Analysis of Comparative Phylogenetic Story by Using Autosomal Markers and Mitochondrial Sequences
American Journal of Bioscience and Bioengineering
Volume 6, Issue 1, February 2018, Pages: 5-12
Received: Nov. 21, 2017;
Accepted: Dec. 4, 2017;
Published: Jan. 25, 2018
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Ngo Thi Kim Cuc, Department of Animal Breeding and Genetics, National Institute of Animal Science, Hanoi, Vietnam
Nguyen Thanh Son, Department of Science and International Cooperation, National Institute of Animal Science, Hanoi, Vietnam
The current study aims at the molecular assessment of genetic diversity within and between Vietnamese local chicken populations. On average, a total of 32 individuals per Vietnamese local chicken population was randomly sampled. Nine Vietnamese chickens breeds and 2 The exotic chicken breeds originating from China were used. The DNA polymorphism was assessed using a set of 29 microsatellite markers recommended by FAO. A fragment of 455 bp from the mtDNA D-loop region was amplified. The results showed that at the autosomal level, the Vietnamese local chicken breeds from different agro-ecological zones represent genetically distinct populations. The northern breeds are clearly separated from breed of the South Central Coast and from breed of the Mekong Delta. The Vietnamese local chicken breeds are highly polymorphic and originated from eight maternal lineages. These lineages are present across the country. Two chicken breeds of Chinese origin, Tam Hoang and Luong Phuong, kept in the National Institute of Animal Sciences are genetically distinct from the Vietnamese local breeds. The Vietnamese chicken breeds are genetically separated from the Chinese chicken gene pool.
Ngo Thi Kim Cuc,
Nguyen Thanh Son,
Analysis of Comparative Phylogenetic Story by Using Autosomal Markers and Mitochondrial Sequences, American Journal of Bioscience and Bioengineering.
Vol. 6, No. 1,
2018, pp. 5-12.
Abebe, A. S., Mikko S. and Johansson A. M. (2015). Genetic diversity of five local Swedish chicken breeds detected by microsatellite markers. PloS One. 10:e0120580–e0120580. doi:10.1371/journal.pone.0120580.
Bandelt H. J., Forster P., Sykes B. C. and Richards M. B (1995) Mitochondrial portraits of human populations using median networks. Genetics 141: 743-753.
Berthouly C., Leroy G., Van T. N., Thanh H. H., Bed'Hom B., Nguyen B. T., Vu C. C., Monicat F., Tixier-Boichard M., Verrier E., Maillard J. and Rognon X. (2009) Genetic analysis of local Vietnamese chickens provides evidence of gene flow from wild to domestic populations. BMC Genetics: 10: 1.
Clement M., Posada D. and Crandall K. A. (2000) tcs: a computer program to estimate gene genealogies. Molecular Ecology 9: 1657-1659.
Desjardins P. and Morais R. (1990) Sequence and gene organization of the chicken mitochondrial genome. A novel gene order in higher vertebrates. J Mol Biol 212: 599-634.
Eding H. and Meuwissen T. H. E. (2003) Linear methods to estimate kinships from genetic marker data for the construction of core sets in genetic conservation schemes. Journal of Animal Breeding and Genetics 120: 289–302.
Evanno G., Regnaut, S. and J. Goudet. (2005) Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study: Molecular Ecology 14: 2611-2620.
Excoffier L., Laval G. and Schneider S. (2006) arlequin Version 3.01: An Integrated Software Package for Population Genetics Data Analysis.
FAO (2007) Global Plan of Action for Animal Genetic Resources and the Interlaken Declaration. Rome. http://www.fao.org/ ag/againfo/ programmes/en/ genetics/documents/ Interlaken/GPA_en.pdf). Accessed on 22/08/2009.
Fathi, M. M., I. Al-Homidan, M. I. Motawei, O. K. Abou-Emera, and Zarei, M. F. El-, 2017. Evaluation of genetic diversity of Saudi native chicken populations using microsatellite markers. Poult. Sci. 96: 530–536.
Feulner, P. G. D., Bielfeldt, W., Zachos, F. E., Bradvarovic, J., Eckert, I. and Hartl, G. B. (2004) Mitochondrial DNA and microsatellite analyses of the genetic status of the presumed subspecies Cervus elaphus montanus (Carpathian red deer). Heredity 93: 299-306.
Guo HW, Li C, Wang XN, Li ZJ, Sun GR, Li GX, Liu XJ, Kang XT and Han RL. 2017. Genetic diversity of mtDNA D-loop sequences in four native Chinese chicken breeds. Br Poult Sci. 2017 58: 490-497.
Granevitze Z., Hillel J., Chen G. H., Cuc N. T. K., Feldman M., Eding H. and Weigend S. (2007) Genetic diversity within chicken populations from different continents and management histories. Animal Genetics 38: 576-583.
Huson, D. H., and Bryant, D. (2006) Application of Phylogenetic Networks in Evolutionary Studies. Molecular Biology and Evolution 23 (2): 254-267.
Johnson J. A., Toepfer J. F. and Dunn P. O. (2003) Contrasting patterns of mitochondrial and microsatellite population structure fragmented populations of greater prairie-chickens. Mol. Ecol. 12: 3335-3347.
Kumar S., Tamura K. and Nei M. (2004) mega3: integrated software for molecular evolutionary genetics analysis and sequence alignment. Briefings in Bioinformatics 5: 150-163.
MARD (Vietnam Ministry of Agriculture and Rural Development) (2004) Atlas of domestic animal breeds in Vietnam. Agricultural publishing house, Hanoi, Vietnam.
Mtileni, B. J., F. C. Muchadeyi, A. Maiwashe, E. Groeneveld, L. F. Groeneveld, K. Dzama, and Weigend S. (2011) Genetic diversity and conservation of South African indigenous chicken populations: South African chicken genetic resources. J. Anim. Breed. Genet. 128: 209–218. doi:10.1111/j.1439-0388.2010.00891.
Linh V. T. (2008) The world of rare chickens in Vietnam. Vietbao Newspaper (issued on February 11st), Vietnam.
Liu Y. P., Wu G. S., Yao Y. G., Miao Y. W., Luikart G., Baig M., Beja-Pereira A., Ding Z. L., Palanichamy M. G. and Zhang Y. P. (2006) Multiple maternal origins of chickens: out of the Asian jungles. Molecular Phylogenetics and Evolution 38: 112-119.
Liu Z. G., Lei C. Z., Luo J., Ding C., Chen G. H., Chang H., Wang K. H., Liu X. X., Zhang X. Y., Xiao X. J. and Wu S. L. (2004) Genetic variability of mtDNA sequences in Chinese native chicken breeds. Asian-Australasian Journal of Animal Sciences 17: 903-907.
Lyimo, C. M., A. Weigend, P. L. Msoffe, H. Eding, H. Simianer, and Weigend S. (2014) Global diversity and genetic contributions of chicken populations from African, Asian and European regions. Anim. Genet. 45: 836–848.
Muchadeyi F. C., Eding H., Simianer H., Wollny C. B. A., Groeneveld E. and Weigend S. (2008) Mitochondrial DNA D-loop sequences suggest a Southeast Asian and Indian origin of Zimbabwean village chickens. Animal Genetics 39: 615-622.
Nyiri P. and Saveliev I. (2002) Globalizing Chinese Migration: Trends in Europe and Asia Research in Migration and Ethnic Relations Series. Ashgate Publisher, Aldershot, United Kingdom.
Oka T., Ino Y., Nomura K., Kawashima S., Kuwayama T., Hanada H., Amano T., Takada M., Takahata N., Hayashi Y. and Akishinonomiya F. (2007) Analysis of mtDNA sequences shows Japanese native chickens have multiple origins. Animal Genetics 38: 287-293.
Pritchard J. K., Stephens M. and Donnerly P. (2000) Inference of population structure using multicocus genotype data. Genetics 155: 945-959.
Ramadan S. Kayang B. Inoue E. Nirasawa K. Hayakawa H. Ito S. Inoue-Murayama M. (2012). Evaluation of genetic diversity and conservation priorities for Egyptian chickens Open J. Anim. Sci. 2183 190.
Rosenberg N. A., Pritchard, J. K., Weber, J. L., Cann, H. M. Kidd, K. K. Zhivotovsky, L. A. and Feldman, M. W. (2002) Genetic structure of human populations: Science 298: 2381-2385.
Rosenberg. N. A. (2004) Distruct: a program for the graphical display of population structure. Molecular Ecology Notes 4: 137–138.
Tautz D. (1989) Hypervariability of simple sequences as a general source for polymorphic DNA markers. Nucleic Acids Research 17: 6463-6471.
Taylor K. W. (1983) The birth of Vietnam. Unverstity of California press, London, United Kingdom.
Tieu H. V., Ly L. V., Sat L. V. and Su V. V. (2008) Vietnamese livestock genetic resources conservation & exploitation from 1990 to 2007. Vietnamese Journal of Animal Science and Technology, special volume: 1-10.
Zhang L., Zhang, P., Li, Q., Gaur, U., Liu, Y., Zhu, Q., Zhao, X., Wang, Y., Yin, H., Hu, Y., Liu, A. and Li., D. (2017). Genetic evidence from mitochondrial DNA corroborates the origin of Tibetan chickens. https://doi.org/10.1371/journal.pone.0172945.
Weigend S. and Romanov M. N. (2001) Current strategies for the assessment and evaluation of genetic diversity in chicken resources. World’s Poultry Science Journal 57: 257-288.