Keragaman genetik puyuh Jepang (Coturnix japonica) berdasarkan analisis sekuen DNA mitokondria gen Cytochrome-b

Novisa Adimaka, Muhammad Rifki, Ratih Dewanti, Muhammad Cahyadi

Abstract


Coturnix japonica is a Japanese quail which is commonly raised in Indonesia. The aim of the study was to determine the genetic diversity of Japanese quail (Coturnix japonica) based on complete sequence of mitochondrial DNA Cytochrome b gene analysis. This study used 12 samples of quail blood collected from two different village breeding centres (VBC) representing black and brown plumage lines. Total DNA genome was isolated from whole blood by following the Wizard® Genomic DNA Purification Kit protocol (Promega, USA). The DNA amplification process in this study was carried out using novel forward and reverse primers using Primer3 software. Additionally, PCR products were sequenced and analysed using MEGA 6.0 and DNAsp v.5 softwares. A total of 21 sequences consists of 12 sequences of quail sample and 9 reference sequences obtained from NCBI website were analyzed to construct phylogenetic tree and to evaluate genetic diversity of Japanese quails. The sequence analysis showed that Japanese quail population in this study had kinship with Francolinus pintadeanus and Coturnix chinensis with an 81% bootstrap value. The genetic distance among Japanese quails was ranged from 0.000 to 0.003. In addition, the mean of genetic distance for Japanese quail was 0.002 and the mean of genetic distance for 21 samples was 0.067. Tajima D'test values were -1.35536 for Japanese quail population and -1.38090 for whole population used in this study. The conclusion of this study was the Japanese quail had low genetic diversity based on complete sequence of Mitochondrial DNA Cytochrome b gene analysis that mean Japanese quail had low level of evolution

Keywords


Cytochrome b; genetic diversity; Japanese quail

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References


Avise, J. C. 1994. Molecular Markers, Natu-ral History, and Evolution. New York: Chapman and Hall.

Avise. 2000. Phylogeography: The History and Formation of Species. Cam-bridge: Harvard University Press.

Batubara, A., Noor R. R., Farajallah, A., Tiesnamurti, B., dan Doloksaribu, M. 2011. Karakterisasi molekuler enam subpopulasi kambing lokal Indonesia berdasarkan analisis sekuen daerah D-loop DNA mitokondria. Jurnal Ilmu Ternak dan Veteriner, 16(1), 49-60. doi: http://doi.org/10.14334/jitv.v16i1.634

Bermingham, N. and Luettich, K. 2003. Pol-ymerase chain reaction and its appli-cations. Current Diagnostic Histo-pathology, 9(3), 159-164. doi: https://doi.org/10.1016/S0968-6053(02)00102-3

Brisson, J. A., Nuzhdinand, S. S.V., and Stern, D. L. 2009. Similar patterns of linkage disequilibrium and nucleotide diversity in native and introduced populations of the pea aphid, Acyrthosiphon pisum. BMC Genetics 10(22), 1-10. doi: https://doi.org/10.1186/1471-2156-10-22

Dharmayanti, N. L. P. I. 2011. Filogenetika molekuler: Metode taksonomi organisme berdasarkan sejarah evolusi. Wartazoa, 1(21), 1-10.

Frankham, R., Ballou, J. D. and Briscoe, D. A. 2004. A Primer of Conservation Genetics. Cambridge: Cambridge University Press.

Giuliano, B. and Selph, J. 2005. Quail fact. Proceedings of the 1st quail manage-ment short course. In. Giuliano, B., E. Willcox and A. Willcox. Depart-ment of Wildlife Ecology and Con-servation Institute of Food and Agri-cultural Sciences. Florida Coopera-tive Extension Service, (pp. 9-15). University of Florida, Florida.

Handiwirawan, E. 2006. Keragaman molekuler dalam suatu populasi. Prosiding Lokakarya Nasional Pengelolaan dan Perlindungan Sumber Daya Genetik di Indonesia: Manfaat Ekonomi untuk Mewujudkan Ketahanan Nasional, 20 Desember 2006: 138-144. Bogor, Indonesia.

Hines, T. 2005. Past and present bobwhite management in south central Florida. Proceedings of the 1st quail manage-ment shortcourse. In. Giuliano, B., E. Willcox and A. Willcox. Department of Wildlife Ecology and Conserva-tion Institute of Food and Agricultural Sciences. Florida Cooperative Extension Service, (pp. 2-8). University of Florida, Florida.

Liu, G. and Zhang, Y. 2016. Next-generation resequencing the complete mitochondrial genome of Japanese quail (Coturnix japonica). Mi-tochondrial DNA Part B: Resources, 1(1), 937-938. doi: https://doi.org/10.1080/23802359.2016.1258343

Mulyani, Y., Purwanto, A. dan Nurruhwati, I. 2011. Perbandingan beberapa metode isolasi DNA untuk deteksi dini koi herpes virus (khv) pada ikan mas (Cyprinus carpio l.). Jurnal Akuatika, 2(1), 1-16.

Nei, M., and Kumar, S. 2000. Molecular Evolution and Phylogenetics. Eng-land, Oxford: Incorporated of the United States of Oxford.

Nielsen, R. and Yang, Z. 1998. Likelihood models for detecting positively se-lected amino acid sites and applica-tions to the Hiv-1 envelope gene. Genetics, 148 (3), 929-936.

Nishibori, M., Shimogiri, T., Hayashi, T., and Yasue, H. 2005. Molecular evidence for hybridization of species in the genus Gallus except for Gallus varius. Journal of Animal Genetics, 36(5), 367-375. doi: https://doi.org/10.1111/j.1365-2052.2005.01318.x

Noor, S., Pramono, H., dan Aziz, S. 2014. Deteksi keragaman spesies bakteri metanogen rumen sapi menggunakan kloning gen 16S rRNA dan sekuensing. Scripta Biologica, 1(4), 1-8. doi: https://doi.org/10.20884/1.sb.2014.1.4.43

Odahara, S., Chung, H. J., Choi, S. H., Yu S. L., Sasazaki, S., Mannen, H., Park, C. S., and Lee, J. H. 2006. Mithocondrial DNA diversity of Ko-rean native goats. Asian-Australasian Journal of Animal Sciences, 19(4), 482-485. doi: https://doi.org/10.5713/ajas.2006.482

Pereira, J. C., Chaves, R., Bastos, E., Leitão, A., and Guedes-Pinto, H. 2011. An efficient method for genomic DNA extraction from different molluscs species. International Journal of Mo-lecular Science, 12 (11), 8086-8095. doi: https://doi.org/10.3390/ijms12118086

Rifki, M., Ratih, D., Nuzul, W., and Cahyadi, M. 2018. Phylogenetic study of black and brown Japanese quail in Indonesia based on mithocondrial d-loop sequence. Journal of Animal Breeding and Ge-nomics, 2(4), 237-244. doi: https://doi.org/10.12972/jabng.20180023

Sawitri, R., dan Takandjandji, M. 2013. Keragaman genetik dan situs polimorfik trenggiling (Manis javanica desmarest, 1822) di penangkaran. Jurnal Penelitian Hutan dan Konservasi Alam, 11(1), 1-11.

doi:https://doi.org/10.20886/jphka.2014.11.1.1-11

Shen, X. J., Suzuki, H., Tsudzuki, M., Ito, S., and Nakamura, T. 1999. Compar-ison of Cytochrome b region among Chinese painted quail, wild-strain quail, and white broiler chicken based on PCR-RFLP analysis. Japan Poultry Science Journal, 36(5), 287-293. doi: https://doi.org/10.2141/jpsa.36.287

Wares, J. P. 2014. Mitochondrial cytochrome b sequence data are not an improvement for species identifica-tion in scleractinian corals. PeerJ, 2(2), 1-8.

doi:https://doi.org/10.7717/peerj.564/fig-1

Wetton, J. H., Braidley, G. L., Tsang, C. S. F., Roney, C. A., Powell, S. L., and Spriggs, A. C. 2002. Generation of a species-specific DNA sequence li-brary of British mammals. A study by the forensic science service for the joint nature conservation committee and the environment and heritage service, (pp. 1-37). Northern, Ireland.

Widayanti, R., Solihin, D. D., Sajuthi, D., dan Perwita, D. 2006. Kajian penanda genetik gen Cytochrome b pada tarsius sp. Jurnal Sain Veteriner, 24(1), 1-8. doi: https://doi.org/10.22146/jsv.349

Widyastuti, W., Mardiati, S. M., dan Saraswati, T. R. 2014. Pertumbuhan puyuh (Coturnix japonica) setelah pemberian tepung kunyit (Curcuma longa l.) pada pakan. Buletin Anatomi dan Fisiologi, 22(2), 12-20.

doi: https://doi.org/10.14710/baf.v22i2.7813




DOI: http://dx.doi.org/10.21776/ub.jiip.2019.029.02.05

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