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Ríos-Utrera Á, Montaño-Bermúdez M, Vega-Murillo VE, Martínez-Velázquez G, Baeza-Rodríguez JJ, Román-Ponce SI. Genetic diversity evolution in the Mexican Charolais cattle population. Anim Biosci 2020; 34:1116-1122. [PMID: 32898959 PMCID: PMC8255882 DOI: 10.5713/ajas.20.0401] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Accepted: 08/16/2020] [Indexed: 11/27/2022] Open
Abstract
Objective The aim was to characterize the genetic diversity evolution of the registered Mexican Charolais cattle population by pedigree analysis. Methods Data consisted of 331,390 pedigree records of animals born from 1934 to 2018. Average complete generation equivalent, generation interval, effective population size (Ne), and effective numbers of founders (fe), ancestors (fa), and founder genomes (Ng) were calculated for seven five-year periods. The inbreeding coefficient was calculated per year of birth, from 1984 to 2018, whereas the gene contribution of the most influential ancestors was calculated for the latter period. Results Average complete generation equivalent consistently increased across periods, from 4.76, for the first period (1984 through 1988), to 7.86, for the last period (2014 through 2018). The inbreeding coefficient showed a relative steadiness across the last seventeen years, oscillating from 0.0110 to 0.0145. During the last period, the average generation interval for the father-offspring pathways was nearly 1 yr. longer than that of the mother-offspring pathways. The effective population size increased steadily since 1984 (105.0) and until 2013 (237.1), but showed a minor decline from 2013 to 2018 (233.2). The population displayed an increase in the fa since 1984 and until 2008; however, showed a small decrease during the last decade. The effective number of founder genomes increased from 1984 to 2003, but revealed loss of genetic variability during the last fifteen years (from 136.4 to 127.7). The fa:fe ratio suggests that the genetic diversity loss was partially caused by formation of genetic bottlenecks in the pedigree; in addition, the Ng:fa ratio indicates loss of founder alleles due to genetic drift. The most influential ancestor explained 1.8% of the total genetic variability in the progeny born from 2014 to 2018. Conclusion Inbreeding, Ne, fa, and Ng are rather beyond critical levels; therefore, the current genetic status of the population is not at risk.
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Affiliation(s)
- Ángel Ríos-Utrera
- Campo Experimental La Posta, Centro de Investigación Regional Golfo-Centro, Instituto Nacional de Investigaciones Forestales, Agrícolas y Pecuarias, Medellín, Veracruz 94277, México
| | - Moisés Montaño-Bermúdez
- CENIDFyMA, Instituto Nacional de Investigaciones Forestales, Agrícolas y Pecuarias, Colón, Querétaro 76280, México
| | | | - Guillermo Martínez-Velázquez
- Campo Experimental Santiago Ixcuintla, Centro de Investigación Regional Pacífico-Centro, Instituto Nacional de Investigaciones Forestales, Agrícolas y Pecuarias, Santiago Ixcuintla, Nayarit 63570, México
| | - Juan José Baeza-Rodríguez
- Campo Experimental Mocochá, Centro de Investigación Regional Pacífico-Sur, Instituto Nacional de Investigaciones Forestales, Agrícolas y Pecuarias, Mocochá, Yucatán 97454, México
| | - Sergio Iván Román-Ponce
- Campo Experimental La Campana, Centro de Investigación Regional Norte-Centro, Instituto Nacional de Investigaciones Forestales, Agrícolas y Pecuarias, Aldama, Chihuahua 32910, México
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Lee SM, Oh JD, Park KD, Do KT. Analysis of genetic characteristics of pig breeds using information on single nucleotide polymorphisms. Asian-Australas J Anim Sci 2018; 32:485-493. [PMID: 30145872 PMCID: PMC6409452 DOI: 10.5713/ajas.18.0304] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Accepted: 08/06/2018] [Indexed: 11/29/2022]
Abstract
Objective This study was undertaken to investigate the genetic characteristics of Berkshire (BS), Landrace (LR), and Yorkshire (YS) pig breeds raised in the Great Grandparents pig farms using the single nucleotide polymorphisms (SNP) information. Methods A total of 25,921 common SNP genotype markers in three pig breeds were used to estimate the expected heterozygosity (HE), polymorphism information content, F-statistics (FST), linkage disequilibrium (LD) and effective population size (Ne). Results The chromosome-wise distribution of FST in BS, LR, and YS populations were within the range of 0–0.36, and the average FST value was estimated to be 0.07±0.06. This result indicated some level of genetic segregation. An average LD (r2) for the BS, LR, and YS breeds was estimated to be approximately 0.41. This study also found an average Ne of 19.9 (BS), 31.4 (LR), and 34.1 (YS) over the last 5th generations. The effective population size for the BS, LR, and YS breeds decreased at a consistent rate from 50th to 10th generations ago. With a relatively faster Ne decline rate in the past 10th generations, there exists possible evidence for intensive selection practices in pigs in the recent past. Conclusion To develop customized chips for the genomic selection of various breeds, it is important to select and utilize SNP based on the genetic characteristics of each breed. Since the improvement efficiency of breed pigs increases sharply by the population size, it is important to increase test units for the improvement and it is desirable to establish the pig improvement network system to expand the unit of breed pig improvement through the genetic connection among breed pig farms.
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Affiliation(s)
- Sang-Min Lee
- Department of Animal Biotechnology, Chonbuk National University, Jeonju 54896, Korea
| | - Jae-Don Oh
- Department of Animal Biotechnology, Chonbuk National University, Jeonju 54896, Korea
| | - Kyung-Do Park
- Department of Animal Biotechnology, Chonbuk National University, Jeonju 54896, Korea
| | - Kyoung-Tag Do
- Department of Animal Biotechnology, Jeju National University, Jeju 63243, Korea
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Shin D, Won KH, Kim SH, Kim YM. Extent of linkage disequilibrium and effective population size of Korean Yorkshire swine. Asian-Australas J Anim Sci 2018; 31:1843-1851. [PMID: 30056677 PMCID: PMC6212734 DOI: 10.5713/ajas.17.0258] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 06/22/2018] [Indexed: 11/27/2022]
Abstract
Objective We aimed to characterize linkage disequilibrium (LD) and effective population size (Ne) in a Korean Yorkshire population using genomic data from thousands of individuals. Methods We genotyped 2,470 Yorkshire individuals from four major Grand-Grand-Parent farms in Korea using the Illumina PorcineSNP60 version2 BeadChip, which covers >61,565 single nucleotide polymorphisms (SNPs) located across all chromosomes and mitochondria. We estimated the expected LD and inferred current Ne as well as ancestral Ne. Results We identified 61,565 SNP from autosomes, mitochondria, and sex chromosomes and characterized the LD of the Yorkshire population, which was relatively high between closely linked markers (>0.55 at 50 kb) and declined with increasing genetic distance. The current Ne of this Korean Yorkshire population was 122.87 (106.90; 138.84), while the historical Ne of Yorkshire pigs suggests that the ancestor Ne has decreased by 99.6% over the last 10,000 generations. Conclusion To maintain genetic diversity of a domesticated animal population, we must carefully consider appropriate breed management methods to avoid inbreeding. Although attenuated selection can affect short-term genetic gain, it is essential for maintaining the long-term genetic variability of the Korean Yorkshire population. Continuous and long-term monitoring would also be needed to maintain the pig population to avoid an unintended reduction of Ne. The best way to preserve a sustainable population is to maintain a sufficient Ne.
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Affiliation(s)
- Donghyun Shin
- Department of Animal Biotechnology, Chonbuk National University, Jeonju, 54896, Korea
| | - Kyeong-Hye Won
- Department of Animal Biotechnology, Chonbuk National University, Jeonju, 54896, Korea
| | | | - Yong-Min Kim
- Korean Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Korea
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Kim S, Cheong HS, Shin HD, Lee SS, Roh HJ, Jeon DY, Cho CY. Genetic diversity and divergence among Korean cattle breeds assessed using a BovineHD single-nucleotide polymorphism chip. Asian-Australas J Anim Sci 2018; 31:1691-1699. [PMID: 30056676 PMCID: PMC6212751 DOI: 10.5713/ajas.17.0419] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Accepted: 06/22/2018] [Indexed: 01/07/2023]
Abstract
Objective In Korea, there are three main cattle breeds, which are distinguished by coat color: Brown Hanwoo (BH), Brindle Hanwoo (BRH), and Jeju Black (JB). In this study, we sought to compare the genetic diversity and divergence among there Korean cattle breeds using a BovineHD chip genotyping array. Methods Sample data were collected from 168 cattle in three populations of BH (48 cattle), BRH (96 cattle), and JB (24 cattle). The single-nucleotide polymorphism (SNP) genotyping was performed using the Illumina BovineHD SNP 777K Bead chip. Results Heterozygosity, used as a measure of within-breed genetic diversity, was higher in BH (0.293) and BRH (0.296) than in JB (0.266). Linkage disequilibrium decay was more rapid in BH and BRH than in JB, reaching an average r2 value of 0.2 before 26 kb in BH and BRH, whereas the corresponding value was reached before 32 kb in JB. Intra-population, inter-population, and Fst analyses were used to identify candidate signatures of positive selection in the genome of a domestic Korean cattle population and 48, 11, and 11 loci were detected in the genomic region of the BRH breed, respectively. A Neighbor-Joining phylogenetic tree showed two main groups: a group comprising BH and BRH on one side and a group containing JB on the other. The runs of homozygosity analysis between Korean breeds indicated that the BRH and JB breeds have high inbreeding within breeds compared with BH. An analysis of differentiation based on a high-density SNP chip showed differences between Korean cattle breeds and the closeness of breeds corresponding to the geographic regions where they are evolving. Conclusion Our results indicate that although the Korean cattle breeds have common features, they also show reliable breed diversity.
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Affiliation(s)
- Seungchang Kim
- Animal Genetic Resources Center, National Institute of Animal Science, RDA, Namwon 55717, Korea
| | - Hyun Sub Cheong
- Department of Genetic Epidemiology, SNP Genetics, Inc., Seoul 04107, Korea
| | - Hyoung Doo Shin
- Department of Genetic Epidemiology, SNP Genetics, Inc., Seoul 04107, Korea.,Department of Life Science, Sogang University, Seoul 04107, Korea
| | - Sung-Soo Lee
- Animal Genetic Resources Center, National Institute of Animal Science, RDA, Namwon 55717, Korea
| | - Hee-Jong Roh
- Animal Genetic Resources Center, National Institute of Animal Science, RDA, Namwon 55717, Korea
| | - Da-Yeon Jeon
- Animal Genetic Resources Center, National Institute of Animal Science, RDA, Namwon 55717, Korea
| | - Chang-Yeon Cho
- Animal Genetic Resources Center, National Institute of Animal Science, RDA, Namwon 55717, Korea
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Krupa E, Žáková E, Krupová Z. Evaluation of inbreeding and genetic variability of five pig breeds in czech republic. Asian-Australas J Anim Sci 2015; 28:25-36. [PMID: 25557673 PMCID: PMC4283186 DOI: 10.5713/ajas.14.0251] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/04/2014] [Revised: 07/10/2014] [Accepted: 08/04/2014] [Indexed: 11/27/2022]
Abstract
The complex analysis of the pedigree records of Czech Landrace (CLA), Czech Large White-dam line (CLWd), Czech Large White-sire line (CLWs), Duroc (DC), and Pietrain (PN) was performed to determine trends of genetic diversity (GD), and to find the main sources of the GD loss. The total size of the pedigree was 132,365, 391,151, 32,913, 13,299, and 7,160 animals in CLA, CLWd, CLWs, DC, and PN, respectively. Animals born in the years 2011 through 2013 were assumed as the reference population. The average pedigree completeness index for one generation back was 95.9%, 97.4%, 91.2%, 89.8%, and 94.2% for appropriate breeds. Number of ancestors explaining 100% of gene pool was 186, 373, 125, 157, and 37 in CLA, CLWd, CLWs, DC, and PN, respectively. The relative proportion of inbred animals (58%, 58%, 54%, 47%, and 25%), the average inbreeding (2.7%, 1.4%, 2.5%, 3.6%, and 1.3%) and the average co-ancestry (3.1%, 1.6%, 3.3%, 4.2%, and 3.3%) were found over the past decade in analysed breeds. The expected inbreeding under random mating increased during the last 10 years in CLWs and PN and varied from 1.27% to 3.2%. The effective population size computed on the basis of inbreeding was 76, 74, 50, 35, and 83 in 2012 in CLA, CLWd, CLWs, DC, and PN, respectively. The shortest generation interval (1.45) was observed for CLWd in sire to son selection pathway. The longest generation interval obtained PN (1.95) in sire to daughter pathway. The average relative GD loss within last generation interval was 7.05%, 4.70%, 9.81%, 7.47%, and 10.46%, respectively. The relative proportion of GD loss due to genetic drift on total GD loss was 85.04%, 84.51%, 89.46%, 86.19%, and 83.68% in CLA, CLWd, CLWs, DC, and PN, respectively. All breeds were characterized by a high proportion of inbred animals, but the average inbreeding was low. The most vulnerable breeds to loss of GD are DC and PN. Therefore, a breeding program should be more oriented to prevent the increase of GD loss in these breeds.
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Affiliation(s)
- E. Krupa
- Corresponding Author: Emil Krupa. Tel: +42-0-267009703, E-mail:
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Alam M, Han KI, Lee DH, Ha JH, Kim JJ. Estimation of Effective Population Size in the Sapsaree: A Korean Native Dog (Canis familiaris). Asian-Australas J Anim Sci 2014; 25:1063-72. [PMID: 25049664 PMCID: PMC4093000 DOI: 10.5713/ajas.2012.12048] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/29/2012] [Revised: 04/16/2012] [Accepted: 04/09/2012] [Indexed: 11/27/2022]
Abstract
Effective population size (Ne) is an important measure to understand population structure and genetic variability in animal species. The objective of this study was to estimate Ne in Sapsaree dogs using the information of rate of inbreeding and genomic data that were obtained from pedigree and the Illumina CanineSNP20 (20K) and CanineHD (170K) beadchips, respectively. Three SNP panels, i.e. Sap134 (20K), Sap60 (170K), and Sap183 (the combined panel from the 20K and 170K), were used to genotype 134, 60, and 183 animal samples, respectively. The Ne estimates based on inbreeding rate ranged from 16 to 51 about five to 13 generations ago. With the use of SNP genotypes, two methods were applied for Ne estimation, i.e. pair-wise r2 values using a simple expectation of distance and r2 values under a non-linear regression with respective distances assuming a finite population size. The average pair-wise Ne estimates across generations using the pairs of SNPs that were located within 5 Mb in the Sap134, Sap60, and Sap183 panels, were 1,486, 1,025 and 1,293, respectively. Under the non-linear regression method, the average Ne estimates were 1,601, 528, and 1,129 for the respective panels. Also, the point estimates of past Ne at 5, 20, and 50 generations ago ranged between 64 to 75, 245 to 286, and 573 to 646, respectively, indicating a significant Ne reduction in the last several generations. These results suggest a strong necessity for minimizing inbreeding through the application of genomic selection or other breeding strategies to increase Ne, so as to maintain genetic variation and to avoid future bottlenecks in the Sapsaree population.
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Affiliation(s)
- M Alam
- Sapsaree Breeding Research Institute, Hayang, Gyeongsan, Gyeongbuk, Korea
| | - K I Han
- Sapsaree Breeding Research Institute, Hayang, Gyeongsan, Gyeongbuk, Korea
| | - D H Lee
- The Korean Sapsaree Foundation, Kyungpook National University, Taegu, Korea
| | - J H Ha
- Department of Biotechnology, Kyungpook National University, Taegu, Korea
| | - J J Kim
- Sapsaree Breeding Research Institute, Hayang, Gyeongsan, Gyeongbuk, Korea
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Zhu M, Zhu B, Wang YH, Wu Y, Xu L, Guo LP, Yuan ZR, Zhang LP, Gao X, Gao HJ, Xu SZ, Li JY. Linkage Disequilibrium Estimation of Chinese Beef Simmental Cattle Using High-density SNP Panels. Asian-Australas J Anim Sci 2014; 26:772-9. [PMID: 25049849 PMCID: PMC4093237 DOI: 10.5713/ajas.2012.12721] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/28/2012] [Revised: 03/18/2013] [Accepted: 02/27/2013] [Indexed: 11/27/2022]
Abstract
Linkage disequilibrium (LD) plays an important role in genomic selection and mapping quantitative trait loci (QTL). In this study, the pattern of LD and effective population size (Ne) were investigated in Chinese beef Simmental cattle. A total of 640 bulls were genotyped with IlluminaBovinSNP50BeadChip and IlluminaBovinHDBeadChip. We estimated LD for each autosomal chromosome at the distance between two random SNPs of <0 to 25 kb, 25 to 50 kb, 50 to 100 kb, 100 to 500 kb, 0.5 to 1 Mb, 1 to 5 Mb and 5 to 10 Mb. The mean values of r2 were 0.30, 0.16 and 0.08, when the separation between SNPs ranged from 0 to 25 kb to 50 to 100 kb and then to 0.5 to 1 Mb, respectively. The LD estimates decreased as the distance increased in SNP pairs, and increased with the increase of minor allelic frequency (MAF) and with the decrease of sample sizes. Estimates of effective population size for Chinese beef Simmental cattle decreased in the past generations and Ne was 73 at five generations ago.
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Affiliation(s)
- M Zhu
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - B Zhu
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Y H Wang
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Y Wu
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - L Xu
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - L P Guo
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Z R Yuan
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - L P Zhang
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - X Gao
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - H J Gao
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - S Z Xu
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - J Y Li
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
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Shin DH, Cho KH, Park KD, Lee HJ, Kim H. Accurate estimation of effective population size in the korean dairy cattle based on linkage disequilibrium corrected by genomic relationship matrix. Asian-Australas J Anim Sci 2014; 26:1672-9. [PMID: 25049757 PMCID: PMC4092893 DOI: 10.5713/ajas.2013.13320] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/04/2013] [Revised: 10/17/2013] [Accepted: 10/02/2013] [Indexed: 11/27/2022]
Abstract
Linkage disequilibrium between markers or genetic variants underlying interesting traits affects many genomic methodologies. In many genomic methodologies, the effective population size (Ne) is important to assess the genetic diversity of animal populations. In this study, dairy cattle were genotyped using the Illumina BovineHD Genotyping BeadChips for over 777,000 SNPs located across all autosomes, mitochondria and sex chromosomes, and 70,000 autosomal SNPs were selected randomly for the final analysis. We characterized more accurate linkage disequilibrium in a sample of 96 dairy cattle producing milk in Korea. Estimated linkage disequilibrium was relatively high between closely linked markers (>0.6 at 10 kb) and decreased with increasing distance. Using formulae that related the expected linkage disequilibrium to Ne, and assuming a constant actual population size, Ne was estimated to be approximately 122 in this population. Historical Ne, calculated assuming linear population growth, was suggestive of a rapid increase Ne over the past 10 generations, and increased slowly thereafter. Additionally, we corrected the genomic relationship structure per chromosome in calculating r(2) and estimated Ne. The observed Ne based on r(2) corrected by genomics relationship structure can be rationalized using current knowledge of the history of the dairy cattle breeds producing milk in Korea.
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Affiliation(s)
- Dong-Hyun Shin
- Department of Agricultural Biotechnology, Animal Biotechnology Major, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Korea
| | - Kwang-Hyun Cho
- Department of Agricultural Biotechnology, Animal Biotechnology Major, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Korea
| | - Kyoung-Do Park
- Department of Agricultural Biotechnology, Animal Biotechnology Major, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Korea
| | - Hyun-Jeong Lee
- Department of Agricultural Biotechnology, Animal Biotechnology Major, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Korea
| | - Heebal Kim
- Department of Agricultural Biotechnology, Animal Biotechnology Major, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Korea
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