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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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Stolle E, Kidner JH, Moritz RFA. Patterns of evolutionary conservation of microsatellites (SSRs) suggest a faster rate of genome evolution in Hymenoptera than in Diptera. Genome Biol Evol 2013; 5:151-62. [PMID: 23292136 PMCID: PMC3595035 DOI: 10.1093/gbe/evs133] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/21/2012] [Indexed: 12/25/2022] Open
Abstract
Microsatellites, or simple sequence repeats (SSRs), are common and widespread DNA elements in genomes of many organisms. However, their dynamics in genome evolution is unclear, whereby they are thought to evolve neutrally. More available genome sequences along with dated phylogenies allowed for studying the evolution of these repetitive DNA elements along evolutionary time scales. This could be used to compare rates of genome evolution. We show that SSRs in insects can be retained for several hundred million years. Different types of microsatellites seem to be retained longer than others. By comparing Dipteran with Hymenopteran species, we found very similar patterns of SSR loss during their evolution, but both taxa differ profoundly in the rate. Relative to divergence time, Diptera lost SSRs twice as fast as Hymenoptera. The loss of SSRs on the Drosophila melanogaster X-chromosome was higher than on the other chromosomes. However, accounting for generation time, the Diptera show an 8.5-fold slower rate of SSR loss than the Hymenoptera, which, in contrast to previous studies, suggests a faster genome evolution in the latter. This shows that generation time differences can have a profound effect. A faster genome evolution in these insects could be facilitated by several factors very different to Diptera, which is discussed in light of our results on the haplodiploid D. melanogaster X-chromosome. Furthermore, large numbers of SSRs can be found to be in synteny and thus could be exploited as a tool to investigate genome structure and evolution.
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Affiliation(s)
- Eckart Stolle
- Department of Zoology, Institute of Biology, Martin-Luther-University Halle-Wittenberg, Halle (Saale), Germany.
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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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Zemanová B, Hájková P, Bryja J, Zima J, Hájková A, Zima J. Development of multiplex microsatellite sets for noninvasive population genetic study of the endangered Tatra chamois. FOLIA ZOOLOGICA 2011. [DOI: 10.25225/fozo.v60.i1.a11.2011] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Barbora Zemanová
- Institute of Vertebrate Biology, Academy of Sciences of the Czech Republic, v.v.i., Department of Population Biology, Květná 8, 603 65 Brno, Czech Republic; e-mails: , , , , ,
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic
| | - Petra Hájková
- Institute of Vertebrate Biology, Academy of Sciences of the Czech Republic, v.v.i., Department of Population Biology, Květná 8, 603 65 Brno, Czech Republic; e-mails: , , , , ,
| | - Josef Bryja
- Institute of Vertebrate Biology, Academy of Sciences of the Czech Republic, v.v.i., Department of Population Biology, Květná 8, 603 65 Brno, Czech Republic; e-mails: , , , , ,
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic
| | - Jan Zima
- Institute of Vertebrate Biology, Academy of Sciences of the Czech Republic, v.v.i., Department of Population Biology, Květná 8, 603 65 Brno, Czech Republic; e-mails: , , , , ,
- Department of Zoology, Faculty of Science, University of South Bohemia, Branišovská 31, 370 05 České Budějovice, Czech Republic
| | - Andrea Hájková
- Institute of Vertebrate Biology, Academy of Sciences of the Czech Republic, v.v.i., Department of Population Biology, Květná 8, 603 65 Brno, Czech Republic; e-mails: , , , , ,
- Department of Zoology, Faculty of Science, Charles University, Viničná 7, 128 44 Prague, Czech Republic
| | - Jan Zima
- Institute of Vertebrate Biology, Academy of Sciences of the Czech Republic, v.v.i., Department of Population Biology, Květná 8, 603 65 Brno, Czech Republic; e-mails: , , , , ,
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Pérez-Pardal L, Royo LJ, Beja-Pereira A, Curik I, Traoré A, Fernández I, Sölkner J, Alonso J, Álvarez I, Bozzi R, Chen S, Ponce de León FA, Goyache F. Y-specific microsatellites reveal an African subfamily in taurine (Bos taurus) cattle. Anim Genet 2010; 41:232-41. [DOI: 10.1111/j.1365-2052.2009.01988.x] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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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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Pérez-Pardal L, Royo LJ, Álvarez I, Ponce de León FA, Fernández I, Casais R, Goyache F. Female segregation patterns of the putative Y-chromosome-specific microsatellite markersINRA124andINRA126do not support their use for cattle population studies. Anim Genet 2009; 40:560-4. [DOI: 10.1111/j.1365-2052.2009.01870.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Pérez T, Albornoz J, Domınguez A. A panel of bovine and caprine microsatellites suitable as markers in chamois. Anim Genet 2008. [DOI: 10.1046/j.1365-2052.2000.00674.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Rejduch B, Kozubska-Sobocinska A, Radko A, Rychlik T, Slota E. The application of genetic markers for cell chimerism diagnosis in lambs. J Anim Breed Genet 2004. [DOI: 10.1111/j.1439-0388.2004.00456.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Payen E, Saidi-Mehtar N, Pailhoux E, Cotinot C. Sheep gene mapping: assignment of ALDOB, CYP19, WT and SOX2 by somatic cell hybrid analysis. Anim Genet 1995; 26:331-3. [PMID: 7486251 DOI: 10.1111/j.1365-2052.1995.tb02668.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Twenty-four hamster-sheep hybrid cell lines representing eleven ovine synteny groups were used to make syntenic assignments for seven loci ALDOB (aldolase B, fructose biophosphate); AMH (anti-Müllerian hormone); CYP19 [cytochrome P450 aromatase, subfamily XIX (aromatization of androgens)]; WT (Wilms' tumour gene); SOX2 (SRY-related HMG-box gene 2); FSHB (follicle-stimulating hormone, beta polypeptide); and SRY (sex region of Y chromosome). These loci were assigned to synteny groups U11(chr2) (ALDOB); U19 (AMH); U3(chr7) (CYP19); and to chromosome 15 (WT) and 1 (SOX2). SRY defines the hybrids containing the Y chromosome.
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Affiliation(s)
- E Payen
- Laboratoire de Biologie Cellulaire et Moléculaire, Bâtiment des Biotechnologies, INRA, Jouy en Josas, France
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Yoo J, Kappes SM, Stone RT, Beattie CW. Linkage analysis assignment of bovine granulocyte colony stimulating factor receptor (G-CSFR) to chromosome 3. Mamm Genome 1995; 6:686-7. [PMID: 8535089 DOI: 10.1007/bf00352388] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- J Yoo
- ARS, Roman L. Hruska U.S. Meat Animal Research Center (MARC), Nebraska 68933-0166, USA
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Vaiman D, Eggen A, Mercier D, Bahri-Darwich I, Grohs C, Bruneau D, Laurent P, Chaput B, Oustry A, Frelat G. A genetic and physical map of bovine chromosome 3. Anim Genet 1995; 26:21-5. [PMID: 7702208 DOI: 10.1111/j.1365-2052.1995.tb02614.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
This paper reports a map of nine polymorphic microsatellite markers previously assigned to bovine chromosome 3 (BTA3) by somatic cell genetics. The linkage group covers 101 cM on the chromosome with an average intermarker distance of 13.9 cM. One marker (INRA200) was isolated from a peak of flow sorted chromosomes 2 and 3. Another marker (INRA197) was derived from a cosmid. The localization of the cosmid by in situ hybridization enabled the orientation of the linkage group on BTA3. Markers were relatively evenly spaced and consequently can be used to complement other mapping data about this chromosome. This establishes a framework of polymorphic markers that can be used to search for quantitative trait loci (QTL).
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Affiliation(s)
- D Vaiman
- Laboratoire de Génétique biochimique et de Cytogénétique, INRA-CRJ, Jouy-en-Josas, France
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Pépin L, Amigues Y, Lépingle A, Berthier JL, Bensaid A, Vaiman D. Sequence conservation of microsatellites between Bos taurus (cattle), Capra hircus (goat) and related species. Examples of use in parentage testing and phylogeny analysis. Heredity (Edinb) 1995; 74 ( Pt 1):53-61. [PMID: 7852099 DOI: 10.1038/hdy.1995.7] [Citation(s) in RCA: 85] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
A panel of 70 bovine microsatellites was tested for amplification from goat DNA. Forty-three could be successfully amplified by PCR, 20 of which were tested for polymorphism. Three were applied for parentage testing in goat families and their exclusion probability evaluated. Fourteen were cloned and sequenced from goat DNA, and goat and bovine sequences were compared to evaluate interspecific conservation. Correlation between the structure of the dinucleotide repeat and the number of alleles was studied and indicated that interruption(s) in the repeat could explain the difference in the levels of polymorphism between the two species. This study provides a valuable in vivo clue to the mechanism generating polymorphism in microsatellites. Sequence conservation was also observed for several microsatellites with two wild species of Bovidae, Nilgaï (Boselaphus tragocamelus) and Himalayan Tur (Capra cylindricornis), and with one species of Cervidae, the fallow deer (Cervus dama). This study showed that an estimated 40 per cent of the microsatellites isolated from cattle will prove useful to study the caprine genome and to characterize economically important genetic loci in this species. Moreover, bovine microsatellites were shown to constitute very useful tools for the study of genetic diversity of the Artiodactyla.
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Affiliation(s)
- L Pépin
- Laboratoire de Génétique Biochimique et de Cytoénétique, INRA-CRJ, Jouy-en-Josas, France
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Affiliation(s)
- E J Payen
- Laboratoire de Biologie Cellulaire et Moléculaire, INRA, Jouy-en-Josas, France
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Vaiman D, Mercier D, Moazami-Goudarzi K, Eggen A, Ciampolini R, Lépingle A, Velmala R, Kaukinen J, Varvio SL, Martin P. A set of 99 cattle microsatellites: characterization, synteny mapping, and polymorphism. Mamm Genome 1994; 5:288-97. [PMID: 7545949 DOI: 10.1007/bf00389543] [Citation(s) in RCA: 208] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Cattle microsatellite clones (136) were isolated from cosmid (10) and plasmid (126) libraries and sequenced. The dinucleotide repeats were studied in each of these sequences and compared with dinucleotide repeats found in other vertebrate species where information was available. The distribution in cattle was similar to that described for other mammals, such as rat, mouse, pig, or human. A major difference resides in the number of sequences present in the bovine genome, which seemed at best one-third as large as in other species. Oligonucleotide primers (117 pairs) were synthesized, and a PCR product of expected size was obtained for 88 microsatellite sequences (75%). Synteny or chromosome assignment was searched for each locus with PCR amplification on a panel of 36 hamster/bovine somatic cell hybrids. Of our bovine microsatellites, eighty-six could be assigned to synteny groups of chromosomes. In addition, 10 other microsatellites--HEL 5, 6, 9, 11, 12, 13 (Kaukinen and Varvio 1993), HEL 4, 7, 14, 15--as well as the microsatellite found in the kappa-casein gene (Fries et al. 1990) were mapped on the hybrids. Microsatellite polymorphism was checked on at least 30 unrelated animals of different breeds. Almost all the autosomal and X Chr microsatellites displayed polymorphism, with the number of alleles varying between two and 44. We assume that these microsatellites could be very helpful in the construction of a primary public linkage map of the bovine genome, with an aim of finding markers for Economic Trait Loci (ETL) in cattle.
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Affiliation(s)
- D Vaiman
- Laboratoire de Génétique biochimique et de Cytogénétique, INRA-CRJ, Jouy-en-Josas, France
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