Variability of Genetically Improved Farmed Tilapia (Gift Tilapia) Crossed With Upm Red Tilapia Hybrids By Mitochondrial DNA Conserved Region Sequence
Yıl 2025,
Cilt: 28 Sayı: 2, 571 - 579, 27.03.2025
Oster F. Nwachı
Awawu Dasuki
Öz
Mitochondrial DNA conserved region (mtDNA CR) segment of a cross between GIFT tilapia and UPM red tilapia, their F1-hybrid (F1) and Backcross (BcF1) was used to define their genetic variability. DNA was extracted from 25 randomly selected specimens of each of the test strains and mtDNA CR primer ORMT-F ORMT-R was used. The MEGA software using Maximum Parsimony (MP) was conducted for the evolutionary analysis of the strains using Tilapia rendalli (AF484717.1 accession numbers from NCBI database). A total of 441 polymorphic regions of 99 sequencing sites were observed, the sites with 12 alignment gaps were missing while the invariable monomorphic sites were 360 (81.6%) with 69 (15.6%) variable polymorphic sites. Parsimony informative sites were 68 with 1 singleton variable site. The conserved regions were effective in discriminating between the sampled fish because they contained important elements that aid replication and expression of the mitochondria genome. The clustering of the strain in the sub-tree of the phylogeny verifies a monophyletic relationship although some of the strains showed more relatedness by their consistent overlap and clustering. Similarly with 0.1 genetic variability conserve region could be used for discrimination between the strains.
Kaynakça
- Ansah, Y. B., Frimpong, E. A., & Hallerman, E. M. (2014). Genetically-improved tilapia strains in Africa: Potential benefits and negative impacts. Sustainability (Switzerland), 6(6), 3697-3721. https://doi.org/10.3390/su6063697
- Bentsen, H. B., Gjerde, B., Eknath, A. E., de Vera, M. S. P., Velasco, R. R., Danting, J. C., Dionisio, E. E., Longalong, F. M., Reyes, R. A., Abella, T. A., Tayame, M. M., Ponzoni, R. W., et al. (2017). Genetic improvement of farmed tilapias: Response to five generations of selection for increased body weight at harvest in Oreochromis niloticus and the further impact of the project. Aquaculture, 468, 206-217. https://doi.org/10.1016/ j.aquaculture.2016.10.018
- Brown, T. A., Cecconi, C., Tkachuk, A. N., Bustamante, C., & Clayton, D. A. (2005). Replication of mitochondrial DNA occurs by strand displacement with alternative light-strand origins, not via a strand-coupled mechanism. Genes & Development, 19, 2466-2476. https://doi.org/10.1101/gad.1352105
- Chakrabarty, P. (2006). Systematics and historical biogeography of Greater Antillean Cichlidae. Molecular Phylogenetics and Evolution, 39, 619-627. https://doi.org/10.1016/j.ympev.2006.01.014
- Clayton, D. A. (1982). Replication of animal mitochondrial DNA. Cell, 28, 693-705. https://doi.org/10.1016/0092-8674(82)90049-6
- Dasuki, A., Esa, Y., Christianus, A., & Ismail, M. F. S. (2023). Genetic variations of Malaysian and Golden Thai strains of climbing perch and their hybrids based on the partial mitochondrial cytochrome oxidase subunit 1 gene. Malaysian Applied Biology, 52(2), 139-146.
- Esa, Y., Shapor, S. S., Daud, S. K., Jeffrine, J., Ryan, R., Adha, K. A., Rahim1, & Soon Guan, T. (2008). Molecular systematics of Mahseers (Cyprinidae) in Malaysia inferred from sequencing of a mitochondrial cytochrome C oxidase I (COI) gene. Pertanika Journal of Tropical Agric. Sci, 31, 263-269.
- FAO (Food and Agriculture Organization of the United Nations). (2009). FishStat Plus Version 2.32. Universal software for fishery statistics time series. Available from http://www.fao.org/fishery/statistics/ software/fishstat/en
- Ferguson, A. J. B., Taggartt, P. A., Prodohl, O., Mcmeel, C., Thompson, C., Stone, P., Mcginnityr, A. H., et al. (1995). Population and conservation. Journal of Fish Biology, 47, 103-126. https://doi.org/10.1111/j.1095-8649.1995.tb06048.x
- Gu, D. E., Mu, X. D., Xu, M., Luo, D., Wei, H., Li, Y. Y., Zhu, Y. J., Luo, J. R., Hu, Y. C., et al. (2016). Identification of wild tilapia species in the main rivers of south China using mitochondrial control region sequence and morphology. Biochemical Systematics and Ecology, 65, 100-107. https://doi.org/10.1016/j.bse.2016.02.007
- Hall, A. T. (2011). BioEdit: An important software for molecular biology. GERF Bulletin of Biosciences, 2, 60-61.
- He, A., Luo, Y., Yang, H., Liu, L., Li, S., Wang, C., et al. (2011). Complete mitochondrial DNA sequences of the Nile tilapia (Oreochromis niloticus) and Blue tilapia (Oreochromis aureus): Genome characterization and phylogeny applications. Molecular Biology Reports, 38(3), 2015-2021. https://doi.org/10.1007/s11033-010-0324-7
- Hidayat, T., Tomohisa, Y., & Motomi, I. (2005). Molecular phylogenetics of subtribe Aeridinae (Orchidaceae): Insights from plastid marker and nuclear ribosomal ITS sequences. Journal of Plant Research, 271-284. https://doi.org/10.1007/s10265-005-0217-3
- Hsieh, C. H., Chang, W. T., Chang, H. C., Hsieh, H. S., Chung, Y. L., & Hwang, D. F. (2010). Puffer fish-based commercial fraud identification in a segment of cytochrome b region by PCR-RFLP analysis. Food Chemistry, 121(4), 1305-1311. https://doi.org/10.1016/j.foodchem.2010.02.004
- Huang, J. L., Chang, H. T., Cheng, R., Hsu, H. H., Pai, T. W., et al. (2004). Identification of simple sequence repeat biomarkers through cross-species comparison in a tag cloud representation. BioMed Research International. 2014(1), 678971.https://doi.org/10.1155/2014/678971
- Jiang, M., Yang, C., & Wen, H. (2004). The complete mitochondrial genome of Aspiorhynchus laticeps and its phylogenetic analysis. Meta Gene, 2(1), 218-225. https://doi.org/10.1016/j.mgene.2014.01.006
- Karamanlidis, A. A., Gaughran, S., Aguilar, A., Dendrinos, P., Huber, D., Pires, R., Schultz, J., & Amato, G. (2016). Shaping species conservation strategies using mtDNA analysis: The case of the elusive Mediterranean monk seal (Monachus monachus). Journal of Molecular Evolution, 193, 71-79. https://doi.org/10.1016/ j.biocon.2015.11.014
- Kimura, M. (1980). A simple method for estimating evolutionary rate of base substitutions through comparative studies of nucleotide sequences. Journal of Molecular Evolution, 16, 111-120. https://doi.org/10.1007/ BF01731581
- Kinaro, Z. O., Xue, L., Nyaundi, K. J., Shen, J., et al. (2015). The mitochondrial genome of an endangered native Singidia tilapia, Oreochromis esculentus: Genome organization and control region polymorphism. Mitochondrial DNA, 1736 (March 2016). https://doi.org/10.3109/19401736.2015.1089493
- Klett, V., & Meyer, A. (2002). What if anything, is a tilapia: Mitochondrial ND2 phylogeny of tilapiines and the evolution of parental care systems in the African cichlid fishes. Molecular Biology and Evolution, 865-883. https://doi.org/10.1093/oxfordjournals.molbev.a004144
- Librado, P., & Rozas, J. (2009). DnaSP v5: A software for comprehensive analysis of DNA polymorphism data. Bioinformatics, 25, 1451-1452. https://doi.org/10.1093/bioinformatics/btp187
- Lim, K. C., Lim, P. E., Chong, V. C., & Lee, K. H. (2015). Molecular and morphological analyses reveal phylogenetic relationships of stingrays focusing on the family Dasyatidae (Myliobatiformes). PLoS ONE, 10(5), e0129411. https://doi.org/10.1371/journal.pone.0129411
- McManus, G. B., & Katz, L. A. (2009). Molecular and morphological methods for identifying plankton: What makes a successful marriage? Journal of Plankton Research, 31(10), 1119-1129. https://doi.org/10.1093/plankt/fbp061
- Nagl, S., Tichy, H., Mayer, W. E., Samonte, I. E., McAndrew, B. J., & Klein, J. (2001). Classification and phylogenetic relationships of African tilapiine fishes inferred from mitochondrial DNA sequences. Molecular Phylogenetics and Evolution, 20 (3), 361-374. https://doi.org/10.1006/mpev.2001.0979
- Nwachi, O. F., Esa, Y., Christianus, A., & Kamarudin, S. M. (2020). Sexual restiveness and colouration between partial diallel cross of genetically improved farmed tilapia 'GIFT' and UPM red tilapia. Jordan Journal of Biological Sciences, 13(2), 219-222
- Nwachi, O. F., & Esa, Y. (2016). A review of production protocols used in producing economically viable monosex tilapia. Journal of Fisheries and Aquatic Science, 11 (January), 1-11. https://doi.org/10.3923/jfas.2016.1.11
- Nyingi, D., De Vos, L., Aman, R., & Agnèse, J. F. (2009). Genetic characterization of an unknown and endangered native population of the Nile tilapia Oreochromis niloticus (Linnaeus, 1758) (Cichlidae; Teleostei) in the Loboi Swamp (Kenya). Aquaculture, 297(1-4), 57-63.
https://doi.org/10.1016/j.aquaculture.2009.09.017
- Ogden, R. (2008). Fisheries forensics: The use of DNA tools for improving compliance, traceability and enforcement in the fishing industry. Fish and Fisheries, 462-472. https://doi.org/10.1111/j.1467-2979.2008.00305.x
- Oladimeji, T. E., Awodiran, M. O., & Komolafe, O. O. (2015). Genetic differentiation studies among natural populations of Tilapia zillii. Notulae Scientia Biologicae, 7(4), 423-429. https://doi.org/10.15835/nsb749649
- Rastogi, G., Dharne, M. S., Walujkar, S., Kumar, A., Patole, M. S., Shouche, Y. S., et al. (2007). Species identification and authentication of tissues of animal origin using mitochondrial and nuclear markers. Meat Science, 76, 666-674. https://doi.org/10.1016/j.meatsci.2007.02.006
- Saitou, N., & Nei, M. (1987). The neighbor-joining method: A new method for reconstructing phylogenetic trees. Molecular Biology and Evolution, 4, 406-425.
- Tamura, K., Stecher, G., Peterson, D., & Filipski, A. (2013). MEGA6: Molecular evolutionary genetics analysis version 6.0. Molecular Biology and Evolution, 30, 2725-2729. https://doi.org/10.1093/molbev/mst197
- Ward, R. D., Zemlak, T. S., Innes, B. H., Last, P. R., & Hebert, P. D. N. (2005). DNA barcoding Australia's fish species. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences, 360, 1847-1857. https://doi.org/10.1098/rstb.2005.1716
- Wu, L., & Yang, J. (2012). Identifications of captive and wild tilapia species existing in Hawaii by mitochondrial DNA control region sequence. PLoS ONE, 7(12), 1-9. https://doi.org/10.1371/journal.pone.0051731
- Xiaowei, L., Dayu, L., Zhiying, Z., Jing-Ling, Z., & Jue, Y. H. (2016). Genetic variation of mitochondrial DNA D-loop sequences from different strains of Nile tilapia (Oreochromis niloticus). Southwest China Journal of Agricultural Science, 8, 2-7.
- Zou, Z., Li, D., Zhu, J., Han, J., Xiao, W., & Yang, H. (2015). Genetic variation among four bred populations of two tilapia strains, based on mitochondrial D-loop sequences. Mitochondrial DNA, 26(3), 426-430. https://doi.org/10.3109/19401736.2013.855735
Variability of Genetically Improved Farmed Tilapia (Gift Tilapia) Crossed With Upm Red Tilapia Hybrids By Mitochondrial DNA Conserved Region Sequence
Yıl 2025,
Cilt: 28 Sayı: 2, 571 - 579, 27.03.2025
Oster F. Nwachı
Awawu Dasuki
Öz
Mitochondrial DNA conserved region (mtDNA CR) segment of a cross between GIFT tilapia and UPM red tilapia, their F1-hybrid (F1) and Backcross (BcF1) was used to define their genetic variability. DNA was extracted from 25 randomly selected specimens of each of the test strains and mtDNA CR primer ORMT-F ORMT-R was used. The MEGA software using Maximum Parsimony (MP) was conducted for the evolutionary analysis of the strains using Tilapia rendalli (AF484717.1 accession numbers from NCBI database). A total of 441 polymorphic regions of 99 sequencing sites were observed, the sites with 12 alignment gaps were missing while the invariable monomorphic sites were 360 (81.6%) with 69 (15.6%) variable polymorphic sites. Parsimony informative sites were 68 with 1 singleton variable site. The conserved regions were effective in discriminating between the sampled fish because they contained important elements that aid replication and expression of the mitochondria genome. The clustering of the strain in the sub-tree of the phylogeny verifies a monophyletic relationship although some of the strains showed more relatedness by their consistent overlap and clustering. Similarly with 0.1 genetic variability conserve region could be used for discrimination between the strains.
Etik Beyan
No potential conflict of interest relevant to this article was reported.
Kaynakça
- Ansah, Y. B., Frimpong, E. A., & Hallerman, E. M. (2014). Genetically-improved tilapia strains in Africa: Potential benefits and negative impacts. Sustainability (Switzerland), 6(6), 3697-3721. https://doi.org/10.3390/su6063697
- Bentsen, H. B., Gjerde, B., Eknath, A. E., de Vera, M. S. P., Velasco, R. R., Danting, J. C., Dionisio, E. E., Longalong, F. M., Reyes, R. A., Abella, T. A., Tayame, M. M., Ponzoni, R. W., et al. (2017). Genetic improvement of farmed tilapias: Response to five generations of selection for increased body weight at harvest in Oreochromis niloticus and the further impact of the project. Aquaculture, 468, 206-217. https://doi.org/10.1016/ j.aquaculture.2016.10.018
- Brown, T. A., Cecconi, C., Tkachuk, A. N., Bustamante, C., & Clayton, D. A. (2005). Replication of mitochondrial DNA occurs by strand displacement with alternative light-strand origins, not via a strand-coupled mechanism. Genes & Development, 19, 2466-2476. https://doi.org/10.1101/gad.1352105
- Chakrabarty, P. (2006). Systematics and historical biogeography of Greater Antillean Cichlidae. Molecular Phylogenetics and Evolution, 39, 619-627. https://doi.org/10.1016/j.ympev.2006.01.014
- Clayton, D. A. (1982). Replication of animal mitochondrial DNA. Cell, 28, 693-705. https://doi.org/10.1016/0092-8674(82)90049-6
- Dasuki, A., Esa, Y., Christianus, A., & Ismail, M. F. S. (2023). Genetic variations of Malaysian and Golden Thai strains of climbing perch and their hybrids based on the partial mitochondrial cytochrome oxidase subunit 1 gene. Malaysian Applied Biology, 52(2), 139-146.
- Esa, Y., Shapor, S. S., Daud, S. K., Jeffrine, J., Ryan, R., Adha, K. A., Rahim1, & Soon Guan, T. (2008). Molecular systematics of Mahseers (Cyprinidae) in Malaysia inferred from sequencing of a mitochondrial cytochrome C oxidase I (COI) gene. Pertanika Journal of Tropical Agric. Sci, 31, 263-269.
- FAO (Food and Agriculture Organization of the United Nations). (2009). FishStat Plus Version 2.32. Universal software for fishery statistics time series. Available from http://www.fao.org/fishery/statistics/ software/fishstat/en
- Ferguson, A. J. B., Taggartt, P. A., Prodohl, O., Mcmeel, C., Thompson, C., Stone, P., Mcginnityr, A. H., et al. (1995). Population and conservation. Journal of Fish Biology, 47, 103-126. https://doi.org/10.1111/j.1095-8649.1995.tb06048.x
- Gu, D. E., Mu, X. D., Xu, M., Luo, D., Wei, H., Li, Y. Y., Zhu, Y. J., Luo, J. R., Hu, Y. C., et al. (2016). Identification of wild tilapia species in the main rivers of south China using mitochondrial control region sequence and morphology. Biochemical Systematics and Ecology, 65, 100-107. https://doi.org/10.1016/j.bse.2016.02.007
- Hall, A. T. (2011). BioEdit: An important software for molecular biology. GERF Bulletin of Biosciences, 2, 60-61.
- He, A., Luo, Y., Yang, H., Liu, L., Li, S., Wang, C., et al. (2011). Complete mitochondrial DNA sequences of the Nile tilapia (Oreochromis niloticus) and Blue tilapia (Oreochromis aureus): Genome characterization and phylogeny applications. Molecular Biology Reports, 38(3), 2015-2021. https://doi.org/10.1007/s11033-010-0324-7
- Hidayat, T., Tomohisa, Y., & Motomi, I. (2005). Molecular phylogenetics of subtribe Aeridinae (Orchidaceae): Insights from plastid marker and nuclear ribosomal ITS sequences. Journal of Plant Research, 271-284. https://doi.org/10.1007/s10265-005-0217-3
- Hsieh, C. H., Chang, W. T., Chang, H. C., Hsieh, H. S., Chung, Y. L., & Hwang, D. F. (2010). Puffer fish-based commercial fraud identification in a segment of cytochrome b region by PCR-RFLP analysis. Food Chemistry, 121(4), 1305-1311. https://doi.org/10.1016/j.foodchem.2010.02.004
- Huang, J. L., Chang, H. T., Cheng, R., Hsu, H. H., Pai, T. W., et al. (2004). Identification of simple sequence repeat biomarkers through cross-species comparison in a tag cloud representation. BioMed Research International. 2014(1), 678971.https://doi.org/10.1155/2014/678971
- Jiang, M., Yang, C., & Wen, H. (2004). The complete mitochondrial genome of Aspiorhynchus laticeps and its phylogenetic analysis. Meta Gene, 2(1), 218-225. https://doi.org/10.1016/j.mgene.2014.01.006
- Karamanlidis, A. A., Gaughran, S., Aguilar, A., Dendrinos, P., Huber, D., Pires, R., Schultz, J., & Amato, G. (2016). Shaping species conservation strategies using mtDNA analysis: The case of the elusive Mediterranean monk seal (Monachus monachus). Journal of Molecular Evolution, 193, 71-79. https://doi.org/10.1016/ j.biocon.2015.11.014
- Kimura, M. (1980). A simple method for estimating evolutionary rate of base substitutions through comparative studies of nucleotide sequences. Journal of Molecular Evolution, 16, 111-120. https://doi.org/10.1007/ BF01731581
- Kinaro, Z. O., Xue, L., Nyaundi, K. J., Shen, J., et al. (2015). The mitochondrial genome of an endangered native Singidia tilapia, Oreochromis esculentus: Genome organization and control region polymorphism. Mitochondrial DNA, 1736 (March 2016). https://doi.org/10.3109/19401736.2015.1089493
- Klett, V., & Meyer, A. (2002). What if anything, is a tilapia: Mitochondrial ND2 phylogeny of tilapiines and the evolution of parental care systems in the African cichlid fishes. Molecular Biology and Evolution, 865-883. https://doi.org/10.1093/oxfordjournals.molbev.a004144
- Librado, P., & Rozas, J. (2009). DnaSP v5: A software for comprehensive analysis of DNA polymorphism data. Bioinformatics, 25, 1451-1452. https://doi.org/10.1093/bioinformatics/btp187
- Lim, K. C., Lim, P. E., Chong, V. C., & Lee, K. H. (2015). Molecular and morphological analyses reveal phylogenetic relationships of stingrays focusing on the family Dasyatidae (Myliobatiformes). PLoS ONE, 10(5), e0129411. https://doi.org/10.1371/journal.pone.0129411
- McManus, G. B., & Katz, L. A. (2009). Molecular and morphological methods for identifying plankton: What makes a successful marriage? Journal of Plankton Research, 31(10), 1119-1129. https://doi.org/10.1093/plankt/fbp061
- Nagl, S., Tichy, H., Mayer, W. E., Samonte, I. E., McAndrew, B. J., & Klein, J. (2001). Classification and phylogenetic relationships of African tilapiine fishes inferred from mitochondrial DNA sequences. Molecular Phylogenetics and Evolution, 20 (3), 361-374. https://doi.org/10.1006/mpev.2001.0979
- Nwachi, O. F., Esa, Y., Christianus, A., & Kamarudin, S. M. (2020). Sexual restiveness and colouration between partial diallel cross of genetically improved farmed tilapia 'GIFT' and UPM red tilapia. Jordan Journal of Biological Sciences, 13(2), 219-222
- Nwachi, O. F., & Esa, Y. (2016). A review of production protocols used in producing economically viable monosex tilapia. Journal of Fisheries and Aquatic Science, 11 (January), 1-11. https://doi.org/10.3923/jfas.2016.1.11
- Nyingi, D., De Vos, L., Aman, R., & Agnèse, J. F. (2009). Genetic characterization of an unknown and endangered native population of the Nile tilapia Oreochromis niloticus (Linnaeus, 1758) (Cichlidae; Teleostei) in the Loboi Swamp (Kenya). Aquaculture, 297(1-4), 57-63.
https://doi.org/10.1016/j.aquaculture.2009.09.017
- Ogden, R. (2008). Fisheries forensics: The use of DNA tools for improving compliance, traceability and enforcement in the fishing industry. Fish and Fisheries, 462-472. https://doi.org/10.1111/j.1467-2979.2008.00305.x
- Oladimeji, T. E., Awodiran, M. O., & Komolafe, O. O. (2015). Genetic differentiation studies among natural populations of Tilapia zillii. Notulae Scientia Biologicae, 7(4), 423-429. https://doi.org/10.15835/nsb749649
- Rastogi, G., Dharne, M. S., Walujkar, S., Kumar, A., Patole, M. S., Shouche, Y. S., et al. (2007). Species identification and authentication of tissues of animal origin using mitochondrial and nuclear markers. Meat Science, 76, 666-674. https://doi.org/10.1016/j.meatsci.2007.02.006
- Saitou, N., & Nei, M. (1987). The neighbor-joining method: A new method for reconstructing phylogenetic trees. Molecular Biology and Evolution, 4, 406-425.
- Tamura, K., Stecher, G., Peterson, D., & Filipski, A. (2013). MEGA6: Molecular evolutionary genetics analysis version 6.0. Molecular Biology and Evolution, 30, 2725-2729. https://doi.org/10.1093/molbev/mst197
- Ward, R. D., Zemlak, T. S., Innes, B. H., Last, P. R., & Hebert, P. D. N. (2005). DNA barcoding Australia's fish species. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences, 360, 1847-1857. https://doi.org/10.1098/rstb.2005.1716
- Wu, L., & Yang, J. (2012). Identifications of captive and wild tilapia species existing in Hawaii by mitochondrial DNA control region sequence. PLoS ONE, 7(12), 1-9. https://doi.org/10.1371/journal.pone.0051731
- Xiaowei, L., Dayu, L., Zhiying, Z., Jing-Ling, Z., & Jue, Y. H. (2016). Genetic variation of mitochondrial DNA D-loop sequences from different strains of Nile tilapia (Oreochromis niloticus). Southwest China Journal of Agricultural Science, 8, 2-7.
- Zou, Z., Li, D., Zhu, J., Han, J., Xiao, W., & Yang, H. (2015). Genetic variation among four bred populations of two tilapia strains, based on mitochondrial D-loop sequences. Mitochondrial DNA, 26(3), 426-430. https://doi.org/10.3109/19401736.2013.855735