Maria Ulfah
Department of Animal Production and Technology, Faculty of Animal Science, Bogor Agricultural University, Bogor-16680, Indonesia
Dyah Perwitasari
Department of Biology, Faculty of Mathematics and Natural Science, Bogor Agricultural University, Bogor-16680, Indonesia
Jakaria .
Department of Animal Production and Technology, Faculty of Animal Science, Bogor Agricultural University, Bogor-16680, Indonesia
Muladno .
Department of Animal Production and Technology, Faculty of Animal Science, Bogor Agricultural University, Bogor-16680, Indonesia
Achmad Farajallah
Department of Biology, Faculty of Mathematics and Natural Science, Bogor Agricultural University, Bogor-16680, Indonesia
ABSTRACT
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.
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How to cite this article
Maria Ulfah, Dyah Perwitasari, Jakaria ., Muladno . and Achmad Farajallah, 2015. Breed Determination for Indonesian Local Chickens Based on Matrilineal Evolution Analysis. International Journal of Poultry Science, 14: 615-621.
DOI: 10.3923/ijps.2015.615.621
URL: https://scialert.net/abstract/?doi=ijps.2015.615.621
DOI: 10.3923/ijps.2015.615.621
URL: https://scialert.net/abstract/?doi=ijps.2015.615.621
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.
CrossRefDirect Link - 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.
Direct Link - 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.
CrossRefDirect Link - 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.
CrossRefPubMedDirect Link - Edgar, R.C., 2004. MUSCLE: Multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res., 32: 1792-1797.
CrossRefDirect Link - 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.
CrossRefDirect Link - 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.
Direct Link - 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.
CrossRefDirect Link - 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.
CrossRefDirect Link - Librado, P. and J. Rozas, 2009. DnaSP v5: A software for comprehensive analysis of DNA polymorphism data. Bioinformatics, 25: 1451-1452.
CrossRefPubMedDirect Link - 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.
CrossRefPubMedDirect Link - 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.
CrossRefDirect Link - 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.
CrossRefDirect Link - 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.
CrossRefDirect Link - 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.
Direct Link - 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.
CrossRefDirect Link - 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.
CrossRefPubMedDirect Link - Ronquist, F. and J.P. Huelsenbeck, 2003. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics, 12: 1572-1574.
CrossRefPubMedDirect Link - 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.
Direct Link - 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.
CrossRefDirect Link - 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.
CrossRefDirect Link - 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.
CrossRefPubMedDirect Link - West, B. and B.X. Zhou, 1988. Did chickens go north? New evidence for domestication. J. Archaeol. Sci., 15: 515-533.
CrossRefDirect Link - 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.
CrossRefDirect Link - 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.
CrossRefDirect Link