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A Genetic Evaluation System for New Zealand White Rabbit Germplasm Resources Based on SSR Markers. Animals (Basel) 2020; 10:ani10081258. [PMID: 32722175 PMCID: PMC7460188 DOI: 10.3390/ani10081258] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 07/15/2020] [Accepted: 07/22/2020] [Indexed: 11/23/2022] Open
Abstract
Simple Summary The New Zealand white rabbit (Oryctolagus cuniculus) is one of the most important breeds of commercial and experimental rabbits in the world, and also one of the most raised rabbit breeds in China. Our goal was to develop a suite of microsatellite markers to aid future conservation genetics research for the Oryctolagus cuniculus breeds. Based on the genetic diversity of 130 New Zealand white rabbits, we obtained a set combination of 22 markers. Then, we performed a genetic analysis of 200 New Zealand white rabbits corresponding to two generations with this combination. It can be used to evaluate the breed conservation of rabbit germplasm resources. Abstract At present, there is an abundance of quality domestic rabbit breeds in China. However, due to the lack of technical standards for the genetic evaluation of rabbit germplasm resources, there have been a number of problems, such as poor breed conservation. By studying the genetic diversity of 130 New Zealand white rabbits (regardless of generation), we obtained the best simple sequence repeat (SSR) marker combination. We found that, when using microsatellite markers for the effective genetic evaluation of domestic rabbits, the number of records should be greater than 60 and the marker number more than 22. Through the comparative analysis of 30 combinations of 22 markers, the optimal combination of 22 markers was determined, and the 22 SSR polymorphic loci were distributed on different chromosomes. We performed a genetic analysis of 200 New Zealand white rabbits corresponding to two generations, using the best SSR polymorphic loci combination. There were no significant differences in the genetic diversity parameters between the two generations of rabbits (p > 0.05), indicating that the characteristics of this excellent rabbit germplasm have been effectively preserved. At the same time, we verified that the established method can be used to evaluate the breed conservation of rabbit germplasm resources.
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Tolesa Z, Bekele E, Tesfaye K, Ben Slimen H, Valqui J, Getahun A, Hartl GB, Suchentrunk F. Mitochondrial and nuclear DNA reveals reticulate evolution in hares (Lepus spp., Lagomorpha, Mammalia) from Ethiopia. PLoS One 2017; 12:e0180137. [PMID: 28767659 PMCID: PMC5540492 DOI: 10.1371/journal.pone.0180137] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Accepted: 06/10/2017] [Indexed: 11/28/2022] Open
Abstract
For hares (Lepus spp., Leporidae, Lagomorpha, Mammalia) from Ethiopia no conclusive molecular phylogenetic data are available. To provide a first molecular phylogenetic model for the Abyssinian Hare (Lepus habessinicus), the Ethiopian Hare (L. fagani), and the Ethiopian Highland Hare (L. starcki) and their evolutionary relationships to hares from Africa, Eurasia, and North America, we phylogenetically analysed mitochondrial ATPase subunit 6 (ATP6; n = 153 / 416bp) and nuclear transferrin (TF; n = 155 / 434bp) sequences of phenotypically determined individuals. For the hares from Ethiopia, genotype composition at twelve microsatellite loci (n = 107) was used to explore both interspecific gene pool separation and levels of current hybridization, as has been observed in some other Lepus species. For phylogenetic analyses ATP6 and TF sequences of Lepus species from South and North Africa (L. capensis, L. saxatilis), the Anatolian peninsula and Europe (L. europaeus, L. timidus) were also produced and additional TF sequences of 18 Lepus species retrieved from GenBank were included as well. Median joining networks, neighbour joining, maximum likelihood analyses, as well as Bayesian inference resulted in similar models of evolution of the three species from Ethiopia for the ATP6 and TF sequences, respectively. The Ethiopian species are, however, not monophyletic, with signatures of contemporary uni- and bidirectional mitochondrial introgression and/ or shared ancestral polymorphism. Lepus habessinicus carries mtDNA distinct from South African L. capensis and North African L. capensis sensu lato; that finding is not in line with earlier suggestions of its conspecificity with L. capensis. Lepus starcki has mtDNA distinct from L. capensis and L. europaeus, which is not in line with earlier suggestions to include it either in L. capensis or L. europaeus. Lepus fagani shares mitochondrial haplotypes with the other two species from Ethiopia, despite its distinct phenotypic and microsatellite differences; moreover, it is not represented by a species-specific mitochondrial haplogroup, suggesting considerable mitochondrial capture by the other species from Ethiopia or species from other parts of Africa. Both mitochondrial and nuclear sequences indicate close phylogenetic relationships among all three Lepus species from Ethiopia, with L. fagani being surprisingly tightly connected to L. habessinicus. TF sequences suggest close evolutionary relationships between the three Ethiopian species and Cape hares from South and North Africa; they further suggest that hares from Ethiopia hold a position ancestral to many Eurasian and North American species.
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Affiliation(s)
- Zelalem Tolesa
- Department of Biology, Hawassa University, Hawassa, Ethiopia
- Zoologisches Institut, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
- Research Institute of Wildlife Ecology, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Endashaw Bekele
- Department of Microbial, Cellular, and Molecular Biology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Kassahun Tesfaye
- Department of Microbial, Cellular, and Molecular Biology, Addis Ababa University, Addis Ababa, Ethiopia
- Centre of Biotechnology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Hichem Ben Slimen
- Institut Supérieur de Biotechnologie de Béja, Avenue Habib Bourguiba, Béja, Tunisia
| | - Juan Valqui
- Zoologisches Institut, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Abebe Getahun
- Department of Zoological Sciences, Addis Ababa University, Addis Ababa, Ethiopia
| | - Günther B. Hartl
- Zoologisches Institut, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Franz Suchentrunk
- Research Institute of Wildlife Ecology, University of Veterinary Medicine Vienna, Vienna, Austria
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Beugin MP, Letty J, Kaerle C, Guitton JS, Muselet L, Queney G, Pontier D. A single multiplex of twelve microsatellite markers for the simultaneous study of the brown hare (Lepus europaeus) and the mountain hare (Lepus timidus). Ecol Evol 2017. [DOI: 10.1002/ece3.2943] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Affiliation(s)
- Marie-Pauline Beugin
- ANTAGENE; Animal Genomics Laboratory; La Tour de Salvagny (Lyon) France
- Univ Lyon; Université Lyon 1; CNRS; Laboratoire de Biométrie et Biologie Evolutive UMR5558; F-69622 Villeurbanne France
| | - Jérôme Letty
- Research Department; National Hunting and Wildlife Agency (ONCFS); Juvignac Nantes France
| | - Cécile Kaerle
- ANTAGENE; Animal Genomics Laboratory; La Tour de Salvagny (Lyon) France
| | - Jean-Sébastien Guitton
- Research Department; National Hunting and Wildlife Agency (ONCFS); Juvignac Nantes France
| | - Lina Muselet
- ANTAGENE; Animal Genomics Laboratory; La Tour de Salvagny (Lyon) France
| | - Guillaume Queney
- ANTAGENE; Animal Genomics Laboratory; La Tour de Salvagny (Lyon) France
| | - Dominique Pontier
- Univ Lyon; Université Lyon 1; CNRS; Laboratoire de Biométrie et Biologie Evolutive UMR5558; F-69622 Villeurbanne France
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Sokos C, Birtsas P, Papaspyropoulos KG, Giannakopoulos A, Athanasiou LV, Manolakou K, Spyrou V, Billinis C. Conservation considerations for a management measure: an integrated approach to hare rearing and release. ENVIRONMENTAL MANAGEMENT 2015; 55:19-30. [PMID: 25344659 DOI: 10.1007/s00267-014-0388-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2014] [Accepted: 10/11/2014] [Indexed: 06/04/2023]
Abstract
Wildlife managers are challenged with the task of deciding whether a management measure is appropriate or not, and furthermore they have to convince others about the merits of their decision. Population decline of some hare species (genus Lepus) has resulted in their Red Listing and conservation measures are being undertaken. Release or restocking is a frequent measure in some countries, and thousands of hares are released annually, mainly for hunting purposes. These hares can be obtained by either intensive or extensive rearing or translocation of the wild animals. Each method entails difficulties and different survival rates in the wild. Survival rates in the wild are low for hares intensively reared in cages but are higher for hares reared extensively in enclosures and wild translocated hares. The benefits of the hare release practice are significantly lower than the action's implementation cost. Hare releases have not increased significantly the wild hare population or the hunting harvest in areas where the practice has been applied. The risk of genetic and evolutionary degradation and pathogen transmission is possible in wild populations. The need for wise management of this practice is evident and the term 'Permitted Transferring Units' should be introduced to denote regions where hares should not be transferred for rearing and release.
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Affiliation(s)
- Christos Sokos
- Laboratory of Microbiology and Parasitology, Faculty of Veterinary Medicine, University of Thessaly, Karditsa, Greece,
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Canu A, Scandura M, Luchetti S, Cossu A, Iacolina L, Bazzanti M, Apollonio M. Influence of management regime and population history on genetic diversity and population structure of brown hares (Lepus europaeus) in an Italian province. EUR J WILDLIFE RES 2013. [DOI: 10.1007/s10344-013-0731-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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Differences in body mass, health status and genetic variation between insular and mainland brown hares (Lepus europaeus) in Sweden. EUR J WILDLIFE RES 2012. [DOI: 10.1007/s10344-012-0633-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Landscape fragmentation and habitat suitability in endangered Italian hare (Lepus corsicanus) and European hare (Lepus europaeus) populations. EUR J WILDLIFE RES 2009. [DOI: 10.1007/s10344-009-0256-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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On shortcomings of using mtDNA sequence divergence for the systematics of hares (genus Lepus): An example from cape hares. Mamm Biol 2008. [DOI: 10.1016/j.mambio.2007.02.003] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Hamill RM, Doyle D, Duke EJ. Microsatellite Analysis of Mountain Hares (Lepus timidus hibernicus): Low Genetic Differentiation and Possible Sex-Bias in Dispersal. J Mammal 2007. [DOI: 10.1644/05-mamm-a-419r1.1] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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Hamill RM, Doyle D, Duke EJ. Spatial patterns of genetic diversity across European subspecies of the mountain hare, Lepus timidus L. Heredity (Edinb) 2006; 97:355-65. [PMID: 16896342 DOI: 10.1038/sj.hdy.6800880] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Fossil evidence shows that populations of species that currently inhabit arctic and boreal regions were not isolated in refugia during glacial periods, but instead maintained populations across large areas of central Europe. These species commonly display little reduction in genetic diversity in northern areas of their range, in contrast to many temperate species. The mountain hare currently inhabits both temperate and arctic-boreal regions. We used nuclear microsatellite and mtDNA sequence data to examine population structure and alternate phylogeographic hypotheses for the mountain hare, that is, temperate type (lower genetic diversity in northern areas) and arctic-boreal type (high northern genetic diversity). Both data sets revealed concordant patterns. Highest allelic richness, expected heterozygosity and mtDNA haplotype diversity were identified in the most northerly subspecies, indicating that this species more closely maps to phylogeographic patterns observed in arctic-boreal rather than temperate species. With regard to population structure, the Alpine and Fennoscandian subspecies were most genetically similar (F(ST) approximately 0.1). These subspecies also clustered together on the mtDNA tree and were assigned with highest likelihood to a common Bayesian cluster. This is consistent with fossil evidence for intermediate populations in the central European plain, persisting well into the postglacial period. In contrast, the geographically close Scottish and Irish populations occupied separate Bayesian clusters, distinct clades on the mtDNA maximum likelihood tree and were genetically divergent from each other (F(ST) > 0.4) indicating the influence of genetic drift, long isolation (possibly dating from the late glacial era) and/or separate postglacial colonisation routes.
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Affiliation(s)
- R M Hamill
- UCD School of Biology and Environmental Science, Belfield, Dublin 4, Ireland.
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Thulin CG, Fang M, Averianov AO. Introgression from Lepus europaeus to L. timidus in Russia revealed by mitochondrial single nucleotide polymorphisms and nuclear microsatellites. Hereditas 2006; 143:68-76. [PMID: 17362337 DOI: 10.1111/j.2006.0018-0661.01952.x] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Hybridisation among wild mammal populations may lead to introgression of genes and genomes over the species barrier. In Sweden, in northern Europe, and on the Iberian Peninsula in southern Europe, mitochondrial DNA from L. timidus occurs among L. europaeus specimens, presumably as a result of interspecific hybridisation. In Russia, the species are believed to hybridise as well, but no investigations have confirmed introgression. Here we develop species diagnostic single nucleotide polymorphisms in the mitochondrial genomes and combine them with analysis of nuclear microsatellite markers to investigate hybridisation and introgression in 71 Lepus specimens from Russia. A total of 58 specimens are typical representatives of either species. An additional nine specimens have slightly intermediate genotypes, potentially as a result of introgression of nuclear genes. Finally, we find three specimens with L. europaeus mitochondrial genome and apparent L. timidus nuclear genome. This indicates that the reciprocal transfer of mtDNA occur among Russian populations of these species. Our observation differs from previous observations of mtDNA introgression in Sweden and Iberia, and provides further support for a reticulated mode of introgression within the genus Lepus.
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Affiliation(s)
- Carl-Gustaf Thulin
- Population Biology and Conservation Biology, Department of Ecology and Evolution, EBC, Uppsala University, Sweden.
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Thulin CG, Stone J, Tegelström H, Walker CW. Species assignment and hybrid identification among Scandinavian hares Lepus europaeus and L. timidus. WILDLIFE BIOLOGY 2006. [DOI: 10.2981/0909-6396(2006)12[29:saahia]2.0.co;2] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
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Estonba A, Solís A, Iriondo M, Sanz-Martín MJ, Pérez-Suárez G, Markov G, Palacios F. The genetic distinctiveness of the three Iberian hare species: Lepus europaeus, L. granatensis, and L. castroviejoi. Mamm Biol 2006. [DOI: 10.1016/j.mambio.2005.08.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Giacometti M, Roganti R, Tann DD, Stahlberger-Saitbekova N, Obexer-Ruff G. Alpine ibexCapra ibex ibexx domestic goatC. aegagrus domesticahybrids in a restricted area of southern Switzerland. WILDLIFE BIOLOGY 2004. [DOI: 10.2981/wlb.2004.018] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Affiliation(s)
- Marco Giacometti
- Marco Giacometti, Wildvet Projects, CH-7605 Stampa, Switzerland -
| | - Renato Roganti
- Renato Roganti & Dario De Tann, Grisons Game and Fish Department, Loestrasse 14, CH-7001 Chur, Switzerland -
| | - Dario De Tann
- Renato Roganti & Dario De Tann, Grisons Game and Fish Department, Loestrasse 14, CH-7001 Chur, Switzerland -
| | - Nasikat Stahlberger-Saitbekova
- Nasikat Stahlberger-Saitbekova & Gabriela Obexer-Ruff, Institute of Animal Breeding, University of Berne, Bremgartenstrasse 109a, CH-3012 Berne, Switzerland -(Gabriela Obexer-Ruff)
| | - Gabriela Obexer-Ruff
- Nasikat Stahlberger-Saitbekova & Gabriela Obexer-Ruff, Institute of Animal Breeding, University of Berne, Bremgartenstrasse 109a, CH-3012 Berne, Switzerland -(Gabriela Obexer-Ruff)
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Thulin CG, Tegelström H. High mtDNA haplotype diversity among introduced Swedish brown haresLepus europaeus. ACTA ACUST UNITED AC 2001. [DOI: 10.1007/bf03192444] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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