International E-publication: Publish Projects, Dissertation, Theses, Books, Souvenir, Conference Proceeding with ISBN.  International E-Bulletin: Information/News regarding: Academics and Research

Molecular markers based characterization and conservation of wild animals

    , ,

Author Affiliations

  • 1Animal Genetics Laboratory, School of Animal and Range Sciences, College of Agriculture and Environmental Sciences; Post Box: 138, Haramaya University, Dire Dawa, Ethiopia
  • 2Animal Genetics Laboratory, School of Animal and Range Sciences, College of Agriculture and Environmental Sciences; Post Box: 138, Haramaya University, Dire Dawa, Ethiopia
  • 3School of Basic and Applied Sciences RNB Global University, Sri Ganganagar Road, Khara, Bikaner - 334601 Rajasthan

Res. J. Recent Sci., Volume 6, Issue (7), Pages 53-62, June,2 (2017)

Abstract

Simultaneous presence of various animal genetic resources in a given area or country is known as animal biodiversity. Africa has rich wildlife resources serving as a major tourist attraction. Wildlife biodiversity (WLBD) is an important asset for developing countries in uplifting their economy. Hence, characterization, conservation and maintenance of WLBD should be given top priority. Global climate change has resulted in the depletion of wildlife habitat and is responsible for extinction of many species. Characterization helps us to distinguish variation within and between different organisms and guide us for proper conservation of populations, species and or strains. Characterization can be done based on phenotype, biochemical polymorphism and molecular based markers. Molecular studies based on mitochondrial DNA (mtDNA) and nuclear DNA are more popular as they save time, minimize long term investigation cost and are efficient in information generation. In this article, we reviewed the various molecular markers used in the characterization of wildlife, namely: Restriction Fragment Length Polymorphism (RFLP), Random Amplification of Polymorphic DNA (RAPD), Amplified Fragment Length Polymorphism (AFLP), Microsatellite and Single Nucleotide Polymorphisms (SNPs).

References

  1. Szaro Robert C. and David Johnston W. (1996)., Biodiversity in mangrove landscapes, theory and practice., Oxford University Press.
  2. Shibru T. (1995)., Protected areas management crises in Ethiopia., Walia., 16, 17-30.
  3. Hilman J.C. (1991)., The current situation in Ethiopia’s wildlife conservation areas., Ethiopian Wildlife Conservation Organization, Addis Ababa.
  4. Newmark W.D., Manyanza D.N., Gamassa D.M. and Sariko H.I. (1994)., The conflict between wildlife and local people living adjacent to protected areas in Tanzania: human density as a predictor., Conservation Biology, 8(1), 249-255.
  5. Schloeder C.A. and Jacobs M. (1993)., Awash National Park Management Plan., Ethiopian Wildlife Conservation Department, Addis Ababa.
  6. World Bank (1997)., World Development Indicators, CD/ROM., International Bank for Reconstruction and Development/World Bank.
  7. Anagaw A. (2008)., Potential for Sustainable trophy sport hunting on Mountain Nyala (Tragelaphus Buxtoni) in the Bale mountains of Ethiopia., Field research progress submitted to BERSEMP.
  8. Frankham R., Ballou J.D. and Briscoe D.A. (2002)., Introduction to Conservation Genetics., Cambridge University Press, New York.
  9. Wan Q.H., Wu H., Fang S.G. and Fujihara T. (2004)., Which genetic marker for which conservation genetics issue?., Wiley-VCHH Verlag GmbH & Co KGaA, Weinheim, 25, 2165-2176.
  10. Smith T.B. and Wayne R.K. (1996)., Molecular Genetic approaches in conservation., Oxford University Press, New York.
  11. Tanksley S.D. and Orton T.J. (1983)., Isozymes in Plant Genetics and Breeding., Amsterdam: Elsevier Science.
  12. Baker C.M., Manwell C. and Labrisky R.F. and Harper J.A. (1966)., Molecular genetics of avian proteins: Egg, blood and tissue proteins of the Ring necked pheasant, Phasianus colchicus L., Comp. Biochem. Physiol., 17(2), 467-476.
  13. Murphy R.W., Sites J.W., Buth D.G. and Haußer C.H. (1996)., Proteins: Isozyme electrophoresis. In: Hillis DM, Moritz C, Mable BK (Eds.) Molecular Systematics., Sinauer Associates, Sunderland, MA, 45, 126.
  14. Sunnucks P. (2000)., Efficient genetic markers for population biology., Tree, 15(5), 199-203.
  15. Mullis K.B., Faloona F., Schaarf S., Saiki R.K., Horn G.T. and Erlich H. (1986)., Specific enzymatic amplification of DNA in vitro: the polymerase chain reaction., Cold Spring Harbor Symposium, Quantitative Biology, 7, 263-273.
  16. Garcia‐Rodriguez A.I., Bowen B.W., Domning D., Mignucci‐Giannoni A.A., Marmontel M., Montoya‐Ospina R.A., Morales‐Vela B., Rudin M., Bonde R.K. and McGuire P.M. (1998)., Phylogeography of the West Indian manatee (Trichechus manatus) how many populations and how many taxa?., Mol, Ecology., 7(9), 1137-1149.
  17. Clark A.M., Branch L.C. and Bowen B.W. (1999)., Effects of natural habitat fragmentation on an endemic lizard: an historical perspective based on an mtDNA gene genealogy., Mol. Ecology., 8(7), 1093-1104.
  18. Karl S.A. and Bowen B.W. (1999)., Evolutionary significant units versus geopolitical taxonomy: molecular systematics of an endangered sea turtle (genus Chelonia)., Conservation Biology., 13(5), 990-999.
  19. Arif I.A. and Khan H.A. (2009)., Molecular markers for biodiversity analysis of wildlife animals: a brief review., Animal Biodiv. Conservation., 32(1), 9-17.
  20. Wallace D.C. (1986)., Mitochondrial genes and disease., Hospital Practice., 21(10), 77-87.
  21. Gray M.W. (1989)., Origin and evolution of mitochondrial DNA., Ann. Rev. Cell. Biol., 5, 25-50.
  22. Clayton D.A. (1991)., Replication and transcription of vertebrate mitochondrial DNA., Ann. Rev. Cell. Biol., 7, 453-478.
  23. Avise J.C. (1991)., Ten unorthodox perspectives on evolution prompted by comparative population findings on mitochondrial DNA., Ann. Rev. Genet., 25, 45-69.
  24. Dianne N., William S. and Claiborne S. (1995)., Molecular evolution of mitochondrial 12S rRNA and cytochrome b sequences in the pantherine linage of Felidae., Mol. Biol. Evol., 12(4), 690-707.
  25. Johnson Warren E., Godoy Jose A., Palomares F., Delibes M., Fernandes M., Revilla E. and O, Phylogenetic and phylogeographic analysis of Iberian Lynx populations., J. Heredity., 95(1), 19-28.
  26. Malisa, A., Gwakisa, P., Balthazary, S., Wasser S.K. and Mutayoba B.M. (2006)., The potential of mitochondrial DNA markers and polymerase chain reaction-restriction fragment length polymorphism for domestic and wild species identification., African J. Biotech., 5(18), 1588-1593.
  27. Zhang, W., Zhang, Z., Shen, F., Rong Hou, Xiaoping Lv and Bisong Yue (2006)., Highly conserved D-loop-like nuclear mitochondrial sequences (Numts) in tiger (Panthera tigris)., J. Genetics., 85(2), 107-116.
  28. Kahl G. (2001)., The Dictionary of Gene Technology., Dictionary of gene technology, Wiley-VCH, Weinheim.
  29. Southern E.M. (1975)., Detection of specific sequences among DNA fragments separated by gel electrophoresis., J. Mol. Biol., 98(3), 503-517.
  30. Botstein D., White R.L., Skolnick M. and Davis R.W. (1980)., Construction of a genetic linkage map in man using restriction fragment length polymorphisms., Human Genetics., 32(3), 314-331.
  31. Collard B.C., Jahufer M.Z., Brouwer J. and Pang E.C.K. (2005)., An introduction to markers, quantitative trait loci (QTL) mappintg and marker-assisted selection for crop improvement: The basic concepts., Euphytica., 142, 169 - 196.
  32. Williams J.G., Kubelik A.R., Livak J., Rafalski J. and Tingey S.V. (1990)., DNA polymorphisms amplified by arbitrary primers are useful as genetic markers., Nucl. Acids Res., 18(22), 6531-6535.
  33. Gachot-Neveu Helene, Lefevre Pavine, Roeder Jean-Jacques, Henry Caroline and Poulle Marie-Lazarine (2009)., Genetic detection of sex-biased and age-biased dispersal in a population of wild carnivore, the red fox, Vulpes vulpes., Zool. Sci., 26(2), 145-152.
  34. Padilla J.A., Martínez-Trancón M., Rabasco A., Parejo J.C., Sansinforiano M.E. and Guijo M.I. (2000)., Genetic variability in the Iberian imperial eagle (Aquila adalberti) demonstrated by RAPD analysis., J Heredity., 91(6), 495-499.
  35. Freitas P.D., Calgaro M.R. and Galetti J.R. (2007)., Genetic diversity within and between broodstocks of the white shrimp Litopenaeus vannamei (Boone, 1931) (Decapoda, Penaeidae) and its implication for the gene pool conservation., Brazilian J. Biol., 67, 939-943.
  36. Gouin N., Grandjean F., Bouchon D., Reynolds Julian D. and Souty-Grosset Catherine (2001)., Population genetic structure of the endangered freshwater crayfish Austropotamobius pallipes, assessed using RAPD markers., Heredity., 87, 80-87.
  37. Fahmi A. and Al-Otaibi S. (2011)., Genetic variation in captive herd of Arabian Oryx., Conservation Biol., 18(5), 1347-1357.
  38. Vos Pieter, Hogers Rene, Bleeker Marjo, Reijans Martin, de Lee Theo van, Hornes Miranda, Friters Adrie, Pot Jerina, Paleman Johan, Kuiper Martin and Zabeau Marc (1995)., AFLP: a new concept for DNA fingerprinting., Nucl. Acids. Res., 23(21), 4407-4414.
  39. Zenger K.R., Stow A.J., Peddemors V., Briscoe D.A. and Harcourt R.G. (2006)., Widespread utility of highly informative AFLP molecular markers across divergent shark species., J Heredity., 97(6), 607-611.
  40. Haig S., Mullins T., Forsman E., Trail Pepper W. and Wennerberg L.I.V. (2004)., Genetic identification of spotted owls, barred owls, and their hybrids: legal implications of hybrid identity., Conservation Biology., 18(5), 1347-1357.
  41. Giannasi N., Thorpe R.S. and Malhotra A. (2001)., The use of amplified fragment length polymorphism in determining species trees at fine taxonomic levels: analysis of a medically important snake, Trimeresurus albolabris., Mol. Ecology., 10, 419-426.
  42. Tautz D. and Rentz M. (1984)., Simple sequences are ubiquitous repetitive components of eukaryotic genomes., Nature., 322, 652-656.
  43. Tautz D. (1989)., Hypervariability of simple sequences as a general source for polymorphic DNA markers., Nucl. Acids Res., 17(16), 6463-6471.
  44. Kruglyak S., Durrett R., Schug M.D. and Aquadro C.F. (1998)., Equilibrium distribution of microsatellite repeats length resulting from a balance between slippage events and point mutations., Proc. Nat. Acad. Sci. USA., 95(18), 10774-10778.
  45. Eblate E.M., Lughano K.J., Sebastian C.D., Peter M.L. and Knut R.H. (2011)., Polymorphic microsatellite markers for genetic studies of African antelope species., African J. Biotech., 10(56), 11817-11820.
  46. Liukkonen T., Kvist L. and Mykrä S. (2012)., Microsatellite markers show distinctiveness of released and wild grey partridges in Finland., Anim. Biodiv. Conservation., 35(2), 419-428.
  47. Subrata S.A. and Storch I. (2012)., A core set of microsatellite markers identified for use in population genetic studies of Purple Swamphen (Porphyrio porphyrio)., Anim. Biodiv. Conservation., 35(1), 23-26.
  48. Syvanen A.C. (2001)., Assessing genetic variation: Genotyping single nucleotide polymorphisms., Nat. Genetics., 2, 930-942.
  49. Brookes A.J. (1999)., The Essence of SNPs., Gene., 234(2), 177-186.
  50. Ren J. (2001)., High throughput Single-strand conformation polymorphism analysis by capillary electrophoresis., J. Chromatography B: Biomed Sci. Appl., 741, 115-128.
  51. Gupta P.K., Roy J.K. and Prasad M. (2001)., Single nucleotide polymorphisms: A new paradigm for molecular marker technology and DNA polymorphism detection with emphasis on their use in plants., Curr.Sci., 80(4), 524-535.
  52. Alacs E.A., Georges A., Robertson J. and Fitzsimons N.N, (2010)., DNA detective: a review of molecular approaches to wildlife forensics., Forensic Sci. Med. Pathol., 6, 180- 194.
  53. Lips Karen R., Brem Forrest, Brenes Roberto, Reeve John D., Alford Ross A., Voyles Jamie, Carey Cynthia, Livo Lauren, Pessier Allan P. and Collins James P. (2006)., Emerging infectious disease and the loss of biodiversity in a Neotropical amphibian community., Proc. Nat. Acad. Sci. USA., 103(9), 3165-3170.
  54. Kaeslin E., Redmond I. and Dudley N. (2012)., Wildlife in a changing climate., Food and Agriculture Organization (F.A.O.), 167.
  55. Ogaden R., Dawnay N. and McEwing R. (2009)., Wildlife DNA forensics - bridging the gap between conservation genetics and law enforcement., Endangering Species Res., 9(3), 179-195.
  56. Peppin L., McEwing R. and Carvalho G.R. (2008)., A DNA-based approach for the forensic identification of Asiatic black bear (Ursus thibetanus) in a traditional Asian medicine., J. Forensic Sci., 53(6), 1358-1362.
  57. Harper C.K., Vermeulen G.J., Clarke A.B., Jacobus I. and Guthrie Alan J. (2013)., Extraction of nuclear DNA from rhinoceros horn and characterization of DNA profiling systems for white (Ceratotherium simum) and black (Diceros bicornis) rhinoceros., Forensic Sci. Int. Genet., 7(4), 428-433.
  58. Lynch M. and Jarrell P.E. (1993)., A method for calibrating molecular clocks and its application to animal mitochondrial DNA., Genetics, 135, 1197-1208.
  59. Xu Yan Chun, Li Bo, Li Wan Shui, Bai Su Ying, Jin Yu, Li Xiao Ping, Gu Ming Bo, Jing Song Yan and Zhang Wei (2005)., Individualization of tiger by using microsatellites., Forensic Sci. Int., 151, 45-51.
  60. Doukakis, P., Pikitch, E. K., Rothschild, A., DeSalle Rob, Amato George and Kolokotronis Sergios-Orestis (2012)., Testing the effectiveness of an international conservation agreement: Market place forensics and CITES caviar trade regulation., PLoS One, 7, e40907.
  61. Abe H., Hayano A. and Inoue-Murayama M. (2012)., Forensic species identification of large macaws using DNA barcodes and microsatellite profiles., Mol. Bio. Rep., 39, 693-699.
  62. Jun J., Han S.H., Jeong T.J., Park Hyun Chul, Lee Byoungyoon and wak Myounghai K. (2011)., Wildlife forensics using mitochondrial DNA sequences: Species identification based on hairs collected in the field and confiscated tanned felidae leathers., Genes & Genomics., 33, 721-726.
  63. Gupta S.K., Sharma C.P. and Singh L. (2014)., DNA typing established as an unambiguous tool for species identification in a dispute case., For. Sci. J., 13(1), 9-14.
  64. Lee E.J., Lee Y.H., Moon S.H., Kim N.Y., Yang M.S., Choi D. and Han M. (2013)., The identification of elephant ivory evidences of illegal trade with mitochondrial cytochrome b gene and hyper variable D-loop region., J. For. Legal Med., 20(3), 174-178.
  65. Dalton D.L. and Kotze A. (2011)., DNA barcoding as a tool for species identification in three forensic wildlife cases in South Africa., For. Sci. Int., 207, 51-54.
  66. Hsieh H.M., Huang L.H., Tsai L.C., Kuo Y., Meng H., Linacre A. and Lee J. (2003)., Species identification of rhinoceros horns using the cytochrome b gene., For. Sci. Int., 136, 1-11.
  67. Baker C.S., Steel D. and Choi Y. (2010)., Genetic evidence of illegal trade in protected whales links Japan with the US and South Korea., Biol. Lett., 6(5), 647-650.
  68. Eaton M.J., Meyers G.L., Kolokotronis S.O., Leslie M.S., Martin A.P. and Amato G. (2010)., Bar-coding bush meat: molecular identification of Central African and South American harvested vertebrates., Conser. Gen., 11, 1389-1404.
  69. Jobin R.M., Patterson D., Zhang Y. (2008)., DNA typing in populations of mule deer for forensic use in the Province of Alberta., For. Sci. Int. Genet., 2(3), 190-197.
  70. Caratti Stefano, Rossi Luca, Sona Bruno, Origlia Silvia, Viara Silvana, Martano Giuseppe, Torre Carlo and Robino Carlo (2010)., Analysis of 11 tetrameric STRs in wild boars for forensic purposes., For. Sci. Int. Genet., 4(5), 339-342.
  71. Sanders J.G., Cribbs J.E., Fienberg H.G., Hulburd G., Katz L. and Palumbi S.R. (2008)., The tip of the tail: Molecular identification of seahorses for sale in apothecary shops and curio stores in California., Conserv. Genet., 9, 65-71.
  72. Gaur A., Singh C.S., Sreenivas A. and Singh L. (2012)., DNA-based identification of a snake in a wine bottle using universal primers: A case of mistaken identity., For. Sci. Int., 214, 51-53.
  73. Wasser S.K., Mailand C., Booth R., Mutayoba B., Kisamo E., Clark B. and Stephens M. (2007)., Using DNA to track the origin of the largest ivory seizure since the 1989 trade ban., Proc. Natl. Acad. Sci., 104(10), 4228-4233.
  74. Lee J.C.I., Tsai L.C., Yang C.Y., Liu C.L., Huang L.H., Linacre A. and Hsieh H.M. (2006)., DNA profiling of Shahtoosh., Electrophoresis, 27(17), 3359-3362.
  75. Panday R., Jha D.K. and Thapa N., Pokharel B. and Aryal N. (2014)., Forensic wildlife parts and their product identification and individualization using DNA barcoding., The Open For. Sci. J., 7, 6-13.