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International Journal of Poultry Science

Year: 2013 | Volume: 12 | Issue: 1 | Page No.: 55-63
DOI: 10.3923/ijps.2013.55.63
Polymorphism of D-Loop Mitochondrial DNA Region and Phylogenetic in Five Indonesian Native Duck Population
Dattadewi Purwantini, Tri Yuwanta, Tety Hartatik and Ismoyowati

Abstract: This research aimed to determine mitochondrial DNA (mtDNA) D-loop region polymorphism and phylogenetic in five Indonesian native ducks population namely Magelang duck, Tegal duck, Mojosari duck, Bali duck and Alabio duck. The significance of this research was applicable to conservation and refinement strategy as well as the improvement of genetic quality by utilizing the available native duck plasma nutfah. It further concerned with determining the genealogy of family, channel, breed or maternal inheritance that bred individuals in native duck population in Indonesia and discovering phylogenetic relations with Mallards duck (Anas platyrhynchos) and the other Anas ducks. Fragment of 718-bp was amplified by PCR and determined the nucleotide sequence of 701-bp. The sequence was then analyzed using Single Nucleotide Polymorphism (SNP) and compared to the standard nucleotide sequence from Anas Platyrhynchos complete genome (HM010684.1) in GenBank Accession. It obtained nucleotide percentage equation of 93.59±8.23%. Phylogenetic investigation used sequencing products and was analyzed using MEGA5 software. Indonesian native ducks have a relatively close genetic relationship with Anas Platyrhynchos and Anas zonorhyncha shown by the genetic distance varying from 0.000-0.786 compared to the other Anas ducks in the world (0.073-1.037) or to Cairina moschata (2.972-5.776). Highly distant genetic variation was found in Magelang duck compared to the other native ducks ranged from 0.000-0.950 to 0.000-0.312. The research concluded that polymorphism of mtDNA D-loop region was found in Indonesian native ducks and had relatively similar maternal inheritance with Anas platyrhyncos dan Anas zonorhyncha.

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How to cite this article
Dattadewi Purwantini, Tri Yuwanta, Tety Hartatik and Ismoyowati , 2013. Polymorphism of D-Loop Mitochondrial DNA Region and Phylogenetic in Five Indonesian Native Duck Population. International Journal of Poultry Science, 12: 55-63.

Keywords: Polymorphism, D-loop DNA mitochondria, phylogenetic and native ducks in Indonesia

REFERENCES
  • Adebambo, A.O., V.A. Mobegi, J.M. Mwacharo, B.M. Oladejo and R.A. Adewale et al., 2010. Lack of phylogeographic structure in nigerian village chickens revealed by mitochondrial DNA D-loop sequence analysis. Int. J. Poult. Sci., 9: 503-507.
    CrossRef    Direct Link    

  • Donne-Gousse, C., V. Laudet and C. Hanni, 2002. A molecular phylogeny of anseriformes based on mitochondrial DNA analysis. Mol. Phylogenet. Evol., 23: 339-356.
    CrossRef    

  • Tu, J.F., Y.H. Huang, S.F. Liu and N. Li, 2009. Complete sequence determination and analysis of Beijing duck mitochondrial genome. Chinese J. Zool., 44: 28-33.
    Direct Link    

  • Xu, S.H., B.W. Bao, J.H. Cheng, J. Huang, H.X. Zhang and G.H. Chen, 2007. Polymorphism analysis on coding and regulation regions of growth hormone gene in duck. Chinese J. Anim. Vet. Sci., 38: 907-912.
    Direct Link    

  • Hetzel, D.J.S., 1985. Duck Breeding Strategies the Indonesia Example. In: Duck Production Science and World Practice, Farrell, D.J. and P. Stapleton (Eds.). University of New England, Armidale NSW., pp: 204-233

  • Ismoyowati and D. Purwantini, 2010. An estimation of genetic variation in indonesian local duck using microsatellite marker. Asian J. Poult. Sci., 4: 198-204.
    CrossRef    

  • Ito, K., H. Nishikawa, T. Shimada, K. Ogawa and Y. Minamiya et al., 2011. Analysis of genetic variation and phylogeny of the predatory bug, Pilophorus typicus, in Japan using mitochondrial gene sequences. J. Insect Sci., Vol. 11
    CrossRef    

  • Kimura, M., 1980. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J. Mol. Evol., 16: 111-120.
    CrossRef    Direct Link    

  • Leekaew, P., T. Songserm, A. Choothesa and U. Boonyaprakob, 2008. A simple method to extract mitochondrial DNA in a non-invasive phylogenetic study of domestic native Thai ducks. Kasetsart J. (Nat. Sci.), 42: 41-50.
    Direct Link    

  • Li, S.H., C.K.L. Yeung, L. Han, M.H. Le, C.X. Wang, P. Ding and C.T. Yao, 2010. Genetic introgression between an introduced babbler, the Chinese hwamei Leucodioptron c. canorum and the endemic Taiwan hwamei L. Taewanus: A multiple marker systems analysis. J. Avian Biol., 41: 64-73.
    CrossRef    Direct Link    

  • Li, H.F., W.Q. Zhu, W.T. Song, J.T. Shu, W. Han and K.W. Chen, 2010. Molecular genetic diversity and origin of Chinese domestic duck breeds. Archiv. Tierzucht., 53: 609-617.
    Direct Link    

  • Liang, Z., C. Wang, H. Yu, X. Peng, Y. Feng, Y. Gong and S. Li, 2010. Molecular cloning, characterization and expression analysis of duck tyrosinase-related protein-1. J. Anim. Vet. Adv., 9: 2102-2108.
    Direct Link    

  • Mundy, N.I., 2005. A window on the genetics of evolution: MC1R and plumage colouration in birds. Proc. Biol Sci., 22: 1633-1640.
    CrossRef    PubMed    Direct Link    

  • Zheng, N., H. Huang, H. Chen, Z. Zhu, Z. Miao, S. Li and X. Dong, 2009. SNP Detection and PCR-RFLP analysis of MC1R gene in mule duck. J. China Poult.,

  • Peters, J.L., K.G. McCracken, Y.N. Zhuravlev, Y. Lu, R.E. Wilson, K.P. Johnson and K.E. Omland, 2005. Phylogenetics of wigeons and allies (Anatidae: Anas): The importance of sampling multiple loci and multiple individuals. Mol. Phylogenet. Evol., 35: 209-224.
    CrossRef    PubMed    Direct Link    

  • Price, T. and A. Bontrager, 2001. Evolutionary genetics: The evolution of plumage patterns. Curr. Biol., 11: R405-R408.
    CrossRef    PubMed    Direct Link    

  • Purwantini, D., Ismoyowati, Prayitno and A.T.A. Sudewo, 2005. Menciptakan bibit unggul itik native berproduksi tinggi. Laporan Hibah Bersaing XII. Proyek Pengkajian dan Penelitian Ilmu Pengetahuan dan Teknologi, Direktorat Jenderal Pendidikan Tinggi Departemen Pendidikan Nasional.

  • Purwanto, H., 2012. Identifikasi DNA dan gen resisten terhadap virus AI (Avian Influenza) pada itik pitalah sebagai sumber daya genetik sumatera barat dengan PCR (Polymerase Chain Reaction). Program Pascasarjana Universitas Andalas Padang. http://pasca.unand.ac.id/id/wp-content/uploads/2011/09/IDENTIFIKASI-DNA-DAN-GEN-RESISTEN-TERHADAP-VIRUS-AI-Avian-Influenza-PADA-ITIK-PITALAH-SEBAGAI-SUMBER-DAYA-GENETIK-SUMATERA-BARAT-DENGAN-PCR-Polymerase-

  • Pyle, P., 2005. Molts and plumages of ducks (Anatinae). Waterbirds, 28: 208-219.
    CrossRef    

  • Rudolph, W., 2002. The indian runner duck: A historical guide. Feathered World, Quoted in Ashton. http://www.pjbs.org/ijps/fin2332.pdf

  • Stevens, L., 1991. Genetics and Evolution of the Domestic Fowl. Cambridge University Press, Cambridge, New York, ISBN: 9780521403177, Pages: 306

  • Tamura, K. and M. Nei, 1993. Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol. Biol. Evol., 10: 512-526.
    CrossRef    PubMed    Direct Link    

  • Tamura, K., D. Peterson, N. Peterson, G. Stecher, M. Nei and S. Kumar, 2011. MEGA5: Molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance and maximum parsimony methods. Mol. Biol. Evol., 28: 2731-2739.
    CrossRef    PubMed    Direct Link    

  • Thompson, J.D., D.G. Higgins and T.J. Gibson, 1994. CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res., 22: 4673-4680.
    CrossRef    PubMed    Direct Link    

  • Tsai, L.C., J.C.I. Lee, S.P. Liao, L.H. Wang, A. Linacre and H.M. Hsieh, 2009. Establishing the mitochondrial DNA D-loop structure of Columba livia. Electrophoresis, 30: 3058-3062.
    CrossRef    PubMed    

  • Wang, C., Z. Liang, W. Yu, Y. Feng, X. Peng, Y.Gong and S. Li, 2011. Polymorphism of the prolactin gene and its association with egg production traits in native Chinese ducks. South Afr. J. Anim. Sci., Vol. 41.,
    CrossRef    

  • Wang, C., S. Li, C. Li, Y. Feng, X. Peng and Y. Gong, 2012. Molecular cloning, expression profile, polymorphism and the genetic effects of the dopamine D1 receptor gene on duck reproductive traits. Mol. Biol. Rep., 39: 9239-9246.
    CrossRef    PubMed    Direct Link    

  • Wilson, B.J., D.M. Martin and H. Nott, 1997. Future genetic improvement in pekin type duck. Proceedings 11th European Symposium on Waterfowl, (ESW'97), Nantes, Fraance, pp: 328-334.

  • Wu, Z.Y., S.C. Zeng, Y.Z. Luo and J.L. Han, 2011. A mystery in sequencing the mitochondrial DNA D-loop from blood samples of domestic mallard duck. J. Biol. Sci., 11: 181-188.
    CrossRef    

  • Yudohusodo, S., 2003. Agribisnis berbasis peternakan menghadapi era perdagangan bebas. Makalah yang Disampaikan pada Acara Peringatan Hari Ulang Tahun ke 37. Fak. Peternakan, UNSOED.

  • Zhang, C.L., Y.H. Wang, M. Xie, M. Chen, X.H. Wang and S.S. Hou, 2010. Mitochondrial coding gene polymorphisms associated with carcass traits in Beijing duck. J. Anim. Vet. Adv., 9: 2522-2525.
    CrossRef    Direct Link    

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