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Lai FY, Lin YC, Ding ST, Chang CS, Chao WL, Wang PH. Development of novel microsatellite markers to analyze the genetic structure of dog populations in Taiwan. Anim Biosci 2022; 35:1314-1326. [PMID: 35240021 PMCID: PMC9449399 DOI: 10.5713/ab.21.0519] [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: 11/26/2021] [Accepted: 02/16/2022] [Indexed: 11/27/2022] Open
Abstract
Objective Alongside the rise of animal-protection awareness in Taiwan, the public has been paying more attention to dog genetic deficiencies due to inbreeding in the pet market. The goal of this study was to isolate novel microsatellite markers for monitoring the genetic structure of domestic dog populations in Taiwan. Methods A total of 113 DNA samples from three dog breeds - beagles (BEs), bichons (BIs), and schnauzers (SCs) - were used in subsequent polymorphic tests applying the 14 novel microsatellite markers that were isolated in this study. Results The results showed that the high level of genetic diversity observed in these novel microsatellite markers provided strong discriminatory power. The estimated probability of identity (P(ID)) and the probability of identity among sibs (P(ID)sib) for the 14 novel microsatellite markers were 1.7×10-12 and 1.6×10-5, respectively. Furthermore, the power of exclusion (PE) for the 14 novel microsatellite markers was 99.98%. The neighbor-joining (NJ) trees constructed among the three breeds indicated that the 14 sets of novel microsatellite markers were sufficient to correctly cluster the BEs, BIs, and SCs. The principal coordinate analysis (PCoA) plot showed that the dogs could be accurately separated by these 14 loci baled on different breeds; moreover, the Beagles from different sources were also distinguished. The first, the second, and the third principal coordinates could be used to explain 44.15, 26.35 and 19.97% of the genetic variation. Conclusion The results of this study could enable powerful monitoring of the genetic structure of domestic dog populations in Taiwan.
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Affiliation(s)
- Fang-Yu Lai
- Key Laboratory of Animal Genetics, Breeding and Bioresources, Department of Animal Science and Technology, College of Bioresources and Agriculture, National Taiwan University, Taipei 10672, Taiwan
| | - Yu-Chen Lin
- Key Laboratory of Animal Genetics, Breeding and Bioresources, Department of Animal Science and Technology, College of Bioresources and Agriculture, National Taiwan University, Taipei 10672, Taiwan
| | - Shih-Torng Ding
- Key Laboratory of Animal Genetics, Breeding and Bioresources, Department of Animal Science and Technology, College of Bioresources and Agriculture, National Taiwan University, Taipei 10672, Taiwan
| | - Chi-Sheng Chang
- Department of Animal Science, Chinese Culture University. No. 55, Hwa-Kang Rd., Yang-Ming-Shan, Taipei City 11114, Taiwan
| | - Wi-Lin Chao
- Department of Animal Industry, Council of Agriculture, Executive Yuan. No. 37, Nanhai Rd., Zhongzheng Dist., Taipei City 100212., Taiwan
| | - Pei-Hwa Wang
- Key Laboratory of Animal Genetics, Breeding and Bioresources, Department of Animal Science and Technology, College of Bioresources and Agriculture, National Taiwan University, Taipei 10672, Taiwan
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Genome-wide single nucleotide polymorphism (SNP) identification and characterization in a non-model organism, the African buffalo (Syncerus caffer), using next generation sequencing. Mamm Biol 2016. [DOI: 10.1016/j.mambio.2016.07.047] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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Miller SM, Clarke AB, Bloomer P, Guthrie AJ, Harper CK. Evaluation of microsatellites for common ungulates in the South African wildlife industry. CONSERV GENET RESOUR 2016. [DOI: 10.1007/s12686-016-0554-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Smitz N, Cornélis D, Chardonnet P, Caron A, de Garine-Wichatitsky M, Jori F, Mouton A, Latinne A, Pigneur LM, Melletti M, Kanapeckas KL, Marescaux J, Pereira CL, Michaux J. Genetic structure of fragmented southern populations of African Cape buffalo (Syncerus caffer caffer). BMC Evol Biol 2014; 14:203. [PMID: 25367154 PMCID: PMC4232705 DOI: 10.1186/s12862-014-0203-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2014] [Accepted: 09/16/2014] [Indexed: 12/03/2022] Open
Abstract
BACKGROUND African wildlife experienced a reduction in population size and geographical distribution over the last millennium, particularly since the 19th century as a result of human demographic expansion, wildlife overexploitation, habitat degradation and cattle-borne diseases. In many areas, ungulate populations are now largely confined within a network of loosely connected protected areas. These metapopulations face gene flow restriction and run the risk of genetic diversity erosion. In this context, we assessed the "genetic health" of free ranging southern African Cape buffalo populations (S.c. caffer) and investigated the origins of their current genetic structure. The analyses were based on 264 samples from 6 southern African countries that were genotyped for 14 autosomal and 3 Y-chromosomal microsatellites. RESULTS The analyses differentiated three significant genetic clusters, hereafter referred to as Northern (N), Central (C) and Southern (S) clusters. The results suggest that splitting of the N and C clusters occurred around 6000 to 8400 years ago. Both N and C clusters displayed high genetic diversity (mean allelic richness (A r ) of 7.217, average genetic diversity over loci of 0.594, mean private alleles (P a ) of 11), low differentiation, and an absence of an inbreeding depression signal (mean F IS = 0.037). The third (S) cluster, a tiny population enclosed within a small isolated protected area, likely originated from a more recent isolation and experienced genetic drift (F IS = 0.062, mean A r = 6.160, P a = 2). This study also highlighted the impact of translocations between clusters on the genetic structure of several African buffalo populations. Lower differentiation estimates were observed between C and N sampling localities that experienced translocation over the last century. CONCLUSIONS We showed that the current genetic structure of southern African Cape buffalo populations results from both ancient and recent processes. The splitting time of N and C clusters suggests that the current pattern results from human-induced factors and/or from the aridification process that occurred during the Holocene period. The more recent S cluster genetic drift probably results of processes that occurred over the last centuries (habitat fragmentation, diseases). Management practices of African buffalo populations should consider the micro-evolutionary changes highlighted in the present study.
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Affiliation(s)
- Nathalie Smitz
- />Departement of Life Sciences-Conservation Genetics, University of Liège, Liège, Belgium
| | - Daniel Cornélis
- />Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), Montpellier, France
| | | | - Alexandre Caron
- />Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), Montpellier, France
- />Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD)-RP-PCP, University of Zimbabwe, Harare, Zimbabwe
- />Mammal Research Institute, Department of Zoology and Entomology, University of Pretoria, Pretoria, South Africa
| | - Michel de Garine-Wichatitsky
- />Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), Montpellier, France
- />Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD)-RP-PCP, University of Zimbabwe, Harare, Zimbabwe
- />Department of Biological Sciences, University of Zimbabwe, Harare, Zimbabwe
| | - Ferran Jori
- />Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), Montpellier, France
- />Mammal Research Institute, Department of Zoology and Entomology, University of Pretoria, Pretoria, South Africa
- />Department of Animal Science and Production, Botswana College of Agriculture, Gaborone, Botswana
| | - Alice Mouton
- />Departement of Life Sciences-Conservation Genetics, University of Liège, Liège, Belgium
| | - Alice Latinne
- />Departement of Life Sciences-Conservation Genetics, University of Liège, Liège, Belgium
- />Institut des Sciences de l’Evolution-CNRS-IRD, Université de Montpellier 2, Montpellier, France
- />Department of Parasitology, Faculty of Veterinary Medicine, Kasetsart University, Bangkok, Thailand
| | - Lise-Marie Pigneur
- />Research Unit in Environmental and Evolutionary Biology, University of Namur, Namur, Belgium
| | - Mario Melletti
- />Independent researcher, Via Di Villa Chigi, Rome, Italy
| | - Kimberly L Kanapeckas
- />Mammal Research Institute, Department of Zoology and Entomology, University of Pretoria, Pretoria, South Africa
- />Department of Genetics and Biochemistry, Clemson University, Clemson, USA
| | - Jonathan Marescaux
- />Research Unit in Environmental and Evolutionary Biology, University of Namur, Namur, Belgium
| | | | - Johan Michaux
- />Departement of Life Sciences-Conservation Genetics, University of Liège, Liège, Belgium
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Gupta A, Lal KK, Punia P, Singh RK, Mohindra V, Sah RS, Kumar R, Luhariya RK, Dwivedi AK, Masih P, Mishra RM, Jena JK. Characterization of polymorphic microsatellite markers and genetic diversity in wild bronze featherback, Notopterus notopterus (Pallas, 1769). Mol Biol Rep 2013; 40:6625-31. [PMID: 24072656 DOI: 10.1007/s11033-013-2776-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2013] [Accepted: 09/14/2013] [Indexed: 11/29/2022]
Abstract
Six polymorphic microsatellite DNA loci were identified in the primitive fish, bronze featherback, Notopterus notopterus for the first time and demonstrated significant population genetic structure. Out of the six primers, one primer (NN90) was specific to N. notopterus (microsatellite sequence within the RAG1 gene) and five primers were product of successful cross-species amplification. Sixty-four primers available from 3 fish species of order Osteoglossiformes and families Notopteridae and Osteoglossidae were tested to amplify homologous microsatellite loci in N. notopterus. Fifteen primer pairs exhibited successful cross-priming PCR product. However, polymorphism was detected only at five loci. To assess the significance of these six loci (including NN90) in population genetic study, 215 samples of N. notopterus from five rivers, viz Satluj, Gomti, Yamuna, Brahmaputra and Mahanadi were analyzed. The five sample sets displayed different diversity levels and observed heterozygosity ranged from 0.6036 to 0.7373. Significant genotype heterogeneity (P < 0.0001) and high FST (0.2205) over all loci indicated that the samples are not drawn from the same genepool. The identified microsatellite loci are promising for use in fine-scale population structure analysis of N. notopterus.
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Affiliation(s)
- Arti Gupta
- National Bureau of Fish Genetic Resources, Canal Ring Road, P.O. Dilkusha, Lucknow, 226002, Uttar Pradesh, India
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Epps CW, Castillo JA, Schmidt-Küntzel A, du Preez P, Stuart-Hill G, Jago M, Naidoo R. Contrasting historical and recent gene flow among African buffalo herds in the Caprivi Strip of Namibia. ACTA ACUST UNITED AC 2013; 104:172-81. [PMID: 23341534 DOI: 10.1093/jhered/ess142] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Population genetic structure is often used to infer population connectivity, but genetic structure may largely reflect historical rather than recent processes. We contrasted genetic structure with recent gene-flow estimates among 6 herds of African buffalo (Syncerus caffer) in the Caprivi Strip, Namibia, using 134 individuals genotyped at 10 microsatellite loci. We tested whether historical and recent gene flows were influenced by distance, potential barriers (rivers), or landscape resistance (distance from water). We also tested at what scales individuals were more related than expected by chance. Genetic structure across the Caprivi Strip was weak, indicating that historically, gene flow was strong and was not affected by distance, barriers, or landscape resistance. Our analysis of simulated data suggested that genetic structure would be unlikely to reflect human disturbances in the last 10-20 generations (75-150 years) because of slow predicted rates of genetic drift, but recent gene-flow estimates would be affected. Recent gene-flow estimates were not consistently affected by rivers or distance to water but showed that isolation by distance appears to be developing. Average relatedness estimates among individuals exceeded random expectations only within herds. We conclude that historically, African buffalo moved freely throughout the Caprivi Strip, whereas recent gene flow has been more restricted. Our findings support efforts to maintain the connectivity of buffalo herds across this region and demonstrate the utility of contrasting genetic inferences from different time scales.
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Affiliation(s)
- Clinton W Epps
- Department of Fisheries and Wildlife, Oregon State University, Corvallis, OR 97331, USA.
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Jakhesara SJ, Rank DN, Kansara JD, Parikh RC, Patel VM, Vataliya PH, Solanki JV. Parentage verification in field progeny testing program of Mehsana buffalo. J Anim Sci 2012; 90:4723-8. [PMID: 22851245 DOI: 10.2527/jas.2011-4353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The present study was undertaken to construct a multiplex microsatellite panel for parentage testing in Mehsana buffalo (Bubalus bubalis). The study was based on a total of 212 Mehsana buffalos (100 dams, 100 daughters, and 12 sires). Genomic DNA was extracted from blood and semen samples. A panel of 10 microsatellite markers (CSSM61, ILSTS29, ILSTS17, ILSTS28, CSSM57, CSSM22, ILSTS61, CSSM8, ETH152, and ILSTS11) was amplified in a single multiplex reaction and analyzed by capillary electrophoresis on an automated DNA sequencer. The expected heterozygosity ranged from 0.642 to 0.833 (mean 0.762). The total exclusion probability using 10 microsatellite loci with 1 known parent was 0.993. Seven out of 10 microsatellite loci revealed relatively high polymorphic information content (>0.7). Eighty-one daughters out of 100 daughters qualified by compatibility according to Mendelism. The results suggest that multiplex microsatellite panel is a fast, robust, reliable, and economic tool to verify the parentage as well as to assign the putative sire to daughters under progeny testing with very high accuracy and hence can be used in routine parentage testing.
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Affiliation(s)
- S J Jakhesara
- Dept. of Animal Biotechnology, Veterinary College, Anand Agricultural University, Anand, Gujarat, India-388001.
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Nagarajan M, Kumar N, Nishanth G, Haribaskar R, Paranthaman K, Gupta J, Mishra M, Vaidhegi R, Kumar S, Ranjan AK, Kumar S. Microsatellite markers of water buffalo, Bubalus bubalis--development, characterisation and linkage disequilibrium studies. BMC Genet 2009; 10:68. [PMID: 19843347 PMCID: PMC2773805 DOI: 10.1186/1471-2156-10-68] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2009] [Accepted: 10/21/2009] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Microsatellite markers are highly polymorphic and widely used in genome mapping and population genetic studies in livestock species. River buffalo, Bubalus bubalis is an economically important livestock species, though only a limited number of microsatellite markers have been reported thus far in this species. RESULTS In the present study, using two different approaches 571 microsatellite markers have been characterized for water buffalo. Of the 571 microsatellite markers, 498 were polymorphic with average heterozygosity of 0.51 on a panel of 24 unrelated buffalo. Fisher exact test was used to detect LD between the marker pairs. Among the 137550 pairs of marker combination, 14.58% pairs showed significant LD (P < 0.05). Further to check the suitability of these microsatellite markers to map these on a radiation hybrid map of buffalo genome, the markers were tested on Chinese hamster genomic DNA for amplification. Only seven of these markers showed amplification in Chinese hamster, and thus 564, of these can be added to the radiation hybrid map of this species. CONCLUSION The high conservation of cattle microsatellite loci in water buffalo promises the usefulness of the cattle microsatellites markers on buffalo. The polymorphic markers characterised in this study will contribute to genetic linkage and radiation hybrid mapping of water buffalo and population genetic studies.
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Affiliation(s)
- Muniyandi Nagarajan
- Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad-500007, India.
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HELLER R, LORENZEN ED, OKELLO JBA, MASEMBE C, SIEGISMUND HR. Mid-Holocene decline in African buffalos inferred from Bayesian coalescent-based analyses of microsatellites and mitochondrial DNA. Mol Ecol 2008; 17:4845-58. [DOI: 10.1111/j.1365-294x.2008.03961.x] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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10
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Nguyen TT, Genini S, Bui LC, Voegeli P, Stranzinger G, Renard JP, Maillard JC, Nguyen BX. Genomic conservation of cattle microsatellite loci in wild gaur (Bos gaurus) and current genetic status of this species in Vietnam. BMC Genet 2007; 8:77. [PMID: 17986322 PMCID: PMC2190770 DOI: 10.1186/1471-2156-8-77] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2007] [Accepted: 11/06/2007] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The wild gaur (Bos gaurus) is an endangered wild cattle species. In Vietnam, the total number of wild gaurs is estimated at a maximum of 500 individuals. Inbreeding and genetic drift are current relevant threats to this small population size. Therefore, information about the genetic status of the Vietnamese wild gaur population is essential to develop strategies for conservation and effective long-term management for this species. In the present study, we performed cross-species amplification of 130 bovine microsatellite markers, in order to evaluate the applicability and conservation of cattle microsatellite loci in the wild gaur genome. The genetic diversity of Vietnamese wild gaur was also investigated, based on data collected from the 117 successfully amplified loci. RESULTS One hundred-thirty cattle microsatellite markers were tested on a panel of 11 animals. Efficient amplifications were observed for 117 markers (90%) with a total of 264 alleles, and of these, 68 (58.1%) gave polymorphic band patterns. The number of alleles per locus among the polymorphic markers ranged from two to six. Thirteen loci (BM1314, BM2304, BM6017, BMC2228, BMS332, BMS911, CSSM023, ETH123, HAUT14, HEL11, HEL5, ILSTS005 and INRA189) distributed on nine different cattle chromosomes failed to amplify wild gaur genomic DNA. Three cattle Y-chromosome specific microsatellite markers (INRA124, INRA126 and BM861) were also highly specific in wild gaur, only displaying an amplification product in the males. Genotype data collected from the 117 successfully amplified microsatellites were used to assess the genetic diversity of this species in Vietnam. Polymorphic Information Content (PIC) values varied between 0.083 and 0.767 with a mean of 0.252 while observed heterozygosities (Ho) ranged from 0.091 to 0.909 (mean of 0.269). Nei's unbiased mean heterozygosity and the mean allele number across loci were 0.298 and 2.2, respectively. CONCLUSION Extensive conservation of cattle microsatellite loci in the wild gaur genome, as shown by our results, indicated a high applicability of bovine microsatellites for genetic characterization and population genetic studies of this species. Moreover, the low genetic diversity observed in Vietnamese wild gaur further underlines the necessity of specific strategies and appropriate management plans to preserve this endangered species from extinction.
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Nguyen TT, Ménétrey F, Genini S, Nguyen VL, Vögeli P, Nguyen BX, Stranzinger G. Application of bovine microsatellite markers on Saola (Pseudoryx nghetinhensis). J Anim Breed Genet 2005; 122:195-8. [PMID: 16130471 DOI: 10.1111/j.1439-0388.2005.00511.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The aim of the present study was to assess the applicability of bovine microsatellite markers on Saola (Pseudoryx nghetinhensis). A total of 127 microsatellite markers were tested on a male and a young female Saola. An efficient amplification was observed for 123 markers (96.8%), 73 markers (59.3%) were polymorphic. Four loci (BM2304, BMS1928, BMS779 and ILSTS006) on cattle chromosomes 1, 4, 7 and 8, respectively, failed to amplify in Saola. Two cattle Y-chromosome-specific microsatellite markers (INRA126 and BM861) were successfully amplified from both sexes in Saola. However, two additional markers (INRA124 and INRA189) on Y-chromosome failed to amplify in the female animal. These results show that most of the bovine microsatellite markers are applicable in Saola and therefore they can be used to study the phylogenetic relationships and the genetic diversity of the Saola population.
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Affiliation(s)
- T T Nguyen
- Institute of Animal Sciences, Swiss Federal Institute of Technology, Zurich, Switzerland
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Kim KS, Min MS, An JH, Lee H. Cross-species amplification of Bovidae microsatellites and low diversity of the endangered Korean goral. ACTA ACUST UNITED AC 2004; 95:521-5. [PMID: 15475399 DOI: 10.1093/jhered/esh082] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The Korean goral (Nemorhaedus caudatus) is an endangered species of wild goat. The conservation and management of this species could benefit from a better understanding of its genetic diversity and structure. Cross-species amplification of 34 Bovidae microsatellite loci was tested on a panel of 6 Korean gorals and 10 domestic goats. After polymerase chain reaction (PCR) optimization, 29 (85.3%) microsatellite loci amplified successfully for the Korean gorals and 27 (79.4%) for the domestic goats. Of the amplified products, 16 (55.2%) were polymorphic in the Korean goral and 22 (81.5%) in domestic goats. Nei's unbiased mean heterozygosity and mean allele number per locus were, respectively, 0.356 and 2.6 in the Korean goral and 0.636 and 4.8 in domestic goats. Low genetic diversity in the Korean gorals observed in this preliminary microsatellite survey suggests an urgent need for further detailed study of genetic diversity in Korean goral populations and a population management strategy based on these studies. Current results of cross-species amplification of domestic Bovidae microsatellites could be employed for the necessary population genetic studies on the Korean goral and other endangered Caprinae species.
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Affiliation(s)
- K-S Kim
- Conservation Genome Resource Bank for Korean Wildlife, Research Institute of Veterinary Science, College of Veterinary Medicine and School of Agricultural Biotechnology, Seoul National University, Seoul 151-742, Korea.
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Arora R, Lakhchaura BD, Prasad RB, Tantia MS, Vijh RK. Genetic diversity analysis of two buffalo populations of northern India using microsatellite markers. J Anim Breed Genet 2004. [DOI: 10.1111/j.1439-0388.2004.00451.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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14
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Mariasegaram M, Pullenayegum S, Jahabar Ali M, Shah RS, Penedo MCT, Wernery U, Sasse J. Isolation and characterization of eight microsatellite markers in Camelus dromedarius and cross-species amplification in C. bactrianus and Lama pacos. Anim Genet 2002; 33:385-7. [PMID: 12354152 DOI: 10.1046/j.1365-2052.2002.00896_6.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Affiliation(s)
- M Mariasegaram
- Central Veterinary Research Laboratory, PO Box 597, Dubai, United Arab Emirates
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Navani N, Jain PK, Gupta S, Sisodia BS, Kumar S. A set of cattle microsatellite DNA markers for genome analysis of riverine buffalo (Bubalus bubalis). Anim Genet 2002; 33:149-54. [PMID: 12047229 DOI: 10.1046/j.1365-2052.2002.00823.x] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
One hundred and eight microsatellite primer pairs, originally identified from cattle, were evaluated for their applicability in buffalo. Eighty-one primer pairs (75%) amplified discrete products, and of these, 61 pairs (56%) gave polymorphic band patterns on a panel of 25 buffaloes. The mean number of alleles per polymorphic marker was 4.50 +/- 0.20, and the mean heterozygosity per polymorphic marker was 0.66 +/- 0.02. Successful genotyping of buffaloes using cattle specific primers suggests that the latter can be a valuable resource for genome analysis in bubaline species.
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Affiliation(s)
- N Navani
- National Bureau of Animal Genetic Resources, Karnal, India
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Van Hooft WF, Groen AF, Prins HHT. Phylogeography of the African buffalo based on mitochondrial and Y-chromosomal loci: Pleistocene origin and population expansion of the Cape buffalo subspecies. Mol Ecol 2002; 11:267-79. [PMID: 11856427 DOI: 10.1046/j.1365-294x.2002.01429.x] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Population genetics and phylogeography of the African buffalo (Syncerus caffer) are inferred from genetic diversity at mitochondrial D-loop hypervariable region I sequences and a Y-chromosomal microsatellite. Three buffalo subspecies from different parts of Africa are included. Nucleotide diversity of the subspecies Cape buffalo at hypervariable region I is high, with little differentiation between populations. A mutation rate of 13-18% substitutions/million years is estimated for hypervariable region I. The nucleotide diversity indicates an estimated female effective population size of 17 000-32 000 individuals. Both mitochondrial and Y-chromosomal diversity are considerably higher in buffalo from central and southwestern Africa than in Cape buffalo, for which several explanations are hypothesized. There are several indications that there was a late middle to late Pleistocene population expansion in Cape buffalo. This also seems to be the period in which Cape buffalo evolved as a separate subspecies, according to the net sequence divergence with the other subspecies. These two observations are in agreement with the hypothesis of a rapid evolution of Cape buffalo based on fossil data. Additionally, there appears to have been a population expansion from eastern to southern Africa, which may be related to vegetation changes. However, as alternative explanations are also possible, further analyses with autosomal loci are needed.
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Affiliation(s)
- W F Van Hooft
- Wageningen University, Department of Environmental Sciences, Tropical Nature Conservation and Vertebrate Ecology Group, Bornsesteeg 69, 6708 PD Wageningen, The Netherlands.
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Baratti M, Alberti A, Groenen M, Veenendaal T, Fulgheri FD. Polymorphic microsatellites developed by cross-species amplifications in common pheasant breeds. Anim Genet 2001; 32:222-5. [PMID: 11531703 DOI: 10.1046/j.1365-2052.2001.00767.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Genetic variability was analysed in two common breeds of pheasant (Phasianus colchicus L. 1758) by means of cross-species amplifications of microsatellite loci: 154 chicken, Gallus gallus and 32 turkey, Meleagris gallopavo, primers were tested for amplification of pheasant DNA. Thirty-six primers (25 specific for chicken and 11 for turkey) amplified pheasant DNA. Fifteen markers yielded specific products and were tested for polymorphism. Eight of them (55%) were polymorphic, with an average polymorphism of two alleles per locus. Specific polymerase chain reaction (PCR) products were sequenced; repeats were found in 11 of the 15 markers, although only two loci showed the same repeat and could be homologous to chicken ones.
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Affiliation(s)
- M Baratti
- Department of Animal Biology and Genetics, University of Florence, Florence, Italy.
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Van Hooft WF, Groen AF, Prins HH. Microsatellite analysis of genetic diversity in African buffalo (Syncerus caffer) populations throughout Africa. Mol Ecol 2000; 9:2017-25. [PMID: 11123614 DOI: 10.1046/j.1365-294x.2000.01101.x] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Genetic diversity in nine African buffalo (Syncerus caffer) populations throughout Africa was analysed with 14 microsatellites to study the effects of rinderpest epidemics and habitat fragmentation during the 20th century. A gradient of declining expected heterozygosity was observed among populations in Save Valley Conservancy (Zimbabwe), and northern and southern Kruger National Park (South Africa). This was explained by a high mortality in northern Kruger National Park during the rinderpest pandemic at the end of the 19th century followed by recolonization from neighbouring populations, resulting in intermediate heterozygosity levels in northern Kruger National Park. In other populations expected heterozygosity was very high, indicating that rinderpest and recent habitat fragmentation had a limited effect on genetic diversity. From expected heterozygosity, estimates of long-term effective population size were derived. Migration rates among populations in eastern and southern Africa were very high, as shown by a weak isolation by distance and significant correlation in allele frequencies between populations. However, there were indications that dry habitats could limit migration. Genetic distances within buffalo in central Africa were relatively large, supporting their status as distinct subspecies. Finally, it was observed that the higher polymorphic microsatellites were less sensitive at detecting isolation by distance and differences in Ne, which may be a result of the high mutation pressure at these loci.
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Affiliation(s)
- W F Van Hooft
- Wageningen University, Department of Environmental Sciences, Tropical Nature Conservation and Vertebrate Ecology Group, Bornsesteeg 69, 6708 PD Wageningen, The Netherlands.
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