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Jin S, Won JI, Kim HJ, Park B, Kim SW, Kim UH, Kang SS, Lee HJ, Moon SJ, Park MS, Sim YT, Jang SS, Kim NY. Polymorphism analysis of tri- and tetranucleotide repeat microsatellite markers in Hanwoo cattle. JOURNAL OF ANIMAL SCIENCE AND TECHNOLOGY 2024; 66:717-725. [PMID: 39165748 PMCID: PMC11331372 DOI: 10.5187/jast.2024.e10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Revised: 12/21/2023] [Accepted: 01/23/2024] [Indexed: 08/22/2024]
Abstract
The Hanwoo traceability system currently utilizes 11 dinucleotide repeat microsatellite (MS) markers. However, dinucleotide repeat markers are known to have a high incidence of polymerase chain reaction (PCR) artifacts, such as stutter bands, which can complicate the accurate reading of alleles. In this study, we examined the polymorphisms of the 11 dinucleotide repeat MS markers currently employed in traceability systems. Additionally, we explored four trinucleotide repeat MS markers and one tetranucleotide repeat MS marker in a sample of 1,106 Hanwoo cattle. We also assessed the potential utility of the tri- and tetranucleotide repeat MS markers. The polymorphic information content (PIC) of the five tri- and tetranucleotide repeat markers ranged from 0.663 to 0.767 (mean: 0.722), sufficiently polymorphic and slightly higher than the mean (0.716) of the current 11 dinucleotide repeat markers. Using all 16 markers, the mean PIC was 0.718. The estimated probability of identity (PI) was 3.13 × 10-12 using the 11 dinucleotide repeat markers, 7.03 × 10-6 using the five tri- and tetranucleotide repeat markers, and 2.39 × 10-17 using all 16 markers; the respective PIhalf-sibs values were 2.69 × 10-9, 1.29 × 10-4, and 3.42 × 10-13; and the respective PIsibs values were 3.89 × 10-5, 9.6 × 10-3, and 3.69 × 10-7. The probability of exclusion1 (PE1) was 0.999864 for the 11 dinucleotide repeat markers, 0.981141 for five of the tri- and tetranucleotide repeat markers, and > 0.99 for all 16 markers; the respective PE2 values were 0.994632, 0.901369, and > 0.99; and the respective PE3 values were 0.998702, > 0.99, and > 0.99. The five investigated tri- and tetranucleotide repeat MS markers can be used in combination with the 11 existing MS markers to improve the accuracy of individual identification and paternity testing in Hanwoo.
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Affiliation(s)
- Shil Jin
- Hanwoo Research Institute, National
Institute of Animal Science, Pyeongchang 25340, Korea
| | - Jeong Il Won
- Hanwoo Research Institute, National
Institute of Animal Science, Pyeongchang 25340, Korea
| | - Hyoun Ju Kim
- Hanwoo Research Institute, National
Institute of Animal Science, Pyeongchang 25340, Korea
| | - Byoungho Park
- Animal Breeding & Genetics
Division, National Institute of Animal Science, Cheonan 31000,
Korea
| | - Sung Woo Kim
- Hanwoo Research Institute, National
Institute of Animal Science, Pyeongchang 25340, Korea
| | - Ui Hyung Kim
- Hanwoo Research Institute, National
Institute of Animal Science, Pyeongchang 25340, Korea
| | - Sung-Sik Kang
- Hanwoo Research Institute, National
Institute of Animal Science, Pyeongchang 25340, Korea
| | - Hyun-Jeong Lee
- Hanwoo Research Institute, National
Institute of Animal Science, Pyeongchang 25340, Korea
| | - Sung Jin Moon
- Hanwoo Research Institute, National
Institute of Animal Science, Pyeongchang 25340, Korea
| | - Myung Sun Park
- Hanwoo Research Institute, National
Institute of Animal Science, Pyeongchang 25340, Korea
| | - Yong Teak Sim
- miDNA Genome Research
institute, Kunsan 54156, Korea
| | - Sun Sik Jang
- Hanwoo Research Institute, National
Institute of Animal Science, Pyeongchang 25340, Korea
| | - Nam Young Kim
- Hanwoo Research Institute, National
Institute of Animal Science, Pyeongchang 25340, Korea
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Oh JD, Song KD, Seo JH, Kim DK, Kim SH, Seo KS, Lim HT, Lee JB, Park HC, Ryu YC, Kang MS, Cho S, Kim ES, Choe HS, Kong HS, Lee HK. Genetic traceability of black pig meats using microsatellite markers. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2014; 27:926-31. [PMID: 25050032 PMCID: PMC4093566 DOI: 10.5713/ajas.2013.13829] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Revised: 03/27/2014] [Accepted: 04/10/2014] [Indexed: 11/27/2022]
Abstract
Pork from Jeju black pig (population J) and Berkshire (population B) has a unique market share in Korea because of their high meat quality. Due to the high demand of this pork, traceability of the pork to its origin is becoming an important part of the consumer demand. To examine the feasibility of such a system, we aim to provide basic genetic information of the two black pig populations and assess the possibility of genetically distinguishing between the two breeds. Muscle samples were collected from slaughter houses in Jeju Island and Namwon, Chonbuk province, Korea, for populations J and B, respectively. In total 800 Jeju black pigs and 351 Berkshires were genotyped at thirteen microsatellite (MS) markers. Analyses on the genetic diversity of the two populations were carried out in the programs MS toolkit and FSTAT. The population structure of the two breeds was determined by a Bayesian clustering method implemented in structure and by a phylogenetic analysis in Phylip. Population J exhibited higher mean number of alleles, expected heterozygosity and observed heterozygosity value, and polymorphism information content, compared to population B. The FIS values of population J and population B were 0.03 and −0.005, respectively, indicating that little or no inbreeding has occurred. In addition, genetic structure analysis revealed the possibility of gene flow from population B to population J. The expected probability of identify value of the 13 MS markers was 9.87×10−14 in population J, 3.17×10−9 in population B, and 1.03×10−12 in the two populations. The results of this study are useful in distinguishing between the two black pig breeds and can be used as a foundation for further development of DNA markers.
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Affiliation(s)
- Jae-Don Oh
- Genomic Informatics Center, Hankyong National University, Anseong 456-649, Korea
| | - Ki-Duk Song
- Genomic Informatics Center, Hankyong National University, Anseong 456-649, Korea
| | - Joo-Hee Seo
- Genomic Informatics Center, Hankyong National University, Anseong 456-649, Korea
| | - Duk-Kyung Kim
- Genomic Informatics Center, Hankyong National University, Anseong 456-649, Korea
| | - Sung-Hoon Kim
- Genomic Informatics Center, Hankyong National University, Anseong 456-649, Korea
| | - Kang-Seok Seo
- Department of Animal Science and Technology, Sunchon National University, Sunchon 540-742, Korea
| | - Hyun-Tae Lim
- Institute of Agriculture and Life Sciences, Gyeongsang National University, Jinju 660-701, Korea
| | - Jae-Bong Lee
- Institute of Agriculture and Life Sciences, Gyeongsang National University, Jinju 660-701, Korea
| | | | - Youn-Chul Ryu
- Major of Animal Science and Biotechnology, Jeju National University, Jeju 690-756, Korea
| | - Min-Soo Kang
- Major of Animal Science and Biotechnology, Jeju National University, Jeju 690-756, Korea
| | | | - Eui-Soo Kim
- Genomic Informatics Center, Hankyong National University, Anseong 456-649, Korea ; Department of Animal Science, Iowa State University, Ames, IA 50011, USA
| | - Ho-Sung Choe
- Department of Animal Biotechnology, Chonbuk National University, Jeonju 561-756, Korea
| | - Hong-Sik Kong
- Genomic Informatics Center, Hankyong National University, Anseong 456-649, Korea
| | - Hak-Kyo Lee
- Genomic Informatics Center, Hankyong National University, Anseong 456-649, Korea
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Heo EJ, Ko EK, Seo KH, Chon JW, Kim YJ, Park HJ, Wee SH, Moon JS. Comparison of the Microsatellite and Single Nucleotide Polymorphism Methods for Discriminating among Hanwoo (Korean Native Cattle), Imported, and Crossbred Beef in Korea. Korean J Food Sci Anim Resour 2014; 34:763-8. [PMID: 26761672 PMCID: PMC4662190 DOI: 10.5851/kosfa.2014.34.6.763] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Revised: 10/08/2014] [Accepted: 10/12/2014] [Indexed: 11/16/2022] Open
Abstract
The identity of 45 Hanwo and 47 imported beef (non-Hanwoo) samples from USA and Australia were verified using the microsatellite (MS) marker and single nucleotide polymorphism (SNP) methods. Samples were collected from 19 supermarkets located in the city of Seoul and Gyeonggi province, South Korea, from 2009 to 2011. As a result, we obtained a 100% concordance rate between the MS and SNP methods for identifying Hanwoo and non-Hanwoo beef. The MS method presented a 95% higher individual discriminating value for Hanwoo (97.8%) than for non-Hanwoo (61.7%) beef. For further comparison of the MS and SNP methods, blood samples were collected and tested from 54 Hanwoo × Holstein crossbred cattle (first, second, and third generations). By using the SNP and MS methods, we correctly identified all of the first-generation crossbred cattle as non-Hanwoo; in addition, among the second and third generation crossbreds, the ratio identified as Hanwoo was 20% and 10%, respectively. The MS method used in our study provides more information, but requires sophisticated techniques during each experimental process. By contrast, the SNP method is simple and has a lower error rate. Our results suggest that the MS and SNP methods are useful for discriminating Hanwoo from non-Hanwoo breeds.
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Affiliation(s)
- Eun-Jeong Heo
- Ministry of Food and Drug Safety, Cheongwon 363-951, Korea
| | - Eun-Kyung Ko
- Animal and Plant Quarantine Agency, Anyang 430-757, Korea
| | - Kun-Ho Seo
- KU Center for Food Safety, College of Veterinary Medicine, Konkuk University, Seoul 143-701, Korea
| | - Jung-Whan Chon
- KU Center for Food Safety, College of Veterinary Medicine, Konkuk University, Seoul 143-701, Korea
| | - Young-Jo Kim
- Ministry of Food and Drug Safety, Cheongwon 363-951, Korea
| | - Hyun-Jung Park
- Ministry of Food and Drug Safety, Cheongwon 363-951, Korea
| | - Sung-Hwan Wee
- Animal and Plant Quarantine Agency, Anyang 430-757, Korea
| | - Jin-San Moon
- Animal and Plant Quarantine Agency, Anyang 430-757, Korea
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Oh J, Kong H, Lee J, Moon S, Jeon G, Lee H. The Genetic Relationship between Regional Population of Hanwoo Brands (Korean Cattle) Using Microsatellite Markers. Korean J Food Sci Anim Resour 2007. [DOI: 10.5851/kosfa.2007.27.3.357] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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