Breed Determination for Indonesian Local Chickens Based on Matrilineal Evolution Analysis
DOI:
https://doi.org/10.3923/ijps.2015.615.621Keywords:
Breed determination, Indonesian chickens, mtDNA D-loopAbstract
Assessing the molecular characteristic of chickens is the powerful method to differentiate chicken breeds. This study analyses the matrilineal evolution of the Indonesian local chickens based on mitochondrial DNA D-loop region to reveal their genetic diversity and phylogenetic relationships. The estimated genetic diversity of Indonesian local chickens ranged from 0.00171 to 0.01800. Six (6) groups from 67 D-loop haplotypes of Indonesian chickens are observed in this study. The Indonesian local chickens can be differentiated from Saudi Arabian, ornamental and commercial line chickens. However, maintaining genetic variation of certain chicken population will be useful to conserve local genes for future utilization.
References
Berthouly-Salazar, C., X. Rognon, T.N. Van, M. Gely and C.V. Chi et al., 2010. Vietnamese chickens: A gate towards Asian genetic diversity. BMC Genet., Vol. 11.
Cuc, N.T.K., H. Simianer, L.F. Groeneveld and S. Weigend, 2011. Multiple maternal lineages of Vietnamese local chickens inferred by mitochondrial DNA D-loop sequences. Asian Aust. J. Anim. Sci., 24: 155-161.
Dana, N., H.J. Megens, R.P.M.A. Crooijmans, O. Hanotte, J. Mwacharo, M.A.M. Groenen and J.A.M. van Arendonk, 2011. East Asian contributions to Dutch traditional and western commercial chickens inferred from mtDNA analysis. Anim. Genet., 42: 125-133.
Desjardins, P. and R. Morais, 1990. Sequence and gene organization of the chicken mitochondrial genome: A novel gene order in higher vertebrates. J. Mol. Biol., 212: 599-634.
Muladno, 2008. Local chicken genetic resources and production systems in Indonesia. GCP/RAS/228/GER Working Paper No. 6, FAO., Rome.
Edgar, R.C., 2004. MUSCLE: Multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res., 32: 1792-1797.
Granevitze, Z., J. Hillel, G.H. Chen, N.T.K. Cuc, M. Feldman, M. Eding and S. Weigend, 2007. Genetic diversity within chicken populations from different continents and management histories. Anim. Genet., 38: 576-583.
Jakaria, M. Ulfah and D.A. Putri, 2012. Phenotypic characteristics of legund chickens in West Java, Indonesia. Proceedings of the 2nd International Seminar on Animal Industry, July 5-6, 2012, Jakarta, Indonesia, pp: 130-134.
Kanginakudru, S., M. Metta, R.D. Jakati and J. Nagaraju, 2008. Genetic evidence from Indian red jungle fowl corroborates multiple domestication of modern day chicken. BMC Evol. Biol., 8: 174-174.
Kawabe, K., R. Worawut, S. Taura, T. Shimogiri, T. Nishida and S. Okamoto, 2014. Genetic diversity of mtDNA D-loop polymorphisms in Laotian native fowl populations. Asian Aust. J. Anim. Sci., 27: 19-23.
Librado, P. and J. Rozas, 2009. DnaSP v5: A software for comprehensive analysis of DNA polymorphism data. Bioinformatics, 25: 1451-1452.
Liu, Y.P., G.S. Wu, Y.G. Yao, Y.W. Miao and G. Luikart et al., 2006. Multiple maternal origins of chickens: Out of the Asian jungles. Mol. Phylogenet. Evol., 38: 12-19.
Miao, Y.W., M.S. Peng, G.S. Wu, Y.N. Ouyang and Z.Y. Yang et al., 2013. Chicken domestication: An updated perspective based on mitochondrial genomes. Heredity, 110: 277-282.
Mwacharo, J.M., G. Bjornstad, V. Mobegi, K. Nomura and H. Hanada et al., 2011. Mitochondrial DNA reveals multiple introductions of domestic chicken in East Africa. Mol. Phylogenet. Evol., 58: 374-382.
Nishibori, M., M. Hanazono, Y. Yamamoto, M. Tsudzuki and H. Yasue, 2003. Complete nucleotide sequence of mitochondrial DNA in White Leghorn and White Plymouth Rock chickens. Anim. Sci. J., 74: 437-439.
Pramual, P., K. Meeyen, K. Wongpakam and U. Klinhom, 2013. Genetic diversity of Thai native chicken inferred from mitochondrial DNA sequences. Trop. Nat. History, 13: 97-106.
Riztyan, N. Suthama, S.M. Ardiningsasi, S. Shimogiri, K. Kawabe, Y. Kawamoto and S. Okamoto, 2011. Genetic diversity analysis of Indonesian native chickens using SNP markers on the Z chromosome. Anim. Genet. J., 39: 49-53.
Riztyan, T. Katano, T. Shimogiri, K. Kawabe and S. Okamoto, 2011. Genetic diversity and population structure of Indonesian native chickens based on single nucleotide polymorphism markers. Poult. Sci., 90: 2471-2478.
Ronquist, F. and J.P. Huelsenbeck, 2003. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics, 12: 1572-1574.
Sambrook, J. and D.W. Russel, 2000. Molecular Cloning: A Laboratory Manual. 3rd Edn., CSHL Press, New York, USA.
Sartika, T., S. Iskandar, L.H. Prasetyo, H. Takahashi and M. Mitsuru, 2004. Genetic relationships of kampung, pelung, sentul and black kedu chicken using microsatellite DNA Markers: I. Lingkage group of macro chromosome. Indonesian J. Anim. Vet. Sci., 9: 81-86.
Storey, A.A., J.S. Athens, D. Bryant, M. Carson and K. Emery et al., 2012. Investigating the global dispersal of chickens in prehistory using ancient mitochondrial DNA signatures. PloS ONE, Vol. 7.
Sulandari, S., M.S.A. Zein and T. Sartika, 2008. Molecular characterization of Indonesian indigenous chickens based on mitochondrial DNA displacement (D)-loop sequences. HAYATI J. Biosci., 15: 145-154.
Tamura, K., G. Stecher, D. Peterson, A. Filipski and S. Kumar, 2013. MEGA6: Molecular evolutionary genetics analysis version 6.0. Mol. Biol. Evol., 30: 2725-2729.
Ulfah, M., Jakaria and R.T. Tarigan, 2012. Qualitative traits of Walik chickens, The rare Indigenous chicken, in West Java, Indonesia. Proceedings of the 2nd International Seminar on Animal Industry, July 5-6, 2012, Jakarta, Indonesia, pp: 117-123.
West, B. and B.X. Zhou, 1988. Did chickens go north? New evidence for domestication. J. Archaeol. Sci., 15: 515-533.
Yacoub, H.A. and M.M. Fathi, 2013. Phylogenetic analysis using d-loop marker of mtDNA of Saudi native chicken strains. Mitochondr. DNA., 24: 538-551.
Yamamoto, Y., T. Namikawa, I. Okada, M. Nishibori, S.S. Mansjoer and H. Martojo, 1996. Genetical studies on native chickens in Indonesia. Asian Aust. J. Anim. Sci., 9: 405-410.
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