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Marín Navas C, Delgado Bermejo JV, McLean AK, León Jurado JM, Rodriguez de la Borbolla y Ruiberriz de Torres A, Navas González FJ. Discriminant Canonical Analysis of the Contribution of Spanish and Arabian Purebred Horses to the Genetic Diversity and Population Structure of Hispano-Arabian Horses. Animals (Basel) 2021; 11:ani11020269. [PMID: 33494478 PMCID: PMC7912545 DOI: 10.3390/ani11020269] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 01/11/2021] [Accepted: 01/18/2021] [Indexed: 12/19/2022] Open
Abstract
Simple Summary The demographic and genetic diversity structure and the contributions of Spanish (PRE) and Arabian Purebred (PRá) horses to the process of conformation of the Hispano-Arabian (Há) horse breed were evaluated. Genetic diversity parameters (inbreeding coefficient, genetic conservation index, coancestry coefficient, non-random mating degree, relatedness coefficient, maximum, complete, and equivalent generations, and number of offspring) were evaluated using a discriminant canonical analysis to determine the partial contributions of each founder breed to the development of Há horse breed. The calculation of Nei genetic distances suggests the overlapping could be estimated in 29.55% of the gene pool of the Há having a PRE origin while 70.45% of the gene pool of the breed may derive from a PRá origin. Although a progressive loss of founder representation may have occurred, breeding strategies implemented considering mating between animals with the highest genetic conservation indices (GCI) may compensate for its effects. Abstract Genetic diversity and population structure were analyzed using the historical and current pedigree information of the Arabian (PRá), Spanish Purebred (PRE), and Hispano-Arabian (Há) horse breeds. Genetic diversity parameters were computed and a canonical discriminant analysis was used to determine the contributions of ancestor breeds to the genetic diversity of the Há horse. Pedigree records were available for 207,100 animals born between 1884 and 2019. Nei’s distances and the equivalent subpopulations number indicated the existence of a highly structured, integrated population for the Há breed, which is more closely genetically related to PRá than PRE horses. An increase in the length of the generation interval might be an effective solution to reduce the increase in inbreeding found in the studied breeds (8.44%, 8.50%, and 2.89%, for PRá, PRE, and Há, respectively). Wright’s fixation statistics indicated slight interherd inbreeding. Pedigree completeness suggested genetic parameters were highly reliable. High GCI levels found for number of founders and non-founders and their relationship to the evolution of inbreeding permit controlling potential deleterious negative effects from excessively frequent mating between interrelated individuals. For instance, the use of individuals presenting high GCI may balance founders’ gene contributions and consequently preserve genetic diversity levels (current genetic diversity loss in PRá, PRE, and Há is 6%, 7%, and 4%, respectively).
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Affiliation(s)
- Carmen Marín Navas
- Department of Genetics, Faculty of Veterinary Sciences, University of Córdoba, 14071 Córdoba, Spain; (C.M.N.); (J.V.D.B.)
| | - Juan Vicente Delgado Bermejo
- Department of Genetics, Faculty of Veterinary Sciences, University of Córdoba, 14071 Córdoba, Spain; (C.M.N.); (J.V.D.B.)
| | - Amy Katherine McLean
- Department of Animal Science, University of California Davis, Davis, CA 95617, USA;
| | - José Manuel León Jurado
- Centro Agropecuario Provincial de Córdoba, Diputación Provincial de Córdoba, 14071 Córdoba, Spain;
| | | | - Francisco Javier Navas González
- Department of Genetics, Faculty of Veterinary Sciences, University of Córdoba, 14071 Córdoba, Spain; (C.M.N.); (J.V.D.B.)
- Correspondence: ; Tel.: +34-957-21-87-06
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Gül S, Yilmaz O, Gündüz Z, Keskin M, Cemal I, Ata N, Önel SE. The genetic structure of the goat breeds belonging to Northwest part of Fertile Crescent. Small Rumin Res 2020. [DOI: 10.1016/j.smallrumres.2019.09.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Asroush F, Mirhoseini SZ, Badbarin N, Seidavi A, Tufarelli V, Laudadio V, Dario C, Selvaggi M. Genetic characterization of Markhoz goat breed using microsatellite markers. Arch Anim Breed 2018; 61:469-473. [PMID: 32175455 PMCID: PMC7065388 DOI: 10.5194/aab-61-469-2018] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 11/29/2018] [Indexed: 11/30/2022] Open
Abstract
The use of molecular markers can support the management of endangered populations and should be combined with appropriate breeding strategies to improve productive traits avoiding the decline of the breed. The genetic variability at 10 microsatellite loci were investigated in a sample of 100 unrelated Markhoz goats (77 females and 23 males). The investigated population was reared at the Sanandaj Markhoz goat Performance Testing Station in Kurdistan, Iran. Markhoz goat, a multipurpose breed, is one of the most valuable genetic resources in Iran. All the studied loci were found to be polymorphic and a total number of 52 alleles were identified with an average number of alleles of 5.2. Moreover, some population genetic indices, such as observed and expected heterozygosity, observed and expected number of alleles, Shannon's index, Nei's expected heterozygosity, and polymorphism information content were also calculated. Despite the decreasing population size, Markhoz goat genetic diversity is still conserved. The breed seems to have a good level of genetic variability and, as a consequence, a potential margin of adaptability to environment and for future genetic improvement.
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Affiliation(s)
- Fariborz Asroush
- Department of Animal Science, Rasht Branch, Islamic Azad University,
Rasht, Iran
| | | | - Nejat Badbarin
- Department of Animal Science, University of Guilan, Rasht, Iran
| | - Alireza Seidavi
- Department of Animal Science, Rasht Branch, Islamic Azad University,
Rasht, Iran
| | - Vincenzo Tufarelli
- Department DETO – Section of Veterinary Science and Animal Production,
University of Bari, Valenzano, Italy
| | - Vito Laudadio
- Department DETO – Section of Veterinary Science and Animal Production,
University of Bari, Valenzano, Italy
| | - Cataldo Dario
- Department of Agro-Environmental and Territorial Sciences, University
of Bari, Bari, Italy
| | - Maria Selvaggi
- Department of Agro-Environmental and Territorial Sciences, University
of Bari, Bari, Italy
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Tefiel H, Ata N, Chahbar M, Benyarou M, Fantazi K, Yilmaz O, Cemal I, Karaca O, Boudouma D, Gaouar SBS. Genetic characterization of four Algerian goat breeds assessed by microsatellite markers. Small Rumin Res 2018. [DOI: 10.1016/j.smallrumres.2018.01.021] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Mastrangelo S, Tolone M, Montalbano M, Tortorici L, Di Gerlando R, Sardina MT, Portolano B. Population genetic structure and milk production traits in Girgentana goat breed. ANIMAL PRODUCTION SCIENCE 2017. [DOI: 10.1071/an15431] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The aim of this work was to evaluate the genetic status of the Girgentana goat, an endangered breed from Sicily (Italy), using microsatellite markers. Furthermore, as the main purpose of the Girgentana breed is milk production, quantitative milk traits were investigated, including fatty acid profile. Molecular data from CSN1S1, CSN2, CSN1S2, and CSN3 casein genes were also used to infer haplotypes. A total of 264 individuals were collected. Samples of Maltese (n = 41) and Derivata di Siria (n = 33) goat breeds were also used to understand the genetic relationship among breeds. Test-day records for milk production were collected to determine daily milk yield, fat, protein, casein, lactose, and somatic cell count. Individual milk samples were also collected for fatty acid extraction. Wright’s statistics, gene flow, Nei genetic distance, factorial correspondence analysis, and Bayesian assignment test showed the existence of genetic variability and differentiation among breeds. The AMOVA results indicated that 89.96% of the total variance was partitioned within populations. The Girgentana breed appears to have a subdivided population, and has not experienced a recent bottleneck. A high variability in milk yield was observed. Mean morning milk yield was 1448 ± 404 g, with 4.30 ± 0.87% and 3.72 ± 0.44% of fat and protein percentages, respectively. The average somatic cell count found in Girgentana goat milk was higher than the threshold of 1 500 000 cells/mL advised in Europe for fresh milk. Gross milk and fatty acid composition were similar to that reported in the literature for other local goat breeds.
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Seilsuth S, Seo JH, Kong HS, Jeon GJ. Microsatellite Analysis of the Genetic Diversity and Population Structure in Dairy Goats in Thailand. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2016; 29:327-32. [PMID: 26950862 PMCID: PMC4811782 DOI: 10.5713/ajas.15.0270] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Revised: 04/16/2015] [Accepted: 05/25/2015] [Indexed: 11/27/2022]
Abstract
The genetic relationships between different populations and breeds of exotic dairy goats in Thailand were studied using 12 microsatellite markers. Blood samples were obtained from 211 goats from Department of Livestock Development breeding and research farms: 29 Anglonubian (AN), 21 Alpine (AP), 23 Jamunapari (JAM), 50 Saanen (SN), and 88 Toggenburg (TG). Five of the 12 microsatellite markers were found to be polymorphic. A mean of 7.40 alleles per locus was found, with a range from 5 (SPS115 and ETH225) to 11 (TGLA122). We found 24, 27, 19, 32, and 24 alleles in the AN, AP, JAM, SN, and TG breeds, respectively; 37 alleles were present in all breeds. The mean number of alleles in each population ranged from 3.2 (ETH225 locus) to 7.6 (TGLA122 locus). Genetic variability within the breeds was moderate as evidenced by the mean expected heterozygosity of 0.539. The average observed heterozygosity across the 5 markers in all breeds was 0.529 with the maximum observed at the BM1818 locus (0.772) and the minimum at the ETH225 locus (0.248). The observed and expected heterozygosity for all breeds for the 5 microsatellite markers ranged from 0.419 to 0.772 and 0.227 to 0.792, respectively. On the basis of their means, the TGLA122 and BM1818 loci were the most suitable markers for distinguishing genetic diversity among the goats. The estimated average F is value for the breeds ranged from -0.044 (ETH225) to 0.180 (SPS115), while the estimated average F st value ranged from 0.021 (SPS115) to 0.104 (ETH10). These results indicated that TGLA122 and BM1818 markers are suitable to be used for aiding conservation and breeding improvement strategies of dairy.
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Affiliation(s)
- Somkiat Seilsuth
- Faculty of Agriculture and Life Science, Chadrakasem Rajabhat University, Bangkok 10902, Thailand ; Genetic Informatics Center, Hankyong National University, Anseong 456-749, Korea
| | - Joo Hee Seo
- Genetic Informatics Center, Hankyong National University, Anseong 456-749, Korea
| | - Hong Sik Kong
- Genetic Informatics Center, Hankyong National University, Anseong 456-749, Korea
| | - Gwang Joo Jeon
- Genetic Informatics Center, Hankyong National University, Anseong 456-749, Korea
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The impact of selection on population genetic structure in the clam Meretrix petechialis revealed by microsatellite markers. Genetica 2015; 144:1-8. [DOI: 10.1007/s10709-015-9873-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Accepted: 11/13/2015] [Indexed: 11/27/2022]
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Genetic diversity and population structure analysis of native and crossbred goat genetic groups of Kerala, India. Small Rumin Res 2015. [DOI: 10.1016/j.smallrumres.2015.08.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Iquebal MA, Sarika, Dhanda SK, Arora V, Dixit SP, Raghava GPS, Rai A, Kumar D. Development of a model webserver for breed identification using microsatellite DNA marker. BMC Genet 2013; 14:118. [PMID: 24320218 PMCID: PMC3890620 DOI: 10.1186/1471-2156-14-118] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2013] [Accepted: 12/04/2013] [Indexed: 11/10/2022] Open
Abstract
Background Identification of true to breed type animal for conservation purpose is imperative. Breed dilution is one of the major problems in sustainability except cases of commercial crossbreeding under controlled condition. Breed descriptor has been developed to identify breed but such descriptors cover only “pure breed” or true to the breed type animals excluding undefined or admixture population. Moreover, in case of semen, ova, embryo and breed product, the breed cannot be identified due to lack of visible phenotypic descriptors. Advent of molecular markers like microsatellite and SNP have revolutionized breed identification from even small biological tissue or germplasm. Microsatellite DNA marker based breed assignments has been reported in various domestic animals. Such methods have limitations viz. non availability of allele data in public domain, thus each time all reference breed has to be genotyped which is neither logical nor economical. Even if such data is available but computational methods needs expertise of data analysis and interpretation. Results We found Bayesian Networks as best classifier with highest accuracy of 98.7% using 51850 reference allele data generated by 25 microsatellite loci on 22 goat breed population of India. The FST values in the study were seen to be low ranging from 0.051 to 0.297 and overall genetic differentiation of 13.8%, suggesting more number of loci needed for higher accuracy. We report here world’s first model webserver for breed identification using microsatellite DNA markers freely accessible at http://cabin.iasri.res.in/gomi/. Conclusion Higher number of loci is required due to less differentiable population and large number of breeds taken in this study. This server will reduce the cost with computational ease. This methodology can be a model for various other domestic animal species as a valuable tool for conservation and breed improvement programmes.
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Affiliation(s)
| | | | | | | | | | | | | | - Dinesh Kumar
- Centre for Agricultural Bioinformatics, Indian Agricultural Statistics Research Institute, Library Avenue, PUSA, New Delhi 110012, India.
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Visser C, Van Marle-Köster E, Snyman M, Bovenhuis H, Crooijmans R. Quantitative trait loci associated with pre-weaning growth in South African Angora goats. Small Rumin Res 2013. [DOI: 10.1016/j.smallrumres.2012.11.035] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Liu JB, Wang F, Lang X, Zha X, Sun XP, Yue YJ, Feng RL, Yang BH, Guo J. Analysis of Geographic and Pairwise Distances among Chinese Cashmere Goat Populations. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2013; 26:323-33. [PMID: 25049794 PMCID: PMC4093469 DOI: 10.5713/ajas.2012.12500] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/13/2012] [Revised: 01/18/2013] [Accepted: 12/03/2012] [Indexed: 11/27/2022]
Abstract
This study investigated the geographic and pairwise distances of nine Chinese local Cashmere goat populations through the analysis of 20 microsatellite DNA markers. Fluorescence PCR was used to identify the markers, which were selected based on their significance as identified by the Food and Agriculture Organization of the United Nations (FAO) and the International Society for Animal Genetics (ISAG). In total, 206 alleles were detected; the average allele number was 10.30; the polymorphism information content of loci ranged from 0.5213 to 0.7582; the number of effective alleles ranged from 4.0484 to 4.6178; the observed heterozygosity was from 0.5023 to 0.5602 for the practical sample; the expected heterozygosity ranged from 0.5783 to 0.6464; and Allelic richness ranged from 4.7551 to 8.0693. These results indicated that Chinese Cashmere goat populations exhibited rich genetic diversity. Further, the Wright’s F-statistics of subpopulation within total (FST) was 0.1184; the genetic differentiation coefficient (GST) was 0.0940; and the average gene flow (Nm) was 2.0415. All pairwise FST values among the populations were highly significant (p<0.01 or p<0.001), suggesting that the populations studied should all be considered to be separate breeds. Finally, the clustering analysis divided the Chinese Cashmere goat populations into at least four clusters, with the Hexi and Yashan goat populations alone in one cluster. These results have provided useful, practical, and important information for the future of Chinese Cashmere goat breeding.
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Affiliation(s)
- Jian-Bin Liu
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
| | - Fan Wang
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
| | - Xia Lang
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
| | - Xi Zha
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
| | - Xiao-Ping Sun
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
| | - Yao-Jing Yue
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
| | - Rui-Lin Feng
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
| | - Bo-Hui Yang
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
| | - Jian Guo
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
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Assessment of genetic diversity, genetic relationship and bottleneck using microsatellites in some native Turkish goat breeds. Small Rumin Res 2012. [DOI: 10.1016/j.smallrumres.2011.12.005] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Martínez A, Ferrando A, Manunza A, Gómez M, Landi V, Jordana J, Capote J, Badaoui B, Vidal O, Delgado J, Amills M. Inferring the demographic history of a highly endangered goat breed through the analysis of nuclear and mitochondrial genetic signatures. Small Rumin Res 2012. [DOI: 10.1016/j.smallrumres.2011.11.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Rout PK, Thangraj K, Mandal A, Roy R. Genetic variation and population structure in Jamunapari goats using microsatellites, mitochondrial DNA, and milk protein genes. ScientificWorldJournal 2012; 2012:618909. [PMID: 22606053 PMCID: PMC3349149 DOI: 10.1100/2012/618909] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2011] [Accepted: 10/25/2011] [Indexed: 11/17/2022] Open
Abstract
Jamunapari, a dairy goat breed of India, has been gradually declining in numbers in its home tract over the years. We have analysed genetic variation and population history in Jamunapari goats based on 17 microsatellite loci, 2 milk protein loci, mitochondrial hypervariable region I (HVRI) sequencing, and three Y-chromosomal gene sequencing. We used the mitochondrial DNA (mtDNA) mismatch distribution, microsatellite data, and bottleneck tests to infer the population history and demography. The mean number of alleles per locus was 9.0 indicating that the allelic variation was high in all the loci and the mean heterozygosity was 0.769 at nuclear loci. Although the population size is smaller than 8,000 individuals, the amount of variability both in terms of allelic richness and gene diversity was high in all the microsatellite loci except ILST 005. The gene diversity and effective number of alleles at milk protein loci were higher than the 10 other Indian goat breeds that they were compared to. Mismatch analysis was carried out and the analysis revealed that the population curve was unimodal indicating the expansion of population. The genetic diversity of Y-chromosome genes was low in the present study. The observed mean M ratio in the population was above the critical significance value (Mc) and close to one indicating that it has maintained a slowly changing population size. The mode-shift test did not detect any distortion of allele frequency and the heterozygosity excess method showed that there was no significant departure from mutation-drift equilibrium detected in the population. However, the effects of genetic bottlenecks were observed in some loci due to decreased heterozygosity and lower level of M ratio. There were two observed genetic subdivisions in the population supporting the observations of farmers in different areas. This base line information on genetic diversity, bottleneck analysis, and mismatch analysis was obtained to assist the conservation decision and management of the breed.
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Affiliation(s)
- P K Rout
- Central Institute for Research on Goats, Makhdoom, Farah, Mathura, India.
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Gama L, Bressan M. Biotechnology applications for the sustainable management of goat genetic resources. Small Rumin Res 2011. [DOI: 10.1016/j.smallrumres.2011.03.031] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Oliveira J, Ribeiro M, Rocha L, Gomes-Filho M, Delgado J, Martinez A, Menezes M, Bettencourt C, Gama L. Genetic relationships between two homologous goat breeds from Portugal and Brazil assessed by microsatellite markers. Small Rumin Res 2010. [DOI: 10.1016/j.smallrumres.2010.05.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Guan TL, Zeng B, Peng QK, Yue BS, Zou FD. Microsatellite analysis of the genetic structure of captive forest musk deer populations and its implication for conservation. BIOCHEM SYST ECOL 2009. [DOI: 10.1016/j.bse.2009.04.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Kumar D, Sharma R, Pandey AK, Gour DS, Malik G, Ahlawat SPS, Jain A. Genetic diversity and bottleneck analysis of Indian bellary sheep by microsatellite markers. RUSS J GENET+ 2007. [DOI: 10.1134/s1022795407090050] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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