Evaluation of Genetic Variation in Oreochromis Tilapia Species from South-South Nigeria using Mitochondrial DNA Hypervariable Region

Article Sidebar

pdf epub
Published: Oct 2, 2024
DOI: https://doi.org/10.26538/tjnpr/v8i9.41
Keywords:
Genetic distance, River, Selection, Tilapia, Variation

Main Article Content

Ekerette E. Ekerette
Department of Genetics and Biotechnology, Faculty of Biological Sciences, University of Calabar P.M.B 1115, Calabar, Nigeria
Owoidihe M. Etukudo
Department of Biological Sciences, Faculty of Computing and Applied Sciences, Topfaith University, P.M.B 1875, Mkpatak, Akwa Ibom State, Nigeria
Jude N. Efienokwu
Department of Science Laboratory, School of Applied Sciences, Delta State Polytechnic, P.M.B 1030, Ogwashi-uku, Delta State, Nigeria
Hannah E. Etta
Department of Animal and Environmental Biology, Faculty of Biological Sciences, University of Cross River State, P.M.B 1123, Calabar, Nigeria
Inyang. I. Henry
Department of Microbiology, Faculty of Biological Scienaces, University of Cross River State, P.M.B 1123, Calabar, Nigeria
Paul B. Ekpo
Department of Genetics and Biotechnology, Faculty of Biological Sciences, University of Calabar P.M.B 1115, Calabar, Nigeria
Ndem E. Edu
Department of Genetics and Biotechnology, Faculty of Biological Sciences, University of Calabar P.M.B 1115, Calabar, Nigeria
Reagan B. Agbor
Department of Genetics and Biotechnology, Faculty of Biological Sciences, University of Calabar P.M.B 1115, Calabar, Nigeria
Uduak. L. Edem
Department of Genetics and Biotechnology, Faculty of Biological Sciences, University of Calabar P.M.B 1115, Calabar, Nigeria 
Ekei V. Ikpeme
Department of Genetics and Biotechnology, Faculty of Biological Sciences, University of Calabar P.M.B 1115, Calabar, Nigeria 

Abstract

Understanding genetic variation among species is essential for effective selection and breeding enhancements. This study was conducted to assess the genetic diversity among three tilapia species (Oreochromis niloticus, Oreochromis aureus, and Oreochromis mossambicus) from several rivers located in South-South Nigeria. A total of 300 samples representing the three species were used for this research. Blood samples were collected from all individuals for DNA extraction, amplification, and sequencing of the mitochondrial (mt) control region. Analysis of mitochondrial DNA revealed that Oreochromis aureus exhibited the greatest number of polymorphic sites, with a total of 225, compared to Oreochromis niloticus and Oreochromis mossambicus, which had 129 and 84 polymorphic sites, respectively. The number of haplotypes was highest in O. niloticus with five, while O. aureus and O. mossambicus each had three haplotypes. O. niloticus also demonstrated the highest haplotype diversity (0.796), whereas O. aureus showed the highest nucleotide diversity (0.139). The largest genetic distance was found between O. aureus and O. mossambicus (0.388), whereas the smallest genetic distance was noted between O. niloticus and O. mossambicus (0.217). Enhancing tilapia production in Nigeria can be achieved by selectively breeding tilapia from the Itu, Ethiope, and New Calabar Rivers, which exhibited high genetic variation.

Downloads

Download data is not yet available.

Article Details

How to Cite
Ekerette, E. E., Etukudo, O. M., Efienokwu, J. N., Etta, H. E., Henry, I. I., Ekpo, P. B., Edu, N. E., Agbor, R. B., Edem, U. L., & Ikpeme, E. V. (2024). Evaluation of Genetic Variation in Oreochromis Tilapia Species from South-South Nigeria using Mitochondrial DNA Hypervariable Region. Tropical Journal of Natural Product Research (TJNPR), 8(9), 8527-8536. https://doi.org/10.26538/tjnpr/v8i9.41
Issue
Vol. 8 No. 9 (2024): Tropical Journal of Natural Product Research (TJNPR)
Section
Articles
Creative Commons License

This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License.

How to Cite

Ekerette, E. E., Etukudo, O. M., Efienokwu, J. N., Etta, H. E., Henry, I. I., Ekpo, P. B., Edu, N. E., Agbor, R. B., Edem, U. L., & Ikpeme, E. V. (2024). Evaluation of Genetic Variation in Oreochromis Tilapia Species from South-South Nigeria using Mitochondrial DNA Hypervariable Region. Tropical Journal of Natural Product Research (TJNPR), 8(9), 8527-8536. https://doi.org/10.26538/tjnpr/v8i9.41

References

Tran N, Chu L, Chan CY, Genschick S, Phillips MJ, Kefi AS. Fish supply and demand for food security in Sub-Saharan Africa: an analysis of the Zambian fish sector. Mar Policy. 2019; 99:343-350. Doi: https://doi.org/10.1016/j.marpol.2018.11.009.

Food and Agriculture Organization. World food and agriculture statistical yearbook. Rome: Statistics Division; 2022a. Doi: https://doi.org/10.4060/cc2211en.

Tschirley D, Reardon RT, Dolislager M, Snyder J. The rise of a middle class in East and Southern Africa: implications for food system transformation. J Int Dev. 2015; 27(5):628–646. Doi: https://doi.org/10.1002/jid.3107.

Zhou Y and Staatz J. Projected demand and supply for various foods in West Africa: implications for investments and food policy. Food Policy. 2016; 61:198–212. Doi: https://doi.org/10.1016/j.foodpol.2016.04.002.

Thurstan RH and Roberts CM. The past and future of fish consumption: can supplies meet healthy eating recommendations? Mar Pollut Bull. 2014; 89(1–2):5–11. Doi: https://doi.org/10.1016/j.marpolbul.2014.09.016.

Ekerette EE, Ikpeme EV, Udensi OU, Ozoje MO, Etukudo OM, Umoyen AJ, Durosaro SO, Wheto M. Phylogenetics and molecular divergence of tilapia fish [Oreochromis species] using mitochondrial D-loop and cytochrome b regions. Am J Mol Biol. 2018; 8(1):39-57. Doi: https://doi.org/10.4236/ajmb.2018.81004.

Kobayashi M, Msangi S, Batka M, Vannuccini S, Dey MM, Anderson JL. Fish to 2030: the role and opportunity for aquaculture. Aqua Econ Manag. 2015; 19(3):282–300. Doi: https://doi.org/10.1080/13657305.2015.994240.

Organization for Economic Co-operation and Development/Food and Agriculture Organization of the United

Nations (OECD/FAO). OECD-FAO Agricultural Outlook 2017–2026. Paris: OECD Publishing; 2017. Doi: https://doi.org/10.1787/19991142.

Chan CY, Tran N, Pethiyagoda S, Crissman CC, Sulser TB, Phillips MJ. Prospects and challenges of fish for food security in Africa. Global Food Secur. 2019; 20:17-25. Doi: https://doi.org/10.1016/j.gfs.2018.12.002.

Engle C and D’Abramo L. Showcasing research focusing on sustainability of aquaculture enterprises and global food security. J World Aqua Soc. 2016; 47(3):311-313. Doi: https://doi.org/10.1111/jwas.12296.

Engle CR, McNevin A, Racine P, Boyd CE, Paungkaew D, Viriyatum R, Tinh HQ, Minh HN. Economics of sustainable intensification of aquaculture: evidence from shrimp farms in Vietnam and Thailand. J. World Aquac. Soc. 2017; 48(2):227-239. Doi: https://doi.org/10.1111/jwas.12423.

Farmery AK, White A, Allison EH. Identifying policy best-practices to support the contribution of aquatic foods to food and nutrition security. Foods. 2021; 10(7):1589. Doi: https://doi.org/10.3390/foods10071589.

Mikkelsen E, Fanning L, Kreiss C, Billing SL, Dennis J, Filgueira R, Grant J, Krause G, Lipton D, Miller M, Perez J, Stead S, Villasante S. Availability and usefulness of economic data on the effects of aquaculture: a North Atlantic comparative assessment. Rev. Aquac. 2021; 13(1):601-618. Doi: https://doi.org/10.1111/raq.12488.

Bush SR, Pauwelussen A, Badia P, Kruk S, Little D, Luong LT, Newton R, Nhan DT, Rahman MM, Sorgeloos P, Sung YY. Implementing aquaculture technology and innovation platforms in Asia. Aquac. 2021; 530. Doi: https://doi.org/10.1016/j.aquaculture.2020.735822.

Lasner T, Brinker A, Nielsen R, Rad F. Establishing a benchmarking for fish farming – profitability, productivity and energy efficiency of German, Danish and Turkish rainbow trout grow-out systems. Aqua Res. 2017; 48(6):3134-3148. Doi: https://doi.org/10.1111/are.13144.

Shikuku KM, Tran N, Joffre OM, Islam AHMS, Barman BK, Ali S, Rossignoli CM. Lock-ins to the dissemination of genetically improved fish seeds. Agric Syst. 2021; 188. Doi: https://doi.org/10.1016/j.agsy.2020.103042.

FAO. National Aquaculture Sector Overview. Egypt. National Aquaculture Sector Overview Fact Sheets. FAO, Rome; 2020.

Moses M, Chauka LJ, de Koning DJ, Palaiokostas C, Mtolera MSP. Growth performance of five different strains

of Nile tilapia (Oreochromis niloticus) introduced to Tanzania reared in fresh and brackish waters. Sci Rep. 2021; 11(1):11147. Doi: https://doi.org/10.1038/s41598-021-90505-y.

Abd El-Hack ME, El-Saadony MT, Nader MM, Salem HM, El-Tahan AM, Soliman SM, Khafaga AF. Effect of environmental factors on growth performance of Nile tilapia (Oreochromis niloticus). Int J Biometeorol. 2022; 66(11):2183–2194. Doi: https://doi.org/10.1007/s00484-022-02347-6.

Robledo D, Ogwang J, Byakora E, Nascimento-Schulze JC, Benda KK, Fraslin C, Salisbury S, Solimo M, Mayega JF, Beine P, Masembe C, Houston R, Mukiibi R. Genetic diversity and population structure of farmed and wild Nile tilapia (Oreochromis niloticus) in Uganda: The potential for aquaculture selection and breeding programs. Genomics. 2024; 116(1):110781. Doi: https://doi.org/10.1016/j.ygeno.2024.110781.

FAO. FishStatJ: universal software for fishery statistical time series: aquaculture production 1950–2020. FAO, Rome; 2022b.

Biovet SA. Tilapia production in Nigeria [Online]. 2024 [cited Aug 2024] Available from: https://www.veterinariadigital.com/en/articulos/tilapia-production-in-nigeria.

Akinjogunla VF, Usman MD, Muazu TA, Ajeigbe SO, Musa ZA, Ijoh BB, Muhammad YU, Usman BI. Comparative efficacy of anesthetic agents (clove oil and sodium bicarbonate) on cultured African catfish, Clarias gariepinus (Burchell, 1822) and Nile tilapia, Oreochromis niloticus (Linnaeus, 1758). Trop J Nat Prod Res. 2023; 7(8):3800–3805. Doi: https://doi.org/10.26538/tjnpr/v7i8.34.

Kakuhikire CT, Nsubuga FW, Raja R, Kato P. Genetic diversity of Nile tilapia (Oreochromis niloticus, L. 1758) in native and introduced populations in East Africa. J Wildl. Biodivers. 2024; 8(3):296–312. Doi: https://doi.org/10.5281/zenodo.11625514.

Suleiman IO, Moruf RO, Usman BI. Population genetic structure of feral and cultured African catfish (Clarias gariepinus) inferred from random amplified polymorphic DNA in Kano, Nigeria. Trop J Nat Prod Res 2023; 7(3):2650–2654. Doi: https://doi.org/10.26538/tjnpr/v7i3.27.

Makeche MC, Muleya W, Nhiwatiwa T. Characterization of Oreochromis niloticus strains of Lake Kariba culture fisheries using morphological and meristic methods. Am. Sci. Res. J. Eng. Technol. Sci. 2020 74(1), 31-40.

Kwikiriza G, Yegon MJ, Byamugisha N, Beingana A, Atukwatse F, Barekye A, Nattabi JK, Meimberg H. Morphometric Variations of Nile Tilapia (Oreochromis niloticus) (Linnaeus, 1758) Local Strains Collected from Different Fish Farms in South Western Highland Agro-Ecological Zone (SWHAEZ), Uganda: Screening Strains for Aquaculture. Fishes. 2023; 8:217. Doi: https://doi.org/10.3390/fishes8040217.

Ropp AJ, Reece KS, Snyder RA, Song J, Biesack EE, McDowell JR. Fine-scale population structure of the northern hard clam (Mercenaria mercenaria) revealed by genome-wide SNP markers. Evol. Appl. 2023 16, 1422–1437. doi: 10.1111/eva.13577

Abdel-Hamid ZG, Heba AM, El-Kader A, Aboelhassan DM, Mahrous KF. Genetic diversity in Egyptian tilapia species using PCR-RFLP of D-loop mitochondrial DNA gene. Res. J. Pharm. Biol. Chem. Sci. 2014; 5(6):469-475.

Agbebi OT, Echefu CJ, Adeosun IO, Ajibade AH, Adegbite EA, Adebambo AO, Ilori MB, Durosaro SO, Ajibike AB. Mitochondrial diversity and time divergence of commonly cultured cichlids in Nigeria. Br Biotechnol J. 2016; 13(2):1-7. Doi: https://doi.org/10.9734/BBJ/2016/25470.

Luo C, Yang P, Wang S. The complete mitochondrial genome of Sarotherodon galilaeus (Linnaeus, 1758) (Perciformes: Cichlidae) and its phylogenetic placement. Mitochondrial DNA. Part B. 2021; 6(3):920–921. Doi: https://doi.org/10.1080/23802359.2021.1888327.

Mbilinyi WL, Rumisha C, Mwandya AW, Msalya GM. Genetic analysis reveals a substantial proportion of non-targeted tilapias among farmed stocks in Kilosa and Kibaha, Tanzania. Tanzan J Sci. 2023; 49(2):559-567. Doi: https://doi.org/10.4314/tjs.v49i2.24.

Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol. 2013; 30:2725-2729. Doi: https://doi.org/10.1093/molbev/mst197.

Librado P and Rozas J. DnaSP version 5: a software for comprehensive analysis of DNA polymorphism data. Bioinform. 2009; 25:1441-1452. Doi: https://doi.org/10.1093/bioinformatics/btp187.

Nguyen TD, Dinh TN, Mai TT. Genetic diversity of mitochondrial DNA D-loop sequence in Bang Troi chicken breed. Acad J Biol. 2024; 46(1):49–54. Doi: https://doi.org/10.15625/2615-9023/18999.

Guo Y, Gong Y, He Y-m, Yang B-g, Zhang W-y, Chen B-e, Huang Y-f, Zhao Y-j, Zhang D-p, Ma Y-h, Chu M-x, E G-x. Investigation of mitochondrial DNA genetic diversity and phylogeny of goats worldwide. J Integr Agric. 2022; 21(6):1830-1837. Doi: https://doi.org/10.1016/S2095-3119(21)63882-0.

Amorim A, Fernandes T, Taveira N. Mitochondrial DNA in human identification: a review. Peer J. 2019; 10: 1-24. Doi: https://doi.org/10.7717/peerj.7314.

Dong F, Cheng P, Sha H, Yue H, Wan C, Zhang Y, Zhang L, Zhang H, Wei Q. Genetic diversity and population structure analysis of blunt snout bream (Megalobrama amblycephala) in the Yangtze River Basin: Implications for conservation and utilization. Aqua Rep. 2024; 35:101925. Doi: https://doi.org/10.1016/j.aqrep.2024.101925.

Ren Y, Ren YL, Dai JC, Zhao NH, Zhao H, Wei J, Nie ZL. Genetic diversity analysis of Schizothorax biddulphi based on mitochondrial DNA COII and ND4 genes. J Fish Sci China. 2022; 46(12):2274-2285.

Kenthao A, Wangsomnuk PP, Jearranaiprepame P. Genetic variations and population structure in three populations of beardless barb, Cyclocheilichthys apogon (Valenciennes, 1842) inferred from mitochondrial cytochrome b sequences. Mitochondrial DNA. Part A. 2018; 29(1):82-90. Doi: https://doi.org/10.1080/24701394.2016.1242581.

Jiang B, Fu J, Dong Z, Fang M, Zhu W, Wang L. Maternal ancestry analyses of red tilapia strains based on D-loop sequences of seven tilapia populations. Peer J. 2019; 7:1-14. Doi: https://doi.org/10.7717/peerj.7007.

Nyaku ER, Diyaware MY, Suleiman SB, Nwafili SA. Mitochondrial DNA D-loop genetic relatedness and characterization of Nile tilapia (Oreochromis niloticus (Linnaeus, 1758)) from Lakes Alau and Bako, Northeast, Nigeria. J Biotechnol. 2023; 2(1):22-33. Doi: https://doi.org/10.36108/jbt/3202.20.0120.

Angienda PO, Lee HJ, Elmer KR, Abila R, Waindi EN, Meyer A. Genetic structure and gene flow in an endangered native tilapia fish (Oreochromis esculentus) compared to invasive Nile tilapia (Oreochromis niloticus) in Yala swamp, East Africa. Conserv Genet. 2011; 12:243–255. Doi: https://doi.org/10.1007/s10592-010-0136-2.

Kanaka KK, Sukhija N, Chandra Goli R, Singh S, Ganguly I, Dixit SP, Dash A, Malik AA. On the concepts and measures of diversity in the genomics era. Curr. Plant Biol. 2023; 33:100278. Doi: https://doi.org/10.1016/j.cpb.2023.100278.

Kavembe GD, Machado-Schiaffino G, Meyer A. Pronounced genetic differentiation of small, isolated and fragmented tilapia populations inhabiting the Magadi Soda Lake in Kenya. Hydrobiologia. 2013; 6:1-17. Doi: https://doi.org/10.1007/s10750-013-1648-9.

Dogan I, Dogan N. Genetic distance measures: review. J. Biostat. 2016; 8(1):87-93. Doi: https://doi.org/10.5336/biostatic.2015-49517.

Heulsenbeck JP and Dyer KA. Bayesian estimation of positively selected sites. J. Mol. Evol. 2004; 58:661. Doi: https://doi.org/10.1007/s00239-004-2588-9.

Kosal E. Introductory biology: Ecology, evolution, and biodiversity. [Online]. 2023. [cited Aug 2024] Available from: https://ncstate.pressbooks.pub/introbio181/.

Molles MC. Ecology: concepts and applications. Columbus: McGraw-Hill Higher Learning; 2010.

Loewe L. Negative selection. Nat Educ. 2008; 1(1):59.

Ikpeme EV, Job IE, Ekerette EE. Selection pressure and the maternal lineage of three local chicken genotypes in South- South Nigeria. U6CAU Proceedings (Maiden Edition). 2019; 1(1):100-109.

Rieseberg LH, Widmer A, Arntz AM, Burke JM. Directional selection is the primary cause of phenotypic diversification. Proc Natl Acad Sci. USA. 2002; 99:12242-12245. Doi: https://doi.org/10.1073/pnas.192360899.

Murphy DA, Elyashiv E, Amster G, Sella G. Broad-scale variation in human genetic diversity levels is predicted by purifying selection on coding and non-coding elements. eLife. 2023; 12:e76065. Doi: https://doi.org/10.7554/eLife.76065.

Ajibike AB, Ilori BM, Awotunde EO, Adegboyega AR, Osinbowale AD, Bemji MN, Durosaro SO, Adebambo AO. Genetic diversity and effect of selection at the mitochondrial hypervariable region in major Nigerian indigenous goat breeds. Asian-Australas. J Anim Sci. 2016; 29(5):45-53. Doi: https://doi.org/10.5713/ajas.15.0775.

Meiklejohn CD, Montooth KL, Rand DM. Positive and negative selection on the mitochondrial genome. Trends Genet. 2007; 23:259–263. Doi: https://doi.org/10.1016/j.tig.2007.03.008.

Ekerette EE, Osim PB, Koffi EE, Leo EA, Ikpeme EV, Ozoje MO. Growth and heat tolerance traits in West African Dwarf sheep and variation in CD14 gene. South Asian J Biol Res. 2024; 6(1):15-28.