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Wang Z, Lu G, Gao Y, Yan L, Li M, Hu D, Zhang D. mtDNA CR Evidence Indicates High Genetic Diversity of Captive Forest Musk Deer in Shaanxi Province, China. Animals (Basel) 2023; 13:2191. [PMID: 37443989 DOI: 10.3390/ani13132191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 06/01/2023] [Accepted: 06/01/2023] [Indexed: 07/15/2023] Open
Abstract
Forest musk deer (Moschus berezovskii) are endangered ruminants whose adult males secrete musk. China has been breeding forest musk deer artificially since the 1950s in an effort to restore wild populations, with Shaanxi and Sichuan provinces as the two main sites for captive breeding. Genetic diversity is a significant indicator that determines the long-term viability and status of a population, particularly for species at risk of extinction. In this study, we analyzed the current genetic makeup of seven captive forest musk deer populations in the Shaanxi province, using the mitochondrial DNA (mtDNA) control region (CR) as the molecular marker. We sequenced 604 bp of mtDNA CR, with an average content of A+T higher than G+C. We observed 111 variable sites and 39 different haplotypes from 338 sequences. The nucleotide diversity (Pi) and haplotype diversity (Hd) were 0.02887 and 0.908, respectively. Genetic differentiation between these populations was not significant, and the populations might not have experienced rapid growth. By combining our sequences with previous ones, we identified 65 unique haplotypes with 26 rare haplotypes and estimated a total of 90 haplotypes in Shaanxi province captive populations. The Shaanxi province and Sichuan province obtained 88 haplotypes, the haplotypes from the two populations were mixed together, and the two populations showed moderate genetic differentiation. Our findings suggested that captive forest musk deer populations in the Shaanxi province had high genetic diversity, with a rich founder population of about 90 maternal lines. Additionally, managers could develop genetic management plans for forest musk deer based on the haplotype database. Overall, our study will provide insights and guidelines for the conservation of genetic diversity in captive forest musk deer populations in the Shaanxi province.
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Affiliation(s)
- Zhe Wang
- School of Ecology and Nature Conservation, Beijing Forestry University, Qinghua East Road 35, Beijing 100083, China
| | - Guanjie Lu
- School of Ecology and Nature Conservation, Beijing Forestry University, Qinghua East Road 35, Beijing 100083, China
| | - Yunyun Gao
- School of Ecology and Nature Conservation, Beijing Forestry University, Qinghua East Road 35, Beijing 100083, China
| | - Liping Yan
- School of Ecology and Nature Conservation, Beijing Forestry University, Qinghua East Road 35, Beijing 100083, China
| | - Mingzhe Li
- China Wildlife Conservation Association, Beijing 100714, China
| | - Defu Hu
- School of Ecology and Nature Conservation, Beijing Forestry University, Qinghua East Road 35, Beijing 100083, China
| | - Dong Zhang
- School of Ecology and Nature Conservation, Beijing Forestry University, Qinghua East Road 35, Beijing 100083, China
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Giontella A, Cardinali I, Lancioni H, Giovannini S, Pieramati C, Silvestrelli M, Sarti FM. Mitochondrial DNA Survey Reveals the Lack of Accuracy in Maremmano Horse Studbook Records. Animals (Basel) 2020; 10:E839. [PMID: 32408648 PMCID: PMC7278429 DOI: 10.3390/ani10050839] [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: 04/01/2020] [Revised: 04/30/2020] [Accepted: 05/09/2020] [Indexed: 11/16/2022] Open
Abstract
* Correspondence: andrea [...].
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Affiliation(s)
- Andrea Giontella
- Department of Veterinary Medicine—Sportive Horse Research Center, University of Perugia, via S.Costanzo 4, 06123 Perugia, Italy; (C.P.); (M.S.)
| | - Irene Cardinali
- Department of Chemistry, Biology and Biotechnology, University of Perugia, via - Elce di Sotto, 8, 06123 Perugia, Italy; (I.C.); (H.L.)
| | - Hovirag Lancioni
- Department of Chemistry, Biology and Biotechnology, University of Perugia, via - Elce di Sotto, 8, 06123 Perugia, Italy; (I.C.); (H.L.)
| | - Samira Giovannini
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, Borgo XX Giugno, 74, 06121 Perugia, Italy; (S.G.); (F.M.S.)
| | - Camillo Pieramati
- Department of Veterinary Medicine—Sportive Horse Research Center, University of Perugia, via S.Costanzo 4, 06123 Perugia, Italy; (C.P.); (M.S.)
| | - Maurizio Silvestrelli
- Department of Veterinary Medicine—Sportive Horse Research Center, University of Perugia, via S.Costanzo 4, 06123 Perugia, Italy; (C.P.); (M.S.)
| | - Francesca Maria Sarti
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, Borgo XX Giugno, 74, 06121 Perugia, Italy; (S.G.); (F.M.S.)
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Deshpande K, Perez E, Leyva N, Suarez M, Mills DK. Genetic Structure of the Big Summit Herd and Neighboring Wild Horse Populations Inhabiting Herd Management Areas of Oregon. WEST N AM NATURALIST 2019. [DOI: 10.3398/064.079.0109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Affiliation(s)
- Ketaki Deshpande
- International Forensic Research Institute, Florida International University, Miami, FL 33199
| | - Evelyn Perez
- International Forensic Research Institute, Florida International University, Miami, FL 33199
| | - Natalie Leyva
- International Forensic Research Institute, Florida International University, Miami, FL 33199
| | - Merly Suarez
- Department of Biological Sciences, Florida International University, Miami, FL 33199
| | - DeEtta K. Mills
- International Forensic Research Institute, Florida International University, Miami, FL 33199
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Ristov S, Brajkovic V, Cubric-Curik V, Michieli I, Curik I. MaGelLAn 1.0: a software to facilitate quantitative and population genetic analysis of maternal inheritance by combination of molecular and pedigree information. Genet Sel Evol 2016; 48:65. [PMID: 27613390 PMCID: PMC5018160 DOI: 10.1186/s12711-016-0242-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Accepted: 08/29/2016] [Indexed: 11/23/2022] Open
Abstract
Background Identification of genes or even nucleotides that are responsible for quantitative and adaptive trait variation is a difficult task due to the complex interdependence between a large number of genetic and environmental factors. The polymorphism of the mitogenome is one of the factors that can contribute to quantitative trait variation. However, the effects of the mitogenome have not been comprehensively studied, since large numbers of mitogenome sequences and recorded phenotypes are required to reach the adequate power of analysis. Current research in our group focuses on acquiring the necessary mitochondria sequence information and analysing its influence on the phenotype of a quantitative trait. To facilitate these tasks we have produced software for processing pedigrees that is optimised for maternal lineage analysis. Results We present MaGelLAn 1.0 (maternal genealogy lineage analyser), a suite of four Python scripts (modules) that is designed to facilitate the analysis of the impact of mitogenome polymorphism on quantitative trait variation by combining molecular and pedigree information. MaGelLAn 1.0 is primarily used to: (1) optimise the sampling strategy for molecular analyses; (2) identify and correct pedigree inconsistencies; and (3) identify maternal lineages and assign the corresponding mitogenome sequences to all individuals in the pedigree, this information being used as input to any of the standard software for quantitative genetic (association) analysis. In addition, MaGelLAn 1.0 allows computing the mitogenome (maternal) effective population sizes and probability of mitogenome (maternal) identity that are useful for conservation management of small populations. Conclusions MaGelLAn is the first tool for pedigree analysis that focuses on quantitative genetic analyses of mitogenome data. It is conceived with the purpose to significantly reduce the effort in handling and preparing large pedigrees for processing the information linked to maternal lines. The software source code, along with the manual and the example files can be downloaded at http://lissp.irb.hr/software/magellan-1-0/ and https://github.com/sristov/magellan. Electronic supplementary material The online version of this article (doi:10.1186/s12711-016-0242-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Strahil Ristov
- Ruđer Bošković Institute, Bijenička cesta 54, 10000, Zagreb, Croatia.
| | - Vladimir Brajkovic
- Faculty of Agriculture, University of Zagreb, Svetošimunska cesta 25, 10000, Zagreb, Croatia
| | - Vlatka Cubric-Curik
- Faculty of Agriculture, University of Zagreb, Svetošimunska cesta 25, 10000, Zagreb, Croatia
| | - Ivan Michieli
- Ruđer Bošković Institute, Bijenička cesta 54, 10000, Zagreb, Croatia
| | - Ino Curik
- Faculty of Agriculture, University of Zagreb, Svetošimunska cesta 25, 10000, Zagreb, Croatia
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Winton CL, Plante Y, Hind P, McMahon R, Hegarty MJ, McEwan NR, Davies-Morel MCG, Morgan CM, Powell W, Nash DM. Comparative genetic diversity in a sample of pony breeds from the U.K. and North America: a case study in the conservation of global genetic resources. Ecol Evol 2015; 5:3507-22. [PMID: 26380682 PMCID: PMC4569044 DOI: 10.1002/ece3.1562] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2014] [Revised: 05/14/2015] [Accepted: 05/18/2015] [Indexed: 11/09/2022] Open
Abstract
Most species exist as subdivided ex situ daughter population(s) derived from a single original group of individuals. Such subdivision occurs for many reasons both natural and manmade. Traditional British and Irish pony breeds were introduced to North America (U.S.A. and Canada) within the last 150 years, and subsequently equivalent breed societies were established. We have analyzed selected U.K. and North American equivalent pony populations as a case study for understanding the relationship between putative source and derived subpopulations. Diversity was measured using mitochondrial DNA and a panel of microsatellite markers. Genetic signatures differed between the North American subpopulations according to historical management processes. Founder effect and stochastic drift was apparent, particularly pronounced in some breeds, with evidence of admixture of imported mares of different North American breeds. This demonstrates the importance of analysis of subpopulations to facilitate understanding the genetic effects of past management practices and to lead to informed future conservation strategies.
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Affiliation(s)
- Clare L Winton
- IBERS, Aberystwyth University Aberystwyth, Ceredigion, SY23 3DA, U.K
| | - Yves Plante
- Agriculture and Agri-Food Canada Saskatoon, Saskatchewan, S7N 5A8, Canada
| | - Pamela Hind
- Agriculture and Agri-Food Canada Saskatoon, Saskatchewan, S7N 5A8, Canada
| | - Robert McMahon
- IBERS, Aberystwyth University Aberystwyth, Ceredigion, SY23 3DA, U.K
| | - Matthew J Hegarty
- IBERS, Aberystwyth University Aberystwyth, Ceredigion, SY23 3DA, U.K
| | - Neil R McEwan
- IBERS, Aberystwyth University Aberystwyth, Ceredigion, SY23 3DA, U.K
| | | | - Charly M Morgan
- IBERS, Aberystwyth University Aberystwyth, Ceredigion, SY23 3DA, U.K
| | | | - Deborah M Nash
- IBERS, Aberystwyth University Aberystwyth, Ceredigion, SY23 3DA, U.K
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Čačić M, Cubric-Curik V, Ristov S, Curik I. Computational approach to utilisation of mitochondrial DNA in the verification of complex pedigree errors. Livest Sci 2014. [DOI: 10.1016/j.livsci.2014.09.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Liu G, Xu CQ, Cao Q, Zimmermann W, Songer M, Zhao SS, Li K, Hu DF. Mitochondrial and pedigree analysis in Przewalski's horse populations: implications for genetic management and reintroductions. ACTA ACUST UNITED AC 2013; 25:313-8. [PMID: 23808923 DOI: 10.3109/19401736.2013.800487] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
BACKGROUND AND AIMS Przewalski's horses have been imported from the western zoos to China since 1985. Yet the genetic diversity in China's populations has not been studied, thus lacking of such knowledge inevitably affects this population's management. The aim of this study was to assess genetic diversity in Chinese population of Przewalski's horses via mitochondrial DNA (mtDNA) control region and pedigree analysis. MATERIALS AND METHODS Two captive and one reintroduced populations were examined based on mitochondrial DNA control region variation via fecal sampling from 2010 to 2012, together with pedigree analysis. RESULTS Amplification success rates of fecal mtDNA were as high as 96.2% (93.8%-100%), and were higher for sample in winter than in summer and autumn. Two haplotypes were identified and shared among three populations, but the proportion of individuals with each haplotype varied among the three populations (F(ST) = 0.10874, p = 0.00978). Haplotype diversity in the released population (0.153) was much lower than that in the two captive populations (0.4011 and 0.4966), in accordance with the direction of increase in probability of identity at the dam lines. CONCLUSION Future concerns in Przewalski's horse population management should emphasize on strict reproduction control to minimize inbreeding in captivity, followed by long-term genetic diversity guidelines and non-invasive monitoring in the reintroduction programmes.
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Affiliation(s)
- Gang Liu
- Laboratory of Non-invasive Research Technology for Endangered Species, College of Biological Science and Technology, Beijing Forestry University , Beijing , China
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Bower MA, Whitten M, Nisbet RER, Spencer M, Dominy KM, Murphy AM, Cassidy R, Barrett E, Hill EW, Binns M. Thoroughbred racehorse mitochondrial DNA demonstrates closer than expected links between maternal genetic history and pedigree records. J Anim Breed Genet 2012; 130:227-35. [PMID: 23679948 DOI: 10.1111/j.1439-0388.2012.01018.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2012] [Accepted: 06/16/2012] [Indexed: 11/27/2022]
Abstract
The potential future earnings and therefore value of Thoroughbred foals untested in the racing arena are calculated based on the performance of their forebears. Thus, lineage is of key importance. However, previous research indicates that maternally inherited mitochondrial DNA (mtDNA) does not correspond to maternal lineage according to recorded pedigree, casting doubt on the voracity of historic pedigrees. We analysed mtDNA of 296 Thoroughbred horses from 33 maternal lineages and identified an interesting trend. Subsequent to the founding of the Thoroughbred breed in the 16th century, well-populated maternal lineages were divided into sub-lineages. Only six in 10 of the Thoroughbreds sampled shared mitochondrial haplotype with other members of their maternal lineage, despite having a common maternal ancestor according to pedigree records. However, nine in 10 Thoroughbreds from the 103 sub-lineages sampled shared mtDNA with horses of their maternal pedigree sub-lineage. Thus, Thoroughbred maternal sub-lineage pedigree represents a more accurate breeding record than previously thought. Errors in pedigrees must have occurred largely, though, not exclusively, at sub-lineage foundation events, probably due to incomplete understanding of modes of inheritance in the past, where maternal sub-lineages were founded from individuals, related, but not by female descent.
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Affiliation(s)
- M A Bower
- McDonald Institute for Archaeological Research, University of Cambridge, Cambridge, UK.
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