OPTIMAL RECTION PCR FOR RESEARCH GENETIC DIVERSITY OF TRA CATFISH (Pangasianodon hypophthalmus)
Main Article Content
Abstract
In this experimental study, microsatellite markers for Tra catfish (Pangasianodon hypophthalmus) from previous studies were selected to optimize using the multiplex the process PCR to analyse the genetic diversity of Tra catfish populations in Vietnam. The markers used in the study is a set of seven single microsatellite markers (Ph07, Ph09, Ph41, CB12, CB15, CB18, and PSPG579) that have been optimized for successful PCR reactions in Tra catfish. The initial results of these markers were then applied to assess the genetic the diversity of Tra populations, showing that all microsatellite markers are polymorphic and meaningful when used to assess the genetic variation of Tra catfish populations. The method used in this study was single PCR and optimized for each microsatellite indicator with 4% agarose to analysis polymorphic’ populations. The results show that all indicators have been successfully optimized for PCR reactions on Tra catfish and the markers have a high polymorphism with an averaged amplification of 7.11, Na = 6.19, He = 0.78, and PIC = 0.77 on each marker in the three sample groups. The results will be served as a foundation for next steps on applying the multiplex PCR and support other studies on genetic diversity on Tra catfish.
Keywords
microsatellite, PCR reaction, genetic diversity
Article Details
References
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Botstein, D., White, R. L., Skolnick, M., & Davis, R. W. (1980). Construction of a genetic linkage map in man using restriction fragment length polymorphisms. American journal of human genetics, 32(3), 314-331.
Buchanan, F. C., Galloway, S. M., & Crawford, A. M. (1994). Ovine microsatellites at the OarFCB5, OarFCB19, OarFCB20, OarFCB48, OarFCB129 and OarFCB226 loci. Animal genetics, 25(1), 60.
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Brookes, C., Bright, J. A., Harbison, S., & Buckleton, J. (2012). Characterising stutter in forensic STR multiplexes. Forensic science international. Genetics, 6(1), 58-63. https://doi.org/10.1016/j.fsigen.2011.02.001
Cruz, P., Ibarra, A. M., Mejia-Ruiz, H., Gaffney, P. M., & Pérez-Enríquez, R. (2004). Genetic variability assessed by microsatellites in a breeding program of Pacific white shrimp (Litopenaeus vannamei). Marine biotechnology (New York, N.Y.), 6(2), 157-164. https://doi.org/10.1007/s10126-003-0017-5
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Harr, B., Zangerl, B., & Schlötterer, C. (2000). Removal of microsatellite interruptions by DNA replication slippage: phylogenetic evidence from Drosophila. Molecular biology and evolution, 17(7), 1001-1009. https://doi.org/10.1093/oxfordjournals.molbev.a026381
Hogan, Z. S., & May, B. P. (2002). Twenty‐seven new microsatellites for the migratory Asian catfish family Pangasiidae. Molecular Ecology, 2, 38-41. doi:10.1046/j.1471-8286.2002.00139.x
Hosseinzadeh-Colagar, A., Haghighatnia, M. J., Amiri, Z., Mohadjerani, M., & Tafrihi, M. (2016). Microsatellite (SSR) amplification by PCR usually led to polymorphic bands: Evidence which shows replication slippage occurs in extend or nascent DNA strands. Molecular biology research communications, 5(3), 167-174.
Kimura M., & Crow J. F., (1964). The number of alleles that can be maintained in a finite population. Genetic, 49(4), 725-738.
Miah, G., Rafii, M. Y., Ismail, M. R., Puteh, A. B., Rahim, H. A., Islam, K., & Latif, M. A. (2013). A review of microsatellite markers and their applications in rice breeding programs to improve blast disease resistance. International journal of molecular sciences, 14(11),
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Na-Nakorn, U., Sriphairoj, K., Sukmanomon, S., Poompuang, S., Kamonrat, W., (2006). Polymorphic microsatellite from DNA of the endangered Mekong giant catfish, Pangasianodon gigas (Chevey) and cross-species amplification in three species of Pangasius. Molecular Ecology, 6, 1174-1176.
Nei, M. (1972). Genetic Distance between Populations. The American Naturalist, 106(949), 283-292. Retrieved September 26, 2020, from http://www.jstor.org/stable/2459777
Nguyen, T. D. T., & Geldermann H., (2004). Da dang di truyen mot so giong lon noi Viet Nam va Chau Au dua tren chi thi microsatellite [Genetic diversity of Vietnamese and European pig breeds based on microsatellite markers]. VNU Journal of Science, Natural Science and Technology, 20(4), 1-10.
Nguyen, H. N., & Luu, T. H. G., (2012). Nghien cuu xac dinh da dang di truyen va huyet thong ca Tra (Pagasius hypophthalmus) bang chi thi microsatellite [Assessment of genetic diversity and parental assignment of striped catfish (Pagasius hypophthalmus) using microsatellite markers], Scientific report, Research Institute of Aquaculture No 1.
Nguyen, N. T., Nguyen, T. K. N., Hoang, T. T., Vo, P. K. B. N., Phan, H. H. T., Nguyen, T. L. A. & Pham, C. T., (2019). Da dang di truyen mot so quan the trau noi Viet Nam [Genetic diversity of Vietnamese native buffaloes]. Journal of Animal Science and Technology, 242.
Nguyen, T. P., & Nguyen, A. T., (2018). 50 nam nuoi ca Tra o dong bang song Cuu Long thanh cong va thach thuc trong phat trien ben vung [The success of 50-year striped catfish farming in the Mekong Delta and challeges on sustainable development]. Agricultural Pulishing House.
Pham, A. T., & Nguyen, H. N., (2003). Nghien cuu bien di RFLPs mot so quan the ca Tra (Pangasius hypophthalmus) [Diversity of Tra catfish populations studied by RFLPs]. National Conference on Biotechnology, Hanoi. 724-726.
So, N., & Vockaert, A. M., (2006), Genetic diversity and population history of the migratory catfishes Pangasianodon hypophthalmus and Pangasius bocourti in the Cambodian Mekong River. Fisheries science, 72, 469-476.
Tran, N. H., & Phung, T. T., (2013). Danh gia da dang di truyen loai du sam da voi Keteleeria davidiana (Bertrand) Beissn bang ki thuat RAPD [Assessment of genetic diversity of Keteleeria davidiana (Bertrand) Beissn using RAPD technique]. Journal of Forest Science and Technology, (1), 22-27.
Tran, T. T. H, Nguyen, T. H, Ngo, P. T., & Tran, N. A. H. (2017). Muc do da dang di truyen cua mot so quan the ca Tra su dung chi thi phan tu cytochrome b [Genetic diversity of Tra catfish populations in Vietnam using cytochrome b gene]. Journal of Science, Vinh University, 46(4A), 21-31
Volckaert, F. A. M., Hellemans, B., & Pouyaud, L., (1999). Nine polymorphic microsatellite markers in the SE Asian catfishes Pangasius hypophthalmus and Clarias batrachus. Animal Genetics, 30, 383-384.
Yeh, F.C., Yang, R. C., Boyle, T. B. J., Ye, Z. H., & Mao, J. X. (1997). POPGENE, the User Friendly Shareware for Population Genetic Analysis. Molecular Biology and Biotechnology Centre, University of Alberta, Alberta. http://www.ualberta.ca/~fyeh
Yue, G. H., & Xia, J. H., (2014). Practical Considerations of Molecular Parentage Analysis in Fish. Journal of The World Aquaculture Society, 45(2), 89-103.
Barker, J. S., Moore, S. S., Hetzel, D. J., Evans, D., Tan, S. G., & Byrne, K. (1997). Genetic diversity of Asian water buffalo (Bubalus bubalis): microsatellite variation and a comparison with protein-coding loci. Animal genetics, 28(2), 103-115. https://doi.org/10.1111/j.1365-2052.1997.00085.x
Botstein, D., White, R. L., Skolnick, M., & Davis, R. W. (1980). Construction of a genetic linkage map in man using restriction fragment length polymorphisms. American journal of human genetics, 32(3), 314-331.
Buchanan, F. C., Galloway, S. M., & Crawford, A. M. (1994). Ovine microsatellites at the OarFCB5, OarFCB19, OarFCB20, OarFCB48, OarFCB129 and OarFCB226 loci. Animal genetics, 25(1), 60.
Bui, T. L. H., Le, N. T. T., & Nguyen, V. S, (2017). Thu nghiem xac dinh pha he bang chi thi phan tu Microsatellite tren quan the chon giong ca Tra (Pangasianodon hypophthalmus) [Parentage assignment of selective population of striped catfish (Pangasianodon hypophthalmus) using microsatellite. Journal of Agriculture and Rural development, I, 8-97.
Brookes, C., Bright, J. A., Harbison, S., & Buckleton, J. (2012). Characterising stutter in forensic STR multiplexes. Forensic science international. Genetics, 6(1), 58-63. https://doi.org/10.1016/j.fsigen.2011.02.001
Cruz, P., Ibarra, A. M., Mejia-Ruiz, H., Gaffney, P. M., & Pérez-Enríquez, R. (2004). Genetic variability assessed by microsatellites in a breeding program of Pacific white shrimp (Litopenaeus vannamei). Marine biotechnology (New York, N.Y.), 6(2), 157-164. https://doi.org/10.1007/s10126-003-0017-5
McDaniel, J., & Pillai, S. D. (2002). Gel alignment and band scoring for DNA fingerprinting using Adobe Photoshop. BioTechniques, 32(1), 120-123. https://doi.org/10.2144/02321bc03
Harr, B., Zangerl, B., & Schlötterer, C. (2000). Removal of microsatellite interruptions by DNA replication slippage: phylogenetic evidence from Drosophila. Molecular biology and evolution, 17(7), 1001-1009. https://doi.org/10.1093/oxfordjournals.molbev.a026381
Hogan, Z. S., & May, B. P. (2002). Twenty‐seven new microsatellites for the migratory Asian catfish family Pangasiidae. Molecular Ecology, 2, 38-41. doi:10.1046/j.1471-8286.2002.00139.x
Hosseinzadeh-Colagar, A., Haghighatnia, M. J., Amiri, Z., Mohadjerani, M., & Tafrihi, M. (2016). Microsatellite (SSR) amplification by PCR usually led to polymorphic bands: Evidence which shows replication slippage occurs in extend or nascent DNA strands. Molecular biology research communications, 5(3), 167-174.
Kimura M., & Crow J. F., (1964). The number of alleles that can be maintained in a finite population. Genetic, 49(4), 725-738.
Miah, G., Rafii, M. Y., Ismail, M. R., Puteh, A. B., Rahim, H. A., Islam, K., & Latif, M. A. (2013). A review of microsatellite markers and their applications in rice breeding programs to improve blast disease resistance. International journal of molecular sciences, 14(11),
22499-22528. https://doi.org/10.3390/ijms141122499
Miller, S. A., Dykes, D. D., & Polesky, H. F. (1988). A simple salting out procedure for extracting DNA from human nucleated cells. Nucleic acids research, 16(3), 1215. https://doi.org/10.1093/nar/16.3.1215
Na-Nakorn, U., Sriphairoj, K., Sukmanomon, S., Poompuang, S., Kamonrat, W., (2006). Polymorphic microsatellite from DNA of the endangered Mekong giant catfish, Pangasianodon gigas (Chevey) and cross-species amplification in three species of Pangasius. Molecular Ecology, 6, 1174-1176.
Nei, M. (1972). Genetic Distance between Populations. The American Naturalist, 106(949), 283-292. Retrieved September 26, 2020, from http://www.jstor.org/stable/2459777
Nguyen, T. D. T., & Geldermann H., (2004). Da dang di truyen mot so giong lon noi Viet Nam va Chau Au dua tren chi thi microsatellite [Genetic diversity of Vietnamese and European pig breeds based on microsatellite markers]. VNU Journal of Science, Natural Science and Technology, 20(4), 1-10.
Nguyen, H. N., & Luu, T. H. G., (2012). Nghien cuu xac dinh da dang di truyen va huyet thong ca Tra (Pagasius hypophthalmus) bang chi thi microsatellite [Assessment of genetic diversity and parental assignment of striped catfish (Pagasius hypophthalmus) using microsatellite markers], Scientific report, Research Institute of Aquaculture No 1.
Nguyen, N. T., Nguyen, T. K. N., Hoang, T. T., Vo, P. K. B. N., Phan, H. H. T., Nguyen, T. L. A. & Pham, C. T., (2019). Da dang di truyen mot so quan the trau noi Viet Nam [Genetic diversity of Vietnamese native buffaloes]. Journal of Animal Science and Technology, 242.
Nguyen, T. P., & Nguyen, A. T., (2018). 50 nam nuoi ca Tra o dong bang song Cuu Long thanh cong va thach thuc trong phat trien ben vung [The success of 50-year striped catfish farming in the Mekong Delta and challeges on sustainable development]. Agricultural Pulishing House.
Pham, A. T., & Nguyen, H. N., (2003). Nghien cuu bien di RFLPs mot so quan the ca Tra (Pangasius hypophthalmus) [Diversity of Tra catfish populations studied by RFLPs]. National Conference on Biotechnology, Hanoi. 724-726.
So, N., & Vockaert, A. M., (2006), Genetic diversity and population history of the migratory catfishes Pangasianodon hypophthalmus and Pangasius bocourti in the Cambodian Mekong River. Fisheries science, 72, 469-476.
Tran, N. H., & Phung, T. T., (2013). Danh gia da dang di truyen loai du sam da voi Keteleeria davidiana (Bertrand) Beissn bang ki thuat RAPD [Assessment of genetic diversity of Keteleeria davidiana (Bertrand) Beissn using RAPD technique]. Journal of Forest Science and Technology, (1), 22-27.
Tran, T. T. H, Nguyen, T. H, Ngo, P. T., & Tran, N. A. H. (2017). Muc do da dang di truyen cua mot so quan the ca Tra su dung chi thi phan tu cytochrome b [Genetic diversity of Tra catfish populations in Vietnam using cytochrome b gene]. Journal of Science, Vinh University, 46(4A), 21-31
Volckaert, F. A. M., Hellemans, B., & Pouyaud, L., (1999). Nine polymorphic microsatellite markers in the SE Asian catfishes Pangasius hypophthalmus and Clarias batrachus. Animal Genetics, 30, 383-384.
Yeh, F.C., Yang, R. C., Boyle, T. B. J., Ye, Z. H., & Mao, J. X. (1997). POPGENE, the User Friendly Shareware for Population Genetic Analysis. Molecular Biology and Biotechnology Centre, University of Alberta, Alberta. http://www.ualberta.ca/~fyeh
Yue, G. H., & Xia, J. H., (2014). Practical Considerations of Molecular Parentage Analysis in Fish. Journal of The World Aquaculture Society, 45(2), 89-103.