-1298 (Y.-S.P. & K.H.)
| | - Kyudong Han
- Center for Bio-Medical Engineering Core Facility, Dankook University, Cheonan 31116, Korea; (W.L.); (S.M.)
- Department of Microbiology, College of Science and Technology, Dankook University, Cheonan 31116, Korea
- Correspondence: (Y.-S.P.); (K.H.); Tel.: +82-41-550-1298 (Y.-S.P. & K.H.)
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Gene Expression Profile in Similar Tissues Using Transcriptome Sequencing Data of Whole-Body Horse Skeletal Muscle. Genes (Basel) 2020; 11:genes11111359. [PMID: 33213000 PMCID: PMC7698552 DOI: 10.3390/genes11111359] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 11/11/2020] [Accepted: 11/14/2020] [Indexed: 01/12/2023] Open
Abstract
Horses have been studied for exercise function rather than food production, unlike most livestock. Therefore, the role and characteristics of tissue landscapes are critically understudied, except for certain muscles used in exercise-related studies. In the present study, we compared RNA-Seq data from 18 Jeju horse skeletal muscles to identify differentially expressed genes (DEGs) between tissues that have similar functions and to characterize these differences. We identified DEGs between different muscles using pairwise differential expression (DE) analyses of tissue transcriptome expression data and classified the samples using the expression values of those genes. Each tissue was largely classified into two groups and their subgroups by k-means clustering, and the DEGs identified in comparison between each group were analyzed by functional/pathway level using gene set enrichment analysis and gene level, confirming the expression of significant genes. As a result of the analysis, the differences in metabolic properties like glycolysis, oxidative phosphorylation, and exercise adaptation of the groups were detected. The results demonstrated that the biochemical and anatomical features of a wide range of muscle tissues in horses could be determined through transcriptome expression analysis, and provided proof-of-concept data demonstrating that RNA-Seq analysis can be used to classify and study in-depth differences between tissues with similar properties.
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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; 9:16672. [PMID: 31723199 PMCID: PMC6853925 DOI: 10.1038/s41598-019-53102-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Accepted: 10/18/2019] [Indexed: 12/16/2022] Open
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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Affiliation(s)
- Krishnamoorthy Srikanth
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, Rural Development Administration, Wanju, 55365, Republic of Korea
| | - Nam-Young Kim
- Subtropical Livestock Research Institute, National Institute of Animal Science, Rural Development Administration, Jeju-do, 63242, Republic of Korea
| | - WonCheoul Park
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, Rural Development Administration, Wanju, 55365, Republic of Korea
| | - Jae-Min Kim
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | | | - Kyung-Tai Lee
- Animal Breeding and Genetics Division, National Institute of Animal Science, Rural Development Administration, Wanju, 55365, Republic of Korea
| | - Ju-Hwan Son
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, Rural Development Administration, Wanju, 55365, Republic of Korea
| | - Han-Ha Chai
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, Rural Development Administration, Wanju, 55365, Republic of Korea
| | - Jung-Woo Choi
- College of Animal Life Science, Kangwon National University, Chuncheon, 24341, Republic of Korea
| | - Gul-Won Jang
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, Rural Development Administration, Wanju, 55365, Republic of Korea
| | | | - Youn-Chul Ryu
- Division of Biotechnology, Jeju National University, Jeju, 63243, Republic of Korea
| | - Jin-Wu Nam
- Department of Life Science, Hanyang University, Seoul, 133-791, Republic of Korea
| | - Jong-Eun Park
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, Rural Development Administration, Wanju, 55365, Republic of Korea
| | - Jun-Mo Kim
- Department of Animal Science and Technology, College of Biotechnology and Natural Resources, Chung-Ang University, Ansung-si, 17546, Republic of Korea.
| | - Dajeong Lim
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, Rural Development Administration, Wanju, 55365, Republic of Korea.
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