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Cernohorska H, Kubickova S, Musilova P, Vozdova M, Vodicka R, Rubes J. Supernumerary Marker Chromosome Identified in Asian Elephant ( Elephas maximus). Animals (Basel) 2023; 13:ani13040701. [PMID: 36830488 PMCID: PMC9952010 DOI: 10.3390/ani13040701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 02/14/2023] [Accepted: 02/14/2023] [Indexed: 02/19/2023] Open
Abstract
We identified a small, supernumerary marker chromosome (sSMC) in two phenotypically normal Asian elephants (Elephas maximus): a female (2n = 57,XX,+mar) and her male offspring (2n = 57,XY,+mar). sSMCs are defined as structurally abnormal chromosomes that cannot be identified by conventional banding analysis since they are usually small and often lack distinct banding patterns. Although current molecular techniques can reveal their origin, the mechanism of their formation is not yet fully understood. We determined the origin of the marker using a suite of conventional and molecular cytogenetic approaches that included (a) G- and C-banding, (b) AgNOR staining, (c) preparation of a DNA clone using laser microdissection of the marker chromosome, (d) FISH with commercially available human painting and telomeric probes, and (e) FISH with centromeric DNA derived from the centromeric regions of a marker-free Asian elephant. Moreover, we present new information on the location and number of NORs in Asian and savanna elephants. We show that the metacentric marker was composed of heterochromatin with NORs at the terminal ends, originating most likely from the heterochromatic region of chromosome 27. In this context, we discuss the possible mechanism of marker formation. We also discuss the similarities between sSMCs and B chromosomes and whether the marker chromosome presented here could evolve into a B chromosome in the future.
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Affiliation(s)
- Halina Cernohorska
- Department of Genetics and Reproductive Biotechnologies, Veterinary Research Institute, 62100 Brno, Czech Republic
- Correspondence: ; Tel.: +420-533331425
| | - Svatava Kubickova
- Department of Genetics and Reproductive Biotechnologies, Veterinary Research Institute, 62100 Brno, Czech Republic
| | - Petra Musilova
- Department of Genetics and Reproductive Biotechnologies, Veterinary Research Institute, 62100 Brno, Czech Republic
| | - Miluse Vozdova
- Department of Genetics and Reproductive Biotechnologies, Veterinary Research Institute, 62100 Brno, Czech Republic
| | | | - Jiri Rubes
- Department of Genetics and Reproductive Biotechnologies, Veterinary Research Institute, 62100 Brno, Czech Republic
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Marasinghe MSLRP, Nilanthi RMR, Hathurusinghe HABM, Sooriyabandara MGC, Chandrasekara CHWMRB, Jayawardana KANC, Kodagoda MM, Rajapakse RC, Bandaranayake PCG. Revisiting traditional SSR based methodologies available for elephant genetic studies. Sci Rep 2021; 11:8718. [PMID: 33888797 PMCID: PMC8062488 DOI: 10.1038/s41598-021-88034-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 03/30/2021] [Indexed: 02/02/2023] Open
Abstract
Asian elephant (Elephas maximus) plays a significant role in natural ecosystems and it is considered as an endangered animal. Molecular genetics studies on elephants' dates back to 1990s. Microsatellite markers have been the preferred choice and have played a major role in ecological, evolutionary and conservation research on elephants over the past 20 years. However, technical constraints especially related to the specificity of traditionally developed microsatellite markers have brought to question their application, specifically when degraded samples are utilized for analysis. Therefore, we analyzed the specificity of 24 sets of microsatellite markers frequently used for elephant molecular work. Comparative wet lab analysis was done with blood and dung DNA in parallel with in silico work. Our data suggest cross-amplification of unspecific products when field-collected dung samples are utilized in assays. The necessity of Asian elephant specific set of microsatellites and or better molecular techniques are highlighted.
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Affiliation(s)
- M S L R P Marasinghe
- Department of Wildlife Conservation, 811/A, Jayanthipura Road, Battaramulla, 10120, Sri Lanka
| | - R M R Nilanthi
- Department of Wildlife Conservation, 811/A, Jayanthipura Road, Battaramulla, 10120, Sri Lanka
| | - H A B M Hathurusinghe
- Agricultural Biotechnology Centre, Faculty of Agriculture, University of Peradeniya, Peradeniya, 20400, Sri Lanka
| | - M G C Sooriyabandara
- Department of Wildlife Conservation, 811/A, Jayanthipura Road, Battaramulla, 10120, Sri Lanka
| | - C H W M R B Chandrasekara
- Agricultural Biotechnology Centre, Faculty of Agriculture, University of Peradeniya, Peradeniya, 20400, Sri Lanka
| | - K A N C Jayawardana
- Department of Wildlife Conservation, 811/A, Jayanthipura Road, Battaramulla, 10120, Sri Lanka
| | - M M Kodagoda
- Agricultural Biotechnology Centre, Faculty of Agriculture, University of Peradeniya, Peradeniya, 20400, Sri Lanka
| | - R C Rajapakse
- Department of National Zoological Gardens, Anagarika Dharmapala Mawatha, Dehiwala, 10350, Sri Lanka
| | - P C G Bandaranayake
- Agricultural Biotechnology Centre, Faculty of Agriculture, University of Peradeniya, Peradeniya, 20400, Sri Lanka.
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Rattanayuvakorn S, Tanomtong A, Phimphan S, Sangpakdee W, Pinmongkhonkul S, Phintong K. Karyological Study of Tusker and Tuskless Male Asian Elephant ( Elephas maximus) by Conventional, GTG-, and Ag-NOR Banding Techniques. CYTOLOGIA 2017. [DOI: 10.1508/cytologia.82.349] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Sukjai Rattanayuvakorn
- Department of Science and Mathematics, Faculty of Agriculture and Technology, Rajamangala University of Technology Isan, Surin Campus
| | - Alongklod Tanomtong
- Toxic Substances in Livestock and Aquatic Animals Research Group, Department of Biology, Faculty of Science, Khon Kaen University
| | - Sumalee Phimphan
- Toxic Substances in Livestock and Aquatic Animals Research Group, Department of Biology, Faculty of Science, Khon Kaen University
| | - Wiwat Sangpakdee
- Biology program, Faculty of Science, Udon Thani Rajabhat University
| | | | - Krit Phintong
- Department of Fundamental Science, Faculty of Science and Technology, Surindra Rajabhat University
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Lei R, Brenneman RA, Schmitt DL, Louis EE. Genetic diversity in North American captive Asian elephants. J Zool (1987) 2011. [DOI: 10.1111/j.1469-7998.2011.00851.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Population genetic structure and conservation of Asian elephants (Elephas maximus) across India. Anim Conserv 2005. [DOI: 10.1017/s1367943005002428] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Vidya TNC, Fernando P, Melnick DJ, Sukumar R. Population differentiation within and among Asian elephant (Elephas maximus) populations in southern India. Heredity (Edinb) 2004; 94:71-80. [PMID: 15454948 DOI: 10.1038/sj.hdy.6800568] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Southern India, one of the last strongholds of the endangered Asian elephant (Elephas maximus), harbours about one-fifth of the global population. We present here the first population genetic study of free-ranging Asian elephants, examining within- and among-population differentiation by analysing mitochondrial DNA (mtDNA) and nuclear microsatellite DNA differentiation across the Nilgiris-Eastern Ghats, Anamalai, and Periyar elephant reserves of southern India. Low mtDNA diversity and 'normal' microsatellite diversity were observed. Surprisingly, the Nilgiri population, which is the world's single largest Asian elephant population, had only one mtDNA haplotype and lower microsatellite diversity than the two other smaller populations examined. There was almost no mtDNA or microsatellite differentiation among localities within the Nilgiris, an area of about 15,000 km2. This suggests extensive gene flow in the past, which is compatible with the home ranges of several hundred square kilometres of elephants in southern India. Conversely, the Nilgiri population is genetically distinct at both mitochondrial and microsatellite markers from the two more southerly populations, Anamalai and Periyar, which in turn are not genetically differentiated from each other. The more southerly populations are separated from the Nilgiris by only a 40-km-wide stretch across a gap in the Western Ghats mountain range. These results variably indicate the importance of population bottlenecks, social organization, and biogeographic barriers in shaping the distribution of genetic variation among Asian elephant populations in southern India.
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Affiliation(s)
- T N C Vidya
- Centre for Ecological Sciences, Indian Institute of Science, Bangalore 560012, India.
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Vandebona H, Goonesekere N, Tiedemann R, Ratnasooriya W, Gunasekera M. Sequence variation at two mitochondrial genes in the Asian elephant (Elephas maximus) population of Sri Lanka. Mamm Biol 2002. [DOI: 10.1078/1616-5047-00030] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Fernando P, Pfrender ME, Encalada SE, Lande R. Mitochondrial DNA variation, phylogeography and population structure of the Asian elephant. Heredity (Edinb) 2000; 84 ( Pt 3):362-72. [PMID: 10762406 DOI: 10.1046/j.1365-2540.2000.00674.x] [Citation(s) in RCA: 92] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We report the first genetic analysis of free-ranging Asian elephants (Elephas maximus). We sampled 118 elephants from Sri Lanka, Bhutan/North India, and Laos/Vietnam by extracting DNA from dung, PCR amplifying and sequencing 630 nucleotides of mitochondrial DNA, including part of the variable left domain of the control region. Comparison with African elephant (Loxodonta africana) sequences indicated a relatively slow molecular clock in the Proboscidea with a sequence divergence of approximately 1%/Myr. Genetic diversity within Asian elephants was low, suggesting a small long-term effective population size. Seventeen haplotypes were identified within Asian elephants, which clustered into two well-differentiated assemblages with an estimated Pliocene divergence of 2.5-3.5 million years ago. The two assemblages showed incomplete geographical partitioning, suggesting allopatric divergence and secondary admixture. On the mainland, little genetic differentiation was observed between elephant populations of Bhutan and India or Laos and Vietnam. A significant difference in haplotype frequencies but relatively weak subdivision was observed between the regions Bhutan-India and Laos-Vietnam. Significant genetic differentiation was observed between the mainland and Sri Lanka, and between northern, mid-latitude and southern regions in Sri Lanka.
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Affiliation(s)
- P Fernando
- Department of Biology, University of Oregon, Eugene, OR 97403, USA.
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