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Hori M, Takada H, Nakane Y, Minami M, Inoue E. Genetic Analysis Reveals Dispersal Patterns of Japanese Serow in Two Different Habitats of a Mountainous Region. Zoolog Sci 2024; 41:201-209. [PMID: 38587915 DOI: 10.2108/zs230055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 11/13/2023] [Indexed: 04/10/2024]
Abstract
Dispersal increases the costs of feeding and predation risk in the new environment and is reported to be biased toward habitats similar to the natal region in some mammals. The benefits and costs of dispersal often differ between sexes, and most mammals show male-biased dispersal in relation to a polygamous mating system. Japanese serow is generally a solitary and monogamous species. However, recent studies have shown that the sociality of serows on Mt. Asama differs between habitat types. In the mountain forests with low forage availability, solitary habits and social monogamy were observed, while, in alpine grasslands, female grouping and social polygyny were observed, which is probably due to abundant forage availability. We investigated the effects of habitat characteristics and sociality on the dispersal of serows using fecal and tissue samples from two different habitats on Mt. Asama. The Fst value between the two areas was significantly positive, and the mean relatedness within areas was significantly higher than that between areas, which suggests limited gene flow and natal habitat-biased dispersal. Bayesian clustering analysis showed unidirectional gene flow from forest to grassland, which was probably due to the high forage availability of the grassland. Analyses of the assignment index and mean relatedness did not show male-biased dispersal, even in the grassland, where serows were polygynous. Thus, polygyny in the grassland is not linked to male-biased dispersal. In summary, our study suggests that dispersal patterns in Japanese serows are affected by habitat rather than social differences.
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Affiliation(s)
- Maiko Hori
- Toho University, Funabashi, Chiba 274-8510, Japan
| | - Hayato Takada
- Wildlife Management Center, Tokyo University of Agriculture and Technology, Fuchu, Tokyo 183-8509, Japan
- Azabu University, Chuo-ku, Sagamihara, Kanagawa 252-5201, Japan
- Mount Fuji Research Institute, Yamanashi Prefecture Government, Fijiyoshida, Yamanashi 403-0005, Japan
| | - Yuki Nakane
- Toho University, Funabashi, Chiba 274-8510, Japan
| | - Masato Minami
- Azabu University, Chuo-ku, Sagamihara, Kanagawa 252-5201, Japan
| | - Eiji Inoue
- Toho University, Funabashi, Chiba 274-8510, Japan,
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Cetkovská E, Brandlová K, Ogden R, Černá Bolfíková B. Evaluation of the Impact of Population Management on the Genetic Parameters of Selected Spiral-Horned Antelopes. BIOLOGY 2024; 13:104. [PMID: 38392322 PMCID: PMC10886411 DOI: 10.3390/biology13020104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 01/25/2024] [Accepted: 01/30/2024] [Indexed: 02/24/2024]
Abstract
The rapid loss of biodiversity and the associated reduction and fragmentation of habitats means that ex situ populations have become an important part of species conservation. These populations, which are often established from a small number of founders, require careful management to avoid the negative effects of genetic drift and inbreeding. Although the inclusion of molecular data is recommended, their availability for captive breeding management remains limited. The aim of this study was to evaluate the relationship between the levels of genetic diversity in six spiral-horned antelope taxa bred under human care and their respective management strategies, conservation status, demography, and geographic origin, using 10 nuclear DNA microsatellite loci and mitochondrial control region DNA sequences. Our findings include associations between genetic diversity and management intensity but also with the diversity and contribution of wild populations to captive founders, with some populations apparently composed of animals from divergent wild lineages elevating captive genetic diversity. When population sizes are large, the potential advantages of maximizing genetic diversity in widely outcrossed populations may need careful consideration with respect to the potential disruption of adaptive diversity. Genetic data serve as a robust tool for managing captive populations, yet their interpretation necessitates a comprehensive understanding of species biology and history.
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Affiliation(s)
- Ema Cetkovská
- Faculty of Tropical AgriSciences, Czech University of Life Sciences Prague, Kamycka 129, 16500 Prague, Czech Republic
| | - Karolína Brandlová
- Faculty of Tropical AgriSciences, Czech University of Life Sciences Prague, Kamycka 129, 16500 Prague, Czech Republic
| | - Rob Ogden
- Royal (Dick) School of Veterinary Studies and the Roslin Institute, University of Edinburgh, Midlothian EH25 9RG, UK
| | - Barbora Černá Bolfíková
- Faculty of Tropical AgriSciences, Czech University of Life Sciences Prague, Kamycka 129, 16500 Prague, Czech Republic
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Genetic Structure Analysis of 155 Transboundary and Local Populations of Cattle ( Bos taurus, Bos indicus and Bos grunniens) Based on STR Markers. Int J Mol Sci 2023; 24:ijms24055061. [PMID: 36902492 PMCID: PMC10003406 DOI: 10.3390/ijms24055061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 01/31/2023] [Accepted: 02/01/2023] [Indexed: 03/09/2023] Open
Abstract
Every week, 1-2 breeds of farm animals, including local cattle, disappear in the world. As the keepers of rare allelic variants, native breeds potentially expand the range of genetic solutions to possible problems of the future, which means that the study of the genetic structure of these breeds is an urgent task. Providing nomadic herders with valuable resources necessary for life, domestic yaks have also become an important object of study. In order to determine the population genetic characteristics, and clarify the phylogenetic relationships of modern representatives of 155 cattle populations from different regions of the world, we collected a large set of STR data (10,250 individuals), including unique native cattle, 12 yak populations from Russia, Mongolia and Kyrgyzstan, as well as zebu breeds. Estimation of main population genetic parameters, phylogenetic analysis, principal component analysis and Bayesian cluster analysis allowed us to refine genetic structure and provided insights in relationships of native populations, transboundary breeds and populations of domestic yak. Our results can find practical application in conservation programs of endangered breeds, as well as become the basis for future fundamental research.
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Takagi T, Murakami R, Takano A, Torii H, Kaneko S, Tamate HB. A historic religious sanctuary may have preserved ancestral genetics of Japanese sika deer ( Cervus nippon). J Mammal 2023; 104:303-315. [PMID: 37032702 PMCID: PMC10075338 DOI: 10.1093/jmammal/gyac120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 12/10/2022] [Indexed: 01/31/2023] Open
Abstract
Abstract
Deer have been a major resource for human populations for thousands of years. Anthropogenic activities, such as hunting, have influenced the genetic structure and distribution of deer populations. In Japan, wild Japanese sika deer (Cervus nippon) have been hunted since ancient times but have also been historically protected as sacred animals in several sanctuaries. Sika deer have been protected for over a thousand years in the religious sanctuary around the Kasuga Taisha Shrine on the Kii Peninsula, located in the center of Japan. Here, we used short sequence repeats (SSR) and mitochondrial DNA (mtDNA) to investigate the genetic diversity, population structure, and demography of Japanese sika deer inhabiting the Kii Peninsula, Japan, and discuss possible anthropogenic influences. Using SSR, three distinct genetic groups were distinguished on the Kii Peninsula: an Eastern genetic group, a Western genetic group, and an isolated genetic group with individuals in the religious sanctuary of Kasuga Taisha Shrine in Nara city. The isolated genetic sanctuary group had only the mtDNA haplotype S4. The SSR genotype data suggested a newer divergence time of the genetic groups of the religious sanctuary than would have occurred as a result of Late Quaternary climate change. This time scale coincided with the establishment of the sanctuary with Kasuga Taisha Shrine. Thus, the religious protection conserved genetic variation over a thousand years.
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Affiliation(s)
- Toshihito Takagi
- Fukushima University, Graduate School of Symbiotic Systems Science and Technology , Fukushima 960-1296 , Japan
| | - Ryoko Murakami
- Yamagata University, Faculty of Medicine , Yamagata 990-9585 , Japan
| | - Ayako Takano
- Nara University of Education, Center for Natural Environment Education , Nara 630-8528 , Japan
| | - Harumi Torii
- Nara University of Education, Center for Natural Environment Education , Nara 630-8528 , Japan
| | - Shingo Kaneko
- Fukushima University, Faculty of Symbiotic Systems Science , Fukushima 960-1296 , Japan
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Freitas TMS, Dias JM, Veríssimo ACF, Lobo JR, Costa GL, de Moura MI, Landi V, Martínez AM, do Carmo AS, Fioravanti MCS. Population Structure of Curraleiro Pé-Duro Cattle and its Relationship With the Serological Profile Against Pathogens of Economic and Zoonotic Interest. Front Genet 2022; 13:872660. [PMID: 35646103 PMCID: PMC9136223 DOI: 10.3389/fgene.2022.872660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 04/04/2022] [Indexed: 11/13/2022] Open
Abstract
Curraleiro Pé-Duro (CPD) cattle, a Brazilian local breed, are animals that are highly resistant to infectious and parasitic diseases. Strategies for the conservation of the breed and the genetic resistance to diseases should also consider the characteristics of the breed. The objective of this study was to analyze the diversity and population structure of the CPD breed using microsatellite markers and to correlate the serological profiles for causative agents of brucellosis, leptospirosis, neosporosis, leukosis, infectious bovine rhinotracheitis, and bovine viral diarrhea. DNA samples of 608 bovines were amplified and genotyped using 28 microsatellite markers for breed characterization. The genotypes were assigned to three clusters, indicating a substructure population related to the geographic distance. The observed heterozygosity was lower than that expected in most loci, and fixation index (Fst) in the subpopulation values ranged from 0.03073 (ETH3) to 0.402 (INRA63) on cluster 1, from 0.00 (INRA32) to 0.39359 (INRA63) on cluster 2, and from 0.00 (INRA32) to 0.28483 (TGLA53) on cluster 3. The Brucella spp., Neospora caninum, and Bovine Leukemia Virus frequencies were significantly different (p < 0.05) between clusters. The differences between the occurrences of diseases were not sufficient to indicate a genetic subpopulation with increased resistance to infections.
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Affiliation(s)
- Thais Miranda Silva Freitas
- Department of Veterinary Medicine, School of Veterinary and Animal Science, Federal University of Goiás, Goiânia, Brazil
- *Correspondence: Thais Miranda Silva Freitas,
| | - Juliana Moraes Dias
- Department of Veterinary Medicine, School of Veterinary and Animal Science, Federal University of Goiás, Goiânia, Brazil
| | | | - Joyce Rodrigues Lobo
- Department of Veterinary Medicine, School of Veterinary and Animal Science, Federal University of Goiás, Goiânia, Brazil
| | - Gustavo Lage Costa
- Escola de Ciências Médicas e da Vida da Pontifícia Universidade Católica de Goiás, Goiânia, Brazil
| | - Maria Ivete de Moura
- Escola de Ciências Médicas e da Vida da Pontifícia Universidade Católica de Goiás, Goiânia, Brazil
| | | | - Amparo Martínez Martínez
- Department of Genetics, Campus of International Agrifood Excellence, Universidad de Córdoba, Cordoba, Spain
| | - Adriana Santana do Carmo
- Department of Animal Science Medicine, School of Veterinary and Animal Science School, Federal University of Goiás, Goiânia, Brazil
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Svishcheva G, Babayan O, Lkhasaranov B, Tsendsuren A, Abdurasulov A, Stolpovsky Y. Microsatellite Diversity and Phylogenetic Relationships among East Eurasian Bos taurus Breeds with an Emphasis on Rare and Ancient Local Cattle. Animals (Basel) 2020; 10:E1493. [PMID: 32846979 PMCID: PMC7552156 DOI: 10.3390/ani10091493] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 08/10/2020] [Accepted: 08/19/2020] [Indexed: 12/03/2022] Open
Abstract
We report the genetic analysis of 18 population samples of animals, which were taken from cattle (Bos taurus) breeds of European and Asian origins. The main strength of our study is the use of rare and ancient native cattle breeds: the Altai, Ukrainian Grey, Tagil, and Buryat ones. The cattle samples studied have different production purposes, belong to various eco-geographic regions, and consequently have distinct farming conditions. In order to clarify the genetic diversity, phylogenetic relationships and historical origin of the studied breeds, we carried out an analysis of the genetic variation of 14 high-variability microsatellite loci at 1168 genotyped animals. High levels of heterozygosity and allelic richness were identified in four of the ancient local breeds, namely the Kalmyk, Tagil, Kyrgyz native, and Buryat breeds. The greatest phylogenetic distances from a common ancestor were observed for the Yakut and Ukrainian Grey breeds, while the Tagil breed showed the smallest difference. By using clustering approaches, we found that the Altai cattle is genetically close to the Kyrgyz one. Moreover, both the Altai and Kyrgyz breeds exposed genetic divergences from other representatives of the Turano-Mongolian type and genetic relationships with the Brown Swiss and Kostroma breeds. This phenomenon can be explained by the extensive use of the Brown Swiss and Kostroma breeds in the breeding and improvement processes for the Kyrgyz breeds, which have been involved in the process of keeping the Altai cattle. Our results can be valuable for conservation and management purposes.
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Affiliation(s)
- Gulnara Svishcheva
- Vavilov Institute of General Genetics, Russian Academy of Sciences, 119333 Moscow, Russia
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Olga Babayan
- Gordiz Ltd., Skolkovo Innovation Centre, 121205 Moscow, Russia
| | | | - Ariuntuul Tsendsuren
- Institute of General and Experimental Biology, The Mongolian Academy of Sciences, Ulaanbaatar 210351, Mongolia
| | - Abdugani Abdurasulov
- Department of Agriculture, Faculty of Natural Sciences and Geography, Osh State University, 723500 Osh, Kyrgyzstan
| | - Yurii Stolpovsky
- Vavilov Institute of General Genetics, Russian Academy of Sciences, 119333 Moscow, Russia
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Genetic Diversity of Historical and Modern Populations of Russian Cattle Breeds Revealed by Microsatellite Analysis. Genes (Basel) 2020; 11:genes11080940. [PMID: 32824045 PMCID: PMC7463645 DOI: 10.3390/genes11080940] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 08/10/2020] [Accepted: 08/12/2020] [Indexed: 01/24/2023] Open
Abstract
Analysis of ancient and historical DNA has great potential to trace the genetic diversity of local cattle populations during their centuries-long development. Forty-nine specimens representing five cattle breeds (Kholmogor, Yaroslavl, Great Russian, Novgorod, and Holland), dated from the end of the 19th century to the first half of the 20th century, were genotyped for nine polymorphic microsatellite loci. Using a multiple-tube approach, we determined the consensus genotypes of all samples/loci analysed. Amplification errors, including allelic drop-out (ADO) and false alleles (FA), occurred with an average frequency of 2.35% and 0.79%, respectively. A significant effect of allelic length on ADO rate (r2 = 0.620, p = 0.05) was shown. We did not observe significant differences in genetic diversity among historical samples and modern representatives of Kholmogor and Yaroslavl breeds. The unbiased expected heterozygosity values were 0.726–0.774 and 0.708–0.739; the allelic richness values were 2.716–2.893 and 2.661–2.758 for the historical and modern samples, respectively. Analyses of FST and Jost’s D genetic distances, and the results of STRUCTURE clustering, showed the maintenance of a part of historical components in the modern populations of Kholmogor and Yaroslavl cattle. Our study contributes to the conservation of biodiversity in the local Russian genetic resources of cattle.
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Takagi T, Matsumoto Y, Koda R, Tamate HB. Bi-Directional Movement of Deer between Tomogashima Islands and the Western Part of the Kii Peninsula, Japan, with Special Reference to Hybridization between the Japanese Sika Deer (Cervus nippon centralis) and the Introduced Exotic Deer. MAMMAL STUDY 2020. [DOI: 10.3106/ms2019-0048] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Affiliation(s)
- Toshihito Takagi
- Graduate School of Science and Engineering, Yamagata University, Kojirakawa 1-4-12, Yamagata City, Yamagata 990-8560, Japan
| | - Yuki Matsumoto
- Research and Development Section, Anicom Specialty Medical Institute Inc., 2-6-3 Chojamachi 4F, Yokohamashi-Nakaku, Kanagawa 231-0033, Japan
| | - Ryosuke Koda
- Research Institute of Environment, Agriculture and Fisheries, Osaka Prefecture, 10-4 Koyamotomachi, Neyagawa, Osaka 572-0088, Japan
| | - Hidetoshi B. Tamate
- Faculty of Science, Yamagata University, Kojirakawa 1-4-12, Yamagata City, Yamagata 990-8560, Japan
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Danilkin AA, Plakhina DA, Zvychaynaya EY, Domnich AV, Kholodova MV, Sorokin PA, Volokh AM. Siberian Roe Deer (Capreolus pygargus Pallas, 1771) in Ukraine: Analysis of the Mitochondrial and Nuclear DNA. BIOL BULL+ 2018. [DOI: 10.1134/s106235901706005x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Species, sex, and individual identification of Japanese serow (Capricornis crispus) and sika deer (Cervus nippon) in sympatric region based on the fecal DNA samples. CONSERV GENET RESOUR 2017. [DOI: 10.1007/s12686-016-0665-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Moioli B, Napolitano F, Orrù L, Catillo G. Analysis of the genetic diversity between Gentile di Puglia, Sopravissana and Sarda sheep breeds using microsatellite markers. ITALIAN JOURNAL OF ANIMAL SCIENCE 2016. [DOI: 10.4081/ijas.2006.73] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Willems H, Welte J, Hecht W, Reiner G. Temporal variation of the genetic diversity of a German red deer population between 1960 and 2012. EUR J WILDLIFE RES 2016. [DOI: 10.1007/s10344-016-0999-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Carranza J, Salinas M, de Andrés D, Pérez‐González J. Iberian red deer: paraphyletic nature at mtDNA but nuclear markers support its genetic identity. Ecol Evol 2016; 6:905-22. [PMID: 26843924 PMCID: PMC4729781 DOI: 10.1002/ece3.1836] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Revised: 10/07/2015] [Accepted: 10/21/2015] [Indexed: 01/15/2023] Open
Abstract
Red deer populations in the Iberian glacial refugium were the main source for postglacial recolonization and subspecific radiation in north-western Europe. However, the phylogenetic history of Iberian red deer (Cervus elaphus hispanicus) and its relationships with northern European populations remain uncertain. Here, we study DNA sequences at the mitochondrial control region along with STR markers for over 680 specimens from all the main red deer populations in Spain and other west European areas. Our results from mitochondrial and genomic DNA show contrasting patterns, likely related to the nature of these types of DNA markers and their specific processes of change over time. The results, taken together, bring support to two distinct, cryptic maternal lineages for Iberian red deer that predated the last glacial maximum and that have maintained geographically well differentiated until present. Haplotype relationships show that only one of them contributed to the northern postglacial recolonization. However, allele frequencies of nuclear markers evidenced one main differentiation between Iberian and northern European subspecies although also supported the structure of both matrilines within Iberia. Thus, our findings reveal a paraphyletic nature for Iberian red deer but also its genetic identity and differentiation with respect to northern subspecies. Finally, we suggest that maintaining the singularity of Iberian red deer requires preventing not only restocking practices with red deer specimens belonging to other European populations but also translocations between both Iberian lineages.
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Affiliation(s)
- Juan Carranza
- Ungulate Research UnitCátedra de Recursos Cinegéticos y Piscícolas (CRCP)Universidad de Córdoba14071CórdobaSpain
| | - María Salinas
- Ungulate Research UnitCátedra de Recursos Cinegéticos y Piscícolas (CRCP)Universidad de Córdoba14071CórdobaSpain
| | - Damián de Andrés
- Ungulate Research UnitCátedra de Recursos Cinegéticos y Piscícolas (CRCP)Universidad de Córdoba14071CórdobaSpain
- Instituto de AgrobiotecnologíaCSIC‐UPNA‐Gobierno de Navarra31192MutilvaNavarraSpain
| | - Javier Pérez‐González
- Ungulate Research UnitCátedra de Recursos Cinegéticos y Piscícolas (CRCP)Universidad de Córdoba14071CórdobaSpain
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Brenig B, Schütz E. Recent development of allele frequencies and exclusion probabilities of microsatellites used for parentage control in the German Holstein Friesian cattle population. BMC Genet 2016; 17:18. [PMID: 26747197 PMCID: PMC4706708 DOI: 10.1186/s12863-016-0327-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Accepted: 01/04/2016] [Indexed: 11/14/2022] Open
Abstract
Background Methods for parentage control in cattle have changed since their initial implementation in the late 1950’s from blood group typing to more current single nucleotide polymorphism determination. In the early 1990’s, 12 microsatellites were selected by the International Society for Animal Genetics based on their informativeness and robustness in a variety of different cattle breeds. Since then this panel is used as standard in cattle herd book breeding and its application is accompanied by recurrent international comparison tests ensuring permanent validity for the most common commercial dairy and beef cattle breeds for example Holstein Friesian, Simmental, Angus, and Hereford. Although, nearly every parentage can be resolved using these microsatellites, cases with very close relatives became an emerging resolution problem during recent years. This is mainly due to an increase of monomorphism and a trend to the fixation of alleles, although no direct selection against their variability was applied. Thus other effects must be presumed resulting in a loss of polymorphism information content, heterozygosity, and exclusion probabilities. Results To determine changes of allele frequencies and exclusion probabilities, we analyzed the development of these parameters for the 12 microsatellites from 2004 to 2014. One hundred sixty eight thousand recorded Holstein Friesian cattle genotypes were evaluated. During this period certain alleles of nine microsatellites increased significantly (t-values >5). When calculating the exclusion probabilities for 11 microsatellites, reduction was determined for the three situations, i.e. one parent is wrongly identified (p = 0.01), both parents are wrongly identified (p = 0.005), and the genotype of one parent is missing (p = 0.048). With the addition of BM1818 to the marker set in 2009, this development was corrected leading to significant increases in exclusion probabilities. Although, the exclusion probabilities for the three family situations using the 12 microsatellites are >99 %, the clarification of 142 relationships in 40,000 situations where one parent is missing will still be impossible. Twenty-five sires were identified that are responsible for the most significant microsatellite allele increases in the population. The corresponding alleles are mainly associated with milk protein and fat yield, body weight at birth and weaning, as well as somatic cell score, milk fat percentage, and longissimus muscle area. Conclusions Our data show that most of the microsatellites used for parentage control in cattle show directional changes in allele frequencies consistent with the history of artificial selection in the German Holstein population.
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Affiliation(s)
- Bertram Brenig
- Institute of Veterinary Medicine, Georg-August-University Göttingen, Burckhardtweg 2, D-37077, Göttingen, Germany.
| | - Ekkehard Schütz
- Institute of Veterinary Medicine, Georg-August-University Göttingen, Burckhardtweg 2, D-37077, Göttingen, Germany.
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Moreno E, Pérez-González J, Carranza J, Moya-Laraño J. Better Fitness in Captive Cuvier's Gazelle despite Inbreeding Increase: Evidence of Purging? PLoS One 2015; 10:e0145111. [PMID: 26679703 PMCID: PMC4682998 DOI: 10.1371/journal.pone.0145111] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Accepted: 11/27/2015] [Indexed: 11/19/2022] Open
Abstract
Captive breeding of endangered species often aims at preserving genetic diversity and to avoid the harmful effects of inbreeding. However, deleterious alleles causing inbreeding depression can be purged when inbreeding persists over several generations. Despite its great importance both for evolutionary biology and for captive breeding programmes, few studies have addressed whether and to which extent purging may occur. Here we undertake a longitudinal study with the largest captive population of Cuvier's gazelle managed under a European Endangered Species Programme since 1975. Previous results in this population have shown that highly inbred mothers tend to produce more daughters, and this fact was used in 2006 to reach a more appropriate sex-ratio in this polygynous species by changing the pairing strategy (i.e., pairing some inbred females instead of keeping them as surplus individuals in the population). Here, by using studbook data we explore whether purging has occurred in the population by investigating whether after the change in pairing strategy a) inbreeding and homozygosity increased at the population level, b) fitness (survival) increased, and c) the relationship between inbreeding and juvenile survival, was positive. Consistent with the existence of purging, we found an increase in inbreeding coefficients, homozygosity and juvenile survival. In addition, we showed that in the course of the breeding programme the relationship between inbreeding and juvenile survival was not uniform but rather changed over time: it was negative in the early years, flat in the middle years and positive after the change in pairing strategy. We highlight that by allowing inbred individuals to mate in captive stocks we may favour sex-ratio bias towards females, a desirable managing strategy to reduce the surplus of males that force most zoos to use ethical culling and euthanizing management tools. We discuss these possibilities but also acknowledge that many other effects should be considered before implementing inbreeding and purging as elements in management decisions.
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Affiliation(s)
- Eulalia Moreno
- Estación Experimental de Zonas Áridas (CSIC), Dept. Ecología Funcional y Evolutiva, Ctra. de Sacramento s/n, E-04120, La Cañada de San Urbano, Almería, Spain
- * E-mail:
| | - Javier Pérez-González
- Ungulate Research Unit, Cátedra de Recursos Cinegéticos y Piscícolas, Universidad de Córdoba, E-14071, Córdoba, Spain
- Guardería Rural, Mancomunidad Integral de Municipios Centro, E-06810, Calamonte, Badajoz, Spain
| | - Juan Carranza
- Ungulate Research Unit, Cátedra de Recursos Cinegéticos y Piscícolas, Universidad de Córdoba, E-14071, Córdoba, Spain
| | - Jordi Moya-Laraño
- Estación Experimental de Zonas Áridas (CSIC), Dept. Ecología Funcional y Evolutiva, Ctra. de Sacramento s/n, E-04120, La Cañada de San Urbano, Almería, Spain
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Niedziałkowska M, Hundertmark KJ, Jędrzejewska B, Sidorovich VE, Zalewska H, Veeroja R, Solberg EJ, Laaksonen S, Sand H, Solovyev VA, Sagaydak A, Tiainen J, Juškaitis R, Done G, Borodulin VA, Tulandin EA, Niedziałkowski K. The contemporary genetic pattern of European moose is shaped by postglacial recolonization, bottlenecks, and the geographical barrier of the Baltic Sea. Biol J Linn Soc Lond 2015. [DOI: 10.1111/bij.12713] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | - Kris J. Hundertmark
- Mammal Research Institute; Polish Academy of Sciences; Białowieża 17-230 Poland
- Institute of Arctic Biology and Department of Biology and Wildlife; University of Alaska; Fairbanks P.O. Box 757000 AK 99775-7000 USA
| | | | - Vadim E. Sidorovich
- Institute of Zoology; Scientific and Practical Centre for Biological Resources; National Academy of Sciences of Belarus; Minsk BY-220072 Republic of Belarus
| | - Hanna Zalewska
- Mammal Research Institute; Polish Academy of Sciences; Białowieża 17-230 Poland
| | - Rauno Veeroja
- Department of Zoology; Institute of Ecology and Earth Science; University of Tartu; Tartu 51014 Estonia
| | - Erling J. Solberg
- Norwegian Institute for Nature Research; P.O. Box 5685 Sluppen Trondheim NO-7485 Norway
| | | | - Håkan Sand
- Grimsö Research Station; Swedish University of Agricultural Sciences; 73091 Riddarhyttan Sweden
| | - Vyacheslav A. Solovyev
- Department of Animal Ecology; B. M. Zhitkov Russian Research Institute of Game Management and Fur Farming; Kirov 610000 Russia
| | - Andrey Sagaydak
- Mizhrichynskyi Regional Landscape Park; Otrokhy; Kozelets Raion Chernihiv Oblast, Ukraine
| | - Juha Tiainen
- Natural Resources Institute Finland; Helsinki 00790 Finland
| | - Rimvydas Juškaitis
- Institute of Ecology; Nature Research Centre; Vilnius LT-08412 Lithuania
| | - Gundega Done
- Latvian State Forest Research Institute ‘Silava’; Salaspils 2169 Latvia
| | - Vadim A. Borodulin
- Inter-regional Non-governmental Organization ‘Leningrad Association of Hunters and Fishermen’; Sankt Petersburg 190121 Russia
| | - Evgenii A. Tulandin
- Non-commercial Partnership ‘Union of Gamekeepers of the Kostroma Region’; Kostroma Russia
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Okada A, Ito TY, Buuveibaatar B, Lhagvasuren B, Tsunekawa A. Genetic structure in Mongolian gazelles based on mitochondrial and microsatellite markers. Mamm Biol 2015. [DOI: 10.1016/j.mambio.2015.03.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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He Y, Wang ZH, Wang XM. Genetic diversity and population structure of a Sichuan sika deer (Cervus sichuanicus) population in Tiebu Nature Reserve based on microsatellite variation. DONG WU XUE YAN JIU = ZOOLOGICAL RESEARCH 2015; 35:528-36. [PMID: 25465089 DOI: 10.13918/j.issn.2095-8137.2014.6.528] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Abstract
Cervus sichuanicus is a species of sika deer (Cervus nippon Group). To date, research has mainly focused on quantity surveying and behavior studies, with genetic information on this species currently deficient. To provide scientific evidence to assist in the protection of this species, we collected Sichuan sika deer fecal samples from the Sichuan Tiebu Nature Reserve (TNR) and extracted DNA from those samples. Microsatellite loci of bovine were used for PCR amplification. After GeneScan, the genotype data were used to analyze the genetic diversity and population structure of the Sichuan sika deer in TNR. Results showed that the average expected heterozygosity of the Sichuan sika deer population in TNR was 0.562, equivalent to the average expected heterozygosity of endangered animals, such as Procapra przewalskii. Furthermore, 8 of 9 microsatellite loci significantly deviated from the Hardy-Weinberg equilibrium and two groups existed within the Sichuan sika deer TNR population. This genetic structure may be caused by a group of Manchurian sika deer (Cervus hortulorum) released in TNR.
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Affiliation(s)
- Ya He
- School of Life Sciences, East China Normal University, Shanghai 200062, China;Shanghai Science & Technology Museum, 2000 Century Avenue, Shanghai 200127, China
| | - Zheng-Huan Wang
- School of Life Sciences, East China Normal University, Shanghai 200062, China
| | - Xiao-Ming Wang
- School of Life Sciences, East China Normal University, Shanghai 200062, China;Shanghai Science & Technology Museum, 2000 Century Avenue, Shanghai 200127, China .
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Plakhina DA, Zvychaynaya EY, Kholodova MV, Danilkin AA. Identification of European (Capreolus capreolus L.) and Siberian (C. pygargus Pall.) roe deer hybrids by microsatellite marker analysis. RUSS J GENET+ 2014. [DOI: 10.1134/s1022795414070151] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Yamashiro A, Yamashiro T, Mori K, Kamada M. Indirect estimation of Recent Sika Deer (Cervus nippon) Migration in Tsurugi Quasi-National Park, Shikoku, Japan. MAMMAL STUDY 2014. [DOI: 10.3106/041.039.0203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Kiselyova TY, Kantanen J, Vorobyov NI, Podoba BE, Terletsky VP. Linkage disequilibrium analysis for microsatellite loci in six cattle breeds. RUSS J GENET+ 2014. [DOI: 10.1134/s1022795414040048] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Present genetic structure revealed by microsatellites reflects recent history of the Finnish moose (Alces alces). EUR J WILDLIFE RES 2013. [DOI: 10.1007/s10344-013-0712-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Haanes H, Markussen SS, Herfindal I, Røed KH, Solberg EJ, Heim M, Midthjell L, Sæther BE. Effects of inbreeding on fitness-related traits in a small isolated moose population. Ecol Evol 2013; 3:4230-42. [PMID: 24324873 PMCID: PMC3853567 DOI: 10.1002/ece3.819] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2013] [Revised: 08/26/2013] [Accepted: 08/29/2013] [Indexed: 11/18/2022] Open
Abstract
Inbreeding can affect fitness-related traits at different life history stages and may interact with environmental variation to induce even larger effects. We used genetic parentage assignment based on 22 microsatellite loci to determine a 25 year long pedigree for a newly established island population of moose with 20–40 reproducing individuals annually. We used the pedigree to calculate individual inbreeding coefficients and examined for effects of individual inbreeding (f) and heterozygosity on fitness-related traits. We found negative effects of f on birth date, calf body mass and twinning rate. The relationship between f and calf body mass and twinning rate were found to be separate but weaker after accounting for birth date. We found no support for an inbreeding effect on the age-specific lifetime reproductive success of females. The influence of f on birth date was related to climatic conditions during the spring prior to birth, indicating that calves with a low f were born earlier after a cold spring than calves with high f. In years with a warm spring, calf f did not affect birth date. The results suggest that severe inbreeding in moose has both indirect effects on fitness through delayed birth and lower juvenile body mass, as well as separate direct effects, as there still was a significant relationship between f and twinning rate after accounting for birth date and body mass as calf. Consequently, severe inbreeding as found in the study population may have consequences for population growth and extinction risk.
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Affiliation(s)
- Hallvard Haanes
- Centre for Biodiversity Dynamics, Department of Biology, Norwegian University of Science and Technology Trondheim, N-7491, Norway ; Departments of Basic Sciences and Aquatic Medicine, Norwegian School of Veterinary Science PO-8146 Dep, Oslo, N-0033, Norway
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Lerp H, Wronski T, Plath M, Schröter A, Pfenninger M. Phylogenetic and population genetic analyses suggest a potential species boundary between Mountain (Gazella gazella) and Arabian Gazelles (G. arabica) in the Levant. Mamm Biol 2013. [DOI: 10.1016/j.mambio.2012.11.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Zhang F, Jiang Z, Xu A, Zeng Y, Li C. Recent geological events and intrinsic behavior influence the population genetic structure of the chiru and tibetan gazelle on the tibetan plateau. PLoS One 2013; 8:e60712. [PMID: 23637761 PMCID: PMC3634780 DOI: 10.1371/journal.pone.0060712] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2012] [Accepted: 03/04/2013] [Indexed: 11/19/2022] Open
Abstract
The extent to which a species responds to environmental changes is mediated not only by extrinsic processes such as time and space, but also by species-specific ecology. The Qinghai-Tibetan Plateau uplifted approximately 3000 m and experienced at least four major glaciations during the Pleistocene epoch in the Quaternary Period. Consequently, the area experienced concurrent changes in geomorphological structure and climate. Two species, the Tibetan antelope (Pantholops hodgsonii, chiru) and Tibetan gazelle (Procapra picticaudata), both are endemic on the Qinghai-Tibetan Plateau, where their habitats overlap, but have different migratory behaviors: the chiru is inclined to have female-biased dispersal with a breeding migration during the calving season; in contrast, Tibetan gazelles are year-round residents and never migrate distantly. By using coalescence methods we compared mitochondrial control region DNA sequences and variation at nine microsatellite loci in these two species. Coalescent simulations indicate that the chiru and Tibetan gazelle do not share concordant patterns in their genealogies. The non-migratory Tibetan gazelle, that is more vulnerable to the impact of drastic geographic changes such as the elevation of the plateau, glaciations and so on, appears to have a strong population genetic structure with complicated demographic history. Specifically, the Tibetan gazelle population appears to have experienced isolation and divergence with population fluctuations since the Middle Pleistocene (0.781 Ma). However, it showed continued decline since the Upper Pleistocene (0.126 Ma), which may be attributed to the irreversible impact of increased human activities on the plateau. In contrast, the migratory chiru appears to have simply experienced population expansion. With substantial gene flow among regional populations, this species shows no historical population isolation and divergence. Thus, this study adds to many empirical studies that show historical and contemporary extrinsic and intrinsic processes shape the recent evolutionary history and population genetic structure of species.
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Affiliation(s)
- Fangfang Zhang
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Graduate School of the Chinese Academy of Sciences, Beijing, China
| | - Zhigang Jiang
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Graduate School of the Chinese Academy of Sciences, Beijing, China
| | - Aichun Xu
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- School of Life Sciences, Jiliang University, Hangzhou, China
| | - Yan Zeng
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Graduate School of the Chinese Academy of Sciences, Beijing, China
| | - Chunwang Li
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
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Kekkonen J, Wikström M, Brommer JE. Heterozygosity in an isolated population of a large mammal founded by four individuals is predicted by an individual-based genetic model. PLoS One 2012; 7:e43482. [PMID: 23028456 PMCID: PMC3447869 DOI: 10.1371/journal.pone.0043482] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2012] [Accepted: 07/20/2012] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Within-population genetic diversity is expected to be dramatically reduced if a population is founded by a low number of individuals. Three females and one male white-tailed deer Odocoileus virginianus, a North American species, were successfully introduced in Finland in 1934 and the population has since been growing rapidly, but remained in complete isolation from other populations. METHODOLOGY/PRINCIPAL FINDINGS Based on 14 microsatellite loci, the expected heterozygosity H was 0.692 with a mean allelic richness (AR) of 5.36, which was significantly lower than what was found in Oklahoma, U.S.A. (H = 0.742; AR = 9.07), demonstrating that a bottleneck occurred. Observed H was in line with predictions from an individual-based model where the genealogy of the males and females in the population were tracked and the population's demography was included. CONCLUSION Our findings provide a rare within-population empirical test of the founder effect and suggest that founding a population by a small number of individuals need not have a dramatic impact on heterozygosity in an iteroparous species.
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Affiliation(s)
- Jaana Kekkonen
- Department of Biosciences, University of Helsinki, Helsinki, Finland
| | | | - Jon E. Brommer
- Department of Biosciences, University of Helsinki, Helsinki, Finland
- ARONIA Coastal Zone Research Team, Novia University of Applied Sciences & Åbo Akademi University, Ekenäs, Finland
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De La Rosa-Reyna XF, Calderón-Lobato RD, Parra-Bracamonte GM, Sifuentes-Rincón AM, DeYoung RW, García-De León FJ, Arellano-Vera W. Genetic diversity and structure among subspecies of white-tailed deer in Mexico. J Mammal 2012. [DOI: 10.1644/11-mamm-a-212.2] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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Niedziałkowska M, Jędrzejewska B, Wójcik JM, Goodman SJ. Genetic structure of red deer population in northeastern Poland in relation to the history of human interventions. J Wildl Manage 2012. [DOI: 10.1002/jwmg.367] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Niedziałkowska M, Fontaine M, Jędrzejewska B. Factors shaping gene flow in red deer (Cervus elaphus) in seminatural landscapes of central Europe. CAN J ZOOL 2012. [DOI: 10.1139/z11-122] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
We studied gene flow and connectivity between three subpopulations and nine groups of red deer ( Cervus elaphus L., 1758) occurring in forests in northeastern Poland and western Belarus. The red deer in this region mostly originated from translocated individuals that were introduced primarily in the 19th and 20th centuries. The genetic structure of the population has been identified during the previous study. Using 14 microsatellite loci, we detected 14 first-generation migrants between the three subpopulations and 21 among the nine groups of deer. The number of effective migrants (Nm) was estimated to be 2.5 individuals/generation between the subpopulations and 6.2 individuals/generation between the groups. About 80% of first-generation migrants moved less than 150 km. The gene flow of hinds and stags was similar. A least cost path (LCP) analysis was performed using different habitat types: deciduous and mixed forests, coniferous forests, wetlands, meadows, arable lands, scarce settlements, dense settlements, and waters. No significant barriers to dispersal were detected, but individual dispersal was restricted in space by the significant isolation by distance. The best model, explaining the genetic distance (FST/1 – FST) between the forests, suggested that LCP corridor length limited gene flow and high forest cover within LCP corridors increased gene flow among the forests.
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Affiliation(s)
- M. Niedziałkowska
- Mammal Research Institute, Polish Academy of Sciences, 17-230 Białowieża, Poland
| | - M.C. Fontaine
- Institute of Integrative and Comparative Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
- Université Paris-Sud, Laboratoire Ecologie, Systématique et Evolution, UMR 8079, Orsay CEDEX, F-91405; CNRS, UMR 8079, Orsay CEDEX, F-91405
| | - B. Jędrzejewska
- Mammal Research Institute, Polish Academy of Sciences, 17-230 Białowieża, Poland
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Heim BC, Ivy JA, Latch EK. A Suite of Microsatellite Markers Optimized for Amplification of DNA From Addax (Addax nasomaculatus) Blood Preserved on FTA Cards. Zoo Biol 2011; 31:98-106. [DOI: 10.1002/zoo.20420] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2011] [Revised: 07/25/2011] [Accepted: 08/02/2011] [Indexed: 11/11/2022]
Affiliation(s)
- Brett C. Heim
- Department of Biological Sciences; University of Wisconsin-Milwaukee; Milwaukee; Wisconsin
| | | | - Emily K. Latch
- Department of Biological Sciences; University of Wisconsin-Milwaukee; Milwaukee; Wisconsin
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Haanes H, Røed KH, Solberg EJ, Herfindal I, Sæther BE. Genetic discontinuities in a continuously distributed and highly mobile ungulate, the Norwegian moose. CONSERV GENET 2011. [DOI: 10.1007/s10592-011-0214-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Haanes H, Røed KH, Mysterud A, Langvatn R, Rosef O. Consequences for genetic diversity and population performance of introducing continental red deer into the northern distribution range. CONSERV GENET 2010. [DOI: 10.1007/s10592-010-0048-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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35
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Hundertmark KJ, Van Daele LJ. Founder effect and bottleneck signatures in an introduced, insular population of elk. CONSERV GENET 2009. [DOI: 10.1007/s10592-009-0013-z] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Corti P, Shafer ABA, Coltman DW, Festa-Bianchet M. Past bottlenecks and current population fragmentation of endangered huemul deer (Hippocamelus bisulcus): implications for preservation of genetic diversity. CONSERV GENET 2009. [DOI: 10.1007/s10592-009-9997-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Serrano M, Calvo JH, Martínez M, Marcos-Carcavilla A, Cuevas J, González C, Jurado JJ, de Tejada PD. Microsatellite based genetic diversity and population structure of the endangered Spanish Guadarrama goat breed. BMC Genet 2009; 10:61. [PMID: 19785776 PMCID: PMC2761942 DOI: 10.1186/1471-2156-10-61] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2009] [Accepted: 09/29/2009] [Indexed: 11/21/2022] Open
Abstract
Background Assessing genetic biodiversity and population structure of minor breeds through the information provided by neutral molecular markers, allows determination of their extinction risk and to design strategies for their management and conservation. Analysis of microsatellite loci is known to be highly informative in the reconstruction of the historical processes underlying the evolution and differentiation of animal populations. Guadarrama goat is a threatened Spanish breed which actual census (2008) consists of 3057 females and 203 males distributed in 22 populations more or less isolated. The aim of this work is to study the genetic status of this breed through the analysis of molecular data from 10 microsatellites typed in historic and actual live animals. Results The mean expected heterozygosity across loci within populations ranged from 0.62 to 0.77. Genetic differentiation measures were moderate, with a mean FST of 0.074, GST of 0.081 and RST of 0.085. Percentages of variation among and within populations were 7.5 and 92.5, respectively. Bayesian clustering analyses pointed out a population subdivision in 16 clusters, however, no correlation between geographical distances and genetic differences was found. Management factors such as the limited exchange of animals between farmers (estimated gene flow Nm = 3.08) mostly due to sanitary and social constraints could be the major causes affecting Guadarrama goat population subdivision. Conclusion Genetic diversity measures revealed a good status of biodiversity in the Guadarrama goat breed. Since diseases are the first cause affecting the census in this breed, population subdivision would be an advantage for its conservation. However, to maintain private alleles present at low frequencies in such small populations minimizing the inbreeding rate, it would necessitate some mating designs of animals carrying such alleles among populations. The systematic use of molecular markers will facilitate the comprehensive management of these populations, which in combination with the actual breeding program to increase milk yield, will constitute a good strategy to preserve the breed.
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Bray TC, Chikhi L, Sheppy AJ, Bruford MW. The population genetic effects of ancestry and admixture in a subdivided cattle breed. Anim Genet 2009; 40:393-400. [DOI: 10.1111/j.1365-2052.2009.01850.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Carolino I, Sousa CO, Ferreira S, Carolino N, Silva FS, Gama LT. Implementation of a parentage control system in Portuguese beef-cattle with a panel of microsatellite markers. Genet Mol Biol 2009; 32:306-11. [PMID: 21637685 PMCID: PMC3036942 DOI: 10.1590/s1415-47572009005000026] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2008] [Accepted: 09/01/2008] [Indexed: 11/21/2022] Open
Abstract
A study was conducted to assess the feasibility of applying a panel of 10 microsatellite markers in parentage control of beef cattle in Portugal. In the first stage, DNA samples were collected from 475 randomly selected animals of the Charolais, Limousin and Preta breeds. Across breeds and genetic markers, means for average number of alleles, effective number of alleles, expected heterozygosity and polymorphic information content, were 8.20, 4.43, 0.733 and 0.70, respectively. Enlightenment from the various markers differed among breeds, but the set of 10 markers resulted in a combined probability above 0.9995 in the ability to exclude a random putative parent. The marker-set thus developed was later used for parentage control in a group of 140 calves from several breeds, where there was the suspicion of possible faulty parentage recording. Overall, 76.4% of the calves in this group were compatible with the recorded parents, with most incompatibilities due to misidentification of the dam. Efforts must be made to improve the quality of pedigree information, with particular emphasis on information recorded at the calf's birth.
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Affiliation(s)
- Inês Carolino
- Unidade de Investigação de Recursos Genéticos, Reprodução e Melhoramento Animal, Instituto Nacional de Recursos Biológicos, Vale de Santarém Portugal
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Poissant J, Shafer ABA, Davis CS, Mainguy J, Hogg JT, Côté SD, Coltman DW. Genome-wide cross-amplification of domestic sheep microsatellites in bighorn sheep and mountain goats. Mol Ecol Resour 2009; 9:1121-6. [PMID: 21564850 DOI: 10.1111/j.1755-0998.2009.02575.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
We tested for cross-species amplification of microsatellite loci located throughout the domestic sheep (Ovis aries) genome in two north American mountain ungulates (bighorn sheep, Ovis canadensis, and mountain goats, Oreamnos americanus). We identified 247 new polymorphic markers in bighorn sheep (≥ 3 alleles in one of two study populations) and 149 in mountain goats (≥ 2 alleles in a single study population) using 648 and 576 primer pairs, respectively. Our efforts increased the number of available polymorphic microsatellite markers to 327 for bighorn sheep and 180 for mountain goats. The average distance between successive polymorphic bighorn sheep and mountain goat markers inferred from the Australian domestic sheep genome linkage map (mean ± 1 SD) was 11.9 ± 9.2 and 15.8 ± 13.8 centimorgans, respectively. The development of genomic resources in these wildlife species enables future studies of the genetic architecture of trait variation.
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Affiliation(s)
- J Poissant
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada T6G 2E9.
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Qanbari S, Nasab MPE, Osfoori R, Nazari AH. Power of microsatellite markers for analysis of genetic variation and parentage verification in sheep. Pak J Biol Sci 2009; 10:1632-8. [PMID: 19086509 DOI: 10.3923/pjbs.2007.1632.1638] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
We report the genetic analysis of 100 individuals of an elite breeding flock of Afshari sheep with a selected set of eighteen microsatellite markers. A full characterization of this set of eighteen loci was carried out generating allele frequency distributions that were used to estimate the genetic information content of these loci, including genetic variability, inbreeding, individual and parent verification parameters. Disregarding MCMA26 monomorphic pattern, microsatellite loci showed moderate level of polymorphism, as such totally 102 alleles were detected with a mean number of 6 alleles per locus. The average expected heterozygosity was 0.72 (SD = 0.07) and the average Polymorphism Information Content (PIC) was 0.67 (SD = 0.08). Total value of inbreeding based on marker data was estimated as -0.02 so it indicates that inbreeding occurred less than would be expected at random. The overall probability of identity considering all twelve independent loci combined was 3.148E-13 meaning lower than 1 in 31 trillions. The results of this study indicate, despite the selective breeding and closed flock system over a number of generations, a relatively high level of heterozygosity still exists in the representative sheep flock. The high degree of multiallelism and the clear and simple codominant Mendelian inheritance of the set of microsatellites used provide a powerful system for the unique identification of Afshari sheep individuals for fingerprinting purposes and parentage testing.
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Affiliation(s)
- S Qanbari
- Research Institute of Physiology and Biotechnology, University of Zanjan, P.O. Box, 313, Zanjan, Iran
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Haanes H, Røed KH, Flagstad Ø, Rosef O. Genetic structure in an expanding cervid population after population reduction. CONSERV GENET 2008. [DOI: 10.1007/s10592-008-9781-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Kusza S, Nagy I, Sasvári Z, Stágel A, Németh T, Molnár A, Kume K, Bősze Z, Jávor A, Kukovics S. Genetic diversity and population structure of Tsigai and Zackel type of sheep breeds in the Central-, Eastern- and Southern-European regions. Small Rumin Res 2008. [DOI: 10.1016/j.smallrumres.2008.04.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Davis GP, Moore SS, Drinkwater RD, Shorthose WR, Loxton ID, Barendse W, Hetzel DJS. QTL for meat tenderness in the M. longissimus lumborum of cattle. Anim Genet 2008; 39:40-5. [DOI: 10.1111/j.1365-2052.2007.01677.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Esmaeelkhanian S, Torshizi RV. Microsatellite variation in one breed of Iranian sheep with 12 markers. Pak J Biol Sci 2007; 10:4455-4460. [PMID: 19093511 DOI: 10.3923/pjbs.2007.4455.4460] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Polymorphic loci, genetic parameters (Polymorphic Information Content, heterozygosity, Shannon Index, the number of actual alleles, the number of effective alleles) and genetic variation within Balouchi sheep population located in Abbasabad station of Mashad, was assessed using 12 microsatellite markers. The Polymerase Chain Reaction (PCR) reactions were successfully done with all primers except for OarHH62 and OarAE64, one locus (CSSM059) was monomorph, whereas the other 9 loci containing CSSM018, CSSM006, BMS1004, BMS2361, BMS744, BMS799, BMS1316, BMS2213 and TGLA122 were polymorph with 6, 6, 4, 4, 5, 4, 2, 3 and 3 number of alleles, respectively. In this population, heterozygosity varied from 0.5 to 0.72; among 9 polymorphic loci, BMS1316 and BMS2361 had the most and the least diversity, respectively. The study of Shannon Index and Polymorphic Information Content (PIC) indicate the least and the most values for BMS1316 and BMS2213 loci, respectively. The most number of actual alleles were belong to CSSM018 and CSSM006 loci with 6 alleles and the least was belong to BMS1316 locus with 2 alleles. BMS2361 locus had the most and BMS1316 locus had the least number of effective alleles. All loci were at Hardy-Weinberg equilibrium (p < 0.005). In this population, average heterozygosity was estimated as 0.54. In general, it can be concluded that Balouchi sheep population of Abbasabad station in Mashad (in Iran) has approximately high genetic diversity with respect to the studied microsatellites and microsatellite markers have approximately high polymorphism and therefore can be used for genetic studies.
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Egito AA, Paiva SR, Albuquerque MDSM, Mariante AS, Almeida LD, Castro SR, Grattapaglia D. Microsatellite based genetic diversity and relationships among ten Creole and commercial cattle breeds raised in Brazil. BMC Genet 2007; 8:83. [PMID: 18067665 PMCID: PMC2228320 DOI: 10.1186/1471-2156-8-83] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2007] [Accepted: 12/07/2007] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Brazil holds the largest commercial cattle populations worldwide. Local cattle breeds can be classified according to their origin, as exotic or Creole. Exotic breeds imported in the last 100 years, both zebuine and taurine, currently make up the bulk of the intensively managed populations. Locally adapted Creole breeds, originated from cattle introduced by the European conquerors derive from natural selection and events of breed admixture. While historical knowledge exists on the Brazilian Creole breeds very little is known on their genetic composition. The objective of this study was to assess the levels of genetic diversity, phylogenetic relationships and patterns of taurine/zebuine admixture among ten cattle breeds raised in Brazil. RESULTS Significant reduction of heterozygosity exists due both to within-population inbreeding and to breed differentiation in both subspecies (taurine and zebuine). For taurine breeds the number of markers that contribute to breed differentiation is larger than for zebuine. A consistently similar number of alleles was seen in both subspecies for all microsatellites. Four Creole breeds were the most genetically diverse followed by the zebuine breeds, the two specialized taurine breeds and the Creole Caracu. Pairwise genetic differentiation were all significant indicating that all breeds can be considered as genetically independent entities. A STRUCTURE based diagram indicated introgression of indicine genes in the local Creole breeds and suggested that occasional Creole introgression can be detected in some Zebuine animals. CONCLUSION This study reports on a comprehensive study of the genetic structure and diversity of cattle breeds in Brazil. A significant amount of genetic variation is maintained in the local cattle populations. The genetic data show that Brazilian Creole breeds constitute an important and diverse reservoir of genetic diversity for bovine breeding and conservation. The genetic data was able to shed light on a number of issues related to the local breeds origin and structure. The Brazilian Creole breeds are all important and viable targets for conservation for they display peculiar traits both phenotypic and of cultural and historical nature that deserve conservation efforts.
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Affiliation(s)
- Andréa A Egito
- EMBRAPA Recursos Genéticos e Biotecnologia, CP 02372, 70770-970 Brasília, DF, Brazil.
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Torr SJ, Prior A, Wilson PJ, Schofield S. Is there safety in numbers? The effect of cattle herding on biting risk from tsetse flies. MEDICAL AND VETERINARY ENTOMOLOGY 2007; 21:301-311. [PMID: 18092968 DOI: 10.1111/j.1365-2915.2007.00705.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
In sub-Saharan Africa, tsetse (Glossina spp.) transmit species of Trypanosoma which threaten 45-50 million cattle with trypanosomiasis. These livestock are subject to various herding practices which may affect biting rates on individual cattle and hence the probability of infection. In Zimbabwe, studies were made of the effect of herd size and composition on individual biting rates by capturing tsetse as they approached and departed from groups of one to 12 cattle. Flies were captured using a ring of electrocuting nets and bloodmeals were analysed using DNA markers to identify which individual cattle were bitten. Increasing the size of a herd from one to 12 adults increased the mean number of tsetse visiting the herd four-fold and the mean feeding probability from 54% to 71%; the increased probability with larger herds was probably a result of fewer flies per host, which, in turn, reduced the hosts' defensive behaviour. For adults and juveniles in groups of four to eight cattle, > 89% of bloodmeals were from the adults, even when these comprised just 13% of the herd. For groups comprising two oxen, four cows/heifers and two calves, a grouping that reflects the typical composition of communal herds in Zimbabwe, approximately 80% of bloodmeals were from the oxen. Simple models of entomological inoculation rates suggest that cattle herding practices may reduce individual trypanosomiasis risk by up to 90%. These results have several epidemiological and practical implications. First, the gregarious nature of hosts needs to be considered in estimating entomological inoculation rates. Secondly, heterogeneities in biting rates on different cattle may help to explain why disease prevalence is frequently lower in younger/smaller cattle. Thirdly, the cost and effectiveness of tsetse control using insecticide-treated cattle may be improved by treating older/larger hosts within a herd. In general, the patterns observed with tsetse appear to apply to other genera of cattle-feeding Diptera (Stomoxys, Anopheles, Tabanidae) and thus may be important for the development of strategies for controlling other diseases affecting livestock.
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Affiliation(s)
- S J Torr
- Natural Resources Institute, University of Greenwich, Greenwich, U.K.
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Tetens J, Goldammer T, Maddox JF, Cockett NE, Leeb T, Drögemüller C. A radiation hybrid map of sheep chromosome 23 based on ovine BAC-end sequences. Anim Genet 2007; 38:132-40. [PMID: 17326803 DOI: 10.1111/j.1365-2052.2007.01572.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
More than 375,000 BAC-end sequences (BES) of the CHORI-243 ovine BAC library have been deposited in public databases. blastn searches with these BES against HSA18 revealed 1806 unique and significant hits. We used blastn-anchored BES for an in silico prediction of gene content and chromosome assignment of comparatively mapped ovine BAC clones. Ovine BES were selected at approximately 1.3-Mb intervals of HSA18 and incorporated into a human-sheep comparative map. An ovine 5000-rad whole-genome radiation hybrid panel (USUoRH5000) was typed with 70 markers, all of which mapped to OAR23. The resulting OAR23 RH map included 43 markers derived from BES with high and unique BLAST hits to the sequence of the orthologous HSA18, nine EST-derived markers, 16 microsatellite markers taken from the ovine linkage map and two bovine microsatellite markers. Six new microsatellite markers derived from the 43 mapped BES and the two bovine microsatellite markers were linkage-mapped using the International Mapping Flock (IMF). Thirteen additional microsatellite markers were derived from other ovine BES with high and unique BLAST hits to the sequence of the orthologous HSA18 and also positioned on the ovine linkage map but not incorporated into the OAR23 RH map. This resulted in 24 markers in common and in the same order between the RH and linkage maps. Eight of the BES-derived markers were mapped using fluorescent in situ hybridization (FISH), to thereby align the RH and cytogenetic maps. Comparison of the ovine chromosome 23 RH map with the HSA18 map identified and localized three major breakpoints between HSA18 and OAR23. The positions of these breakpoints were equivalent to those previously shown for syntenic BTA24 and HSA18. This study presents evidence for the usefulness of ovine BES when constructing a high-resolution comprehensive map for a single sheep chromosome. The comparative analysis confirms and refines knowledge about chromosomal conservation and rearrangements between sheep, cattle and human. The constructed RH map demonstrates the resolution and utility of the newly constructed ovine RH panel.
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Affiliation(s)
- J Tetens
- Institute for Animal Breeding and Genetics, University of Veterinary Medicine Hannover, Germany
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Genetic structure of introduced European fallow deer (Dama dama dama) in Tasmania, Australia. EUR J WILDLIFE RES 2006. [DOI: 10.1007/s10344-006-0069-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Armstrong E, Postiglioni A, Martínez A, Rincón G, Vega-Pla JL. Microsatellite analysis of a sample of Uruguayan Creole bulls (Bos taurus). Genet Mol Biol 2006. [DOI: 10.1590/s1415-47572006000200012] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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