Genetic diversity of Tambaqui (Teleostei - Characidae) broodstocks from Northern region of Brazil using microsatellite markers
DOI:
https://doi.org/10.5433/1679-0359.2020v41n6Supl2p3249Keywords:
Colossoma macropomum, Conservation, Genetic variability, Microsatellites, SSR.Abstract
The Amazonian fish Tambaqui (Colossoma macropomum) is the most common native species in Brazil. This species has the highest production rate in the Northern region, especially in the State of Rondônia. The genetic evaluation of Tambaqui is an extremely important to increase productivity in fish farms or improve the adaptability in restocking natural populations. The objective of this study was to evaluate the genetic diversity of three Tambaqui broodstocks in Rondônia, Brazil. Six microsatellite markers were used to analyze a total of 89 breeders collected from three fish farms located in Ji-Paraná (JP), Ouro Preto do Oeste (OP) and Presidente Médici (PM). A total of 37 alleles between 140 and 310 bp were found, including the presence of exclusive and low frequency alleles in the three broodstocks. The average values of observed heterozygosity ranged from 0.404 (PM) to 0.499 (JP). The FIS coefficient values were positive for the three broodstocks, demonstrating a deficit of heterozygotes. The Molecular Variance Analysis (AMOVA) showed greater variation within the stocks than between them. The genetic differentiation was moderate and significant between the stocks, with higher differentiation between JP x PM and lower between OP x PM. The Bayesian analysis designated an optimal value of K = 3 groupings. Although there is moderate genetic diversity between broodstocks, the high FIS indicates a possible decline of diversity in the next generations, and therefore, the incorporation of new breeders is suggested to increase the genetic diversity in the three stocks.Downloads
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References
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Peakall, R., & Smouse, P. E. (2012). GenALEx 6.5: Genetic analysis in Excel. Population genetic software for teaching and research-an update. Bioinformatics, 28(19), 2537-2539. doi: 10.1093/bioinformatics/ bts460
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Pritchard, J. K., Stephens, M., & Donnelly, P. (2000). Inference of population structure using multilocus genotype data. Genetics, 155.(2), 945-959.
Ribeiro, R. P., Rodriguez-Rodriguez, M. P., Resende, E. K., Souza, F. P., Povh, J. A., Poveda-Parra, A. R.,... Lopera-Barrero, N. M. (2016). Genetic characteristics of Tambaqui broodstocks in the state of Rondônia, Brazil: implications on production and conservation. Semina: Ciências Agrárias, 37(4, Supl. 1), 2375-2386. doi: 10.5433/1679-0359.2016v37n4Supl1p2375
Rodriguez-Rodriguez, M. P., Lopera-Barrero, N. M., Vargas, L., Albuquerque, D. M., Goes, E. S. D. R., Prado, O. P. P. D., & Ribeiro, R. P. (2013). Caracterização genética de gerações de tilápia Gift por meio de marcadores microssatélites. Pesquisa Agropecuária Brasileira, 48(10), 1385-1393. doi: 10.1590/S0 100-204X2013001000010
Rousset, F. S. (2008). GENEPOP’ 007: a complete re-implementation of the GENEPOP software for Windows and Linux. Molecular Ecology Research, 8(1), 103-106. doi: 10.1111/j.1471-8286.2007.019 31.x
Santos, C. H. A., Santana, G. X., Sá Leitão, C. S., Paula Silva, M. N., & Almeida Val, V. M. F. (2016). Loss of genetic diversity in farmed populations of Colossoma macropomum estimated by microsatellites. Animal Genetics, 47(3), 373-376. doi: 10.1111/age.12422
Santos, M. D. C. F., Hrbek, T., & Farias, I. P. (2009). Microsatellite markers for the tambaqui (Colossoma macropomum, Serrasalmidae, Characiformes), an economically important keystone species of the Amazon River floodplain. Molecular Ecology Resources, 9(3), 874-876. doi: 10.1111/j.1755-0998. 2008.02331.x
Souza, F. P. de, Castro, P. L. D., Goes, E. S. D. R., Ribeiro, R. P., Santos, S. C. A. D., Lima, E. C. S. D., Murari, P. J. F., & Lopera-Barrero, N. M. (2018a). Genetic variability of Prochilodus lineatus in artificial and semi-natural reproduction. Italian Journal of Animal Science, 17(2), 321-325. doi: 10. 1080/1828051X.2017.1365312
Souza, F. P. de, Lima, E. C. S., Castro, P. L., Goes, E. S. R., Ribeiro, R. P., & Lopera-Barrero, N. M. (2018b). Contribuição parental em progênies de Curimba usando diferentes sistemas reprodutivos. Boletim do Instituto de Pesca, 44(1), 74-79. doi: 10.20950/1678-2305.2018.276
Tamura, K., Peterson, D., Peterson, N., Stecher, G., Nei, M., & Kumar, S. (2011). MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods research resource. Molecular Biology Evolution, 28(10), 2731-2739. doi: 10.1093/ molbev/msr121
Waples, R. S. (2015). Testing for Hardy-Weinberg proportions: have we lost the plot? Journal of Heredity, 106(1), 1-19. doi: 10.1093/jhered/esu062
Wright, S. (1978). Evolution and genetics of populations. Variability within and among natural populations (p. 590, v. 4). Chicago: University of Chicago.
Aguiar, J., Schneider, H., Gomes, F., Carneiro, J., Santos, S., Rodrigues, L. R., & Sampaio, I. (2013). Genetic variation in native and farmed populations of Tambaqui (Colossoma macropomum) in the Brazilian Amazon: Regional discrepancies in farming systems. Anais da Academia Brasileira de Ciências, 85(4), 1439-1447. doi: 10.1590/0001-376520130007
Aguiar, J. D. P., Gomes, P. F. F., Hamoy, I. G., Santos, S. E. B. D., Schneider, H., & Sampaio, I. (2018). Loss of genetic variability in the captive stocks of tambaqui, Colossoma macropomum (Cuvier, 1818), at breeding centres in Brazil, and their divergence from wild populations. Aquaculture Research, 49(5), 1914-1925. doi: 10.1111/are.13647
Araujo-Lima, C. R. M. & Goulding, M. (1997). So fruitful fish: ecology, conservation, and aquaculture of the Amazon's Tambaqui. New York: Columbia University Press, 1997.
Azevedo, R. M. D., Santos, H. O. D., Ferreira, R. A., Marçal, R. M., & Silva-Mann, R. (2013). Variabilidade genética em populações de Erythrina velutina Willd. por meio de isoenzimas. Revista Acadêmica: Ciências Agrárias e Ambientais, 11(1), 43-51. doi: 10.7213/academica.10.S01.AO05
Brabo, M. F., Fernando, L., Pereira, S., Abreu, D., Campelo, V., & Veras, G. C. (2016). Cenário atual da produção de pescado no mundo, no Brasil e no estado do Pará: ênfase na aquicultura. Acta of Fisheries and Aquatic Resources, 4(2), 50-58. doi: 10.2312/Actafish.2016.4.2.50-58
Costa, J., Freitas, R., Gomes, A. L., Carneiro, D., & Martins, M. I. (2016). Effect of stocking density on economic performance for Colossoma macropomum (Cuvier, 1816), juvenile in earthen ponds. Latin American Journal of Aquatic Research, 44(1), 165-170. doi: 10.3856/vol44-issue1-fulltext-18
Earl, D. A. & vonHoldt, B. M. (2012). STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method. Conservation Genetics Resources, 4(2), 359-361. doi: 10.1007/s12686-011-9548-7
Evanno, G., Regnaut, S., & Goudet, J. (2005). Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Molecular Ecology, 14(8), 2611-2620. doi: 10.1111/j.1365-294X.2005.02553.x
Excoffier, L., Laval, G., & Schneider, S. (2005). Arlequin ver. 3.0: an integrated software package for population genetics data analysis. Evolutionary Bioinformatics, 1(1), 47-50.
Food and Agriculture Organization (2020). The state of world fisheries and aquaculture 2020. Sustainability in action. Rome: FAO.
Goudet, J. (2002). FSTAT: a program to estimate and test gene diversities and fixation indices (version 2.9.3.2). Lausanne: University of Lausanne, Department of Ecology & Evolution; 2002. Retrieved from http://www2.unil.ch/popgen/softwares/fstat.htm
Jacometo, C. B., Lopera-Barrero, N. M., Rodriguez-Rodriguez, M. D. P., Gomes, P. C., Povh, J. A., Streit Jr, D. P.,.... Ribeiro, R. P. (2010). Variabilidade genética em tambaquis (Teleostei: Characidae) de diferentes regiões do Brasil. Pesquisa Agropecuária Brasileira, 45(5), 481-487. doi: 10.1590/S0100-204X2010000500007
Lopera-Barrero, N. M., Povh, J. A., Ribeiro, R. P., Gomes, P. C., Jacometo, C. B., & Silva, T. L. (2008). Comparison of DNA extraction protocols of fish fin and larvae samples: modified salt (NaCl) extraction. Ciencia e Investigación Agrarria, 35(1), 65-74. doi: 10.4067/S0718-16202008000100008
Lopera-Barrero, N. M., Rodriguez-Rodriguez, M. P., Fornari, D. C., Resende, E. K., Poveda-Parra, A. R., Braccini, G.,… Ribeiro, R. P. (2015). Genetic variability of broodstocks of Tambaqui (Teleostei-Characidae) from the northeast region of Brazil. Semina: Ciências Agrárias, 36(6), 4013-4021. doi: 10. 5433/1679-0359.2015v36n6p4013
Lopera-Barrero, N. M., Santos, S. C. A., Goes, E. S. R., Castro, P. L., Souza, F. P., Poveda-Parra, A. R.,... Ribeiro, R. P. (2016). Monitoramento e conservação genética de populações naturais de Prochilodus lineatus dos rios Pardo, Mogi-Guaçu e Tietê, São Paulo. Arquivo Brasileiro de Medicina Veterinária e Zootecnia, 68(6), 1621-1628. doi: 10.1590/1678-4162-8791
Moraes, A. Neto, Ayres, D. R., Streit, D. P. Jr.,.Lopera-Barrero, N. M., Ferraz, P. B., Fº., Corrêa, R. A. C., Fº.,... Povh, J. A. (2017). Genetic diversity of tambaqui broodstocks in stock enhancement programs. Semina: Ciências Agrárias, 38(3), 1655-1659. doi: 10.5433/1679-0359.2017v38n3p1665
Nei, M. (1978). Estimation of average heterozygosity and genetic distance from a small number of individuals. Genetics, 89(3), 583-590.
Peakall, R., & Smouse, P. E. (2012). GenALEx 6.5: Genetic analysis in Excel. Population genetic software for teaching and research-an update. Bioinformatics, 28(19), 2537-2539. doi: 10.1093/bioinformatics/ bts460
Peixe Br (2020). Anuário Peixe Br da Piscicultura. Recuperado de https://www.peixebr.com.br/anuario-2020/
Pritchard, J. K., Stephens, M., & Donnelly, P. (2000). Inference of population structure using multilocus genotype data. Genetics, 155.(2), 945-959.
Ribeiro, R. P., Rodriguez-Rodriguez, M. P., Resende, E. K., Souza, F. P., Povh, J. A., Poveda-Parra, A. R.,... Lopera-Barrero, N. M. (2016). Genetic characteristics of Tambaqui broodstocks in the state of Rondônia, Brazil: implications on production and conservation. Semina: Ciências Agrárias, 37(4, Supl. 1), 2375-2386. doi: 10.5433/1679-0359.2016v37n4Supl1p2375
Rodriguez-Rodriguez, M. P., Lopera-Barrero, N. M., Vargas, L., Albuquerque, D. M., Goes, E. S. D. R., Prado, O. P. P. D., & Ribeiro, R. P. (2013). Caracterização genética de gerações de tilápia Gift por meio de marcadores microssatélites. Pesquisa Agropecuária Brasileira, 48(10), 1385-1393. doi: 10.1590/S0 100-204X2013001000010
Rousset, F. S. (2008). GENEPOP’ 007: a complete re-implementation of the GENEPOP software for Windows and Linux. Molecular Ecology Research, 8(1), 103-106. doi: 10.1111/j.1471-8286.2007.019 31.x
Santos, C. H. A., Santana, G. X., Sá Leitão, C. S., Paula Silva, M. N., & Almeida Val, V. M. F. (2016). Loss of genetic diversity in farmed populations of Colossoma macropomum estimated by microsatellites. Animal Genetics, 47(3), 373-376. doi: 10.1111/age.12422
Santos, M. D. C. F., Hrbek, T., & Farias, I. P. (2009). Microsatellite markers for the tambaqui (Colossoma macropomum, Serrasalmidae, Characiformes), an economically important keystone species of the Amazon River floodplain. Molecular Ecology Resources, 9(3), 874-876. doi: 10.1111/j.1755-0998. 2008.02331.x
Souza, F. P. de, Castro, P. L. D., Goes, E. S. D. R., Ribeiro, R. P., Santos, S. C. A. D., Lima, E. C. S. D., Murari, P. J. F., & Lopera-Barrero, N. M. (2018a). Genetic variability of Prochilodus lineatus in artificial and semi-natural reproduction. Italian Journal of Animal Science, 17(2), 321-325. doi: 10. 1080/1828051X.2017.1365312
Souza, F. P. de, Lima, E. C. S., Castro, P. L., Goes, E. S. R., Ribeiro, R. P., & Lopera-Barrero, N. M. (2018b). Contribuição parental em progênies de Curimba usando diferentes sistemas reprodutivos. Boletim do Instituto de Pesca, 44(1), 74-79. doi: 10.20950/1678-2305.2018.276
Tamura, K., Peterson, D., Peterson, N., Stecher, G., Nei, M., & Kumar, S. (2011). MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods research resource. Molecular Biology Evolution, 28(10), 2731-2739. doi: 10.1093/ molbev/msr121
Waples, R. S. (2015). Testing for Hardy-Weinberg proportions: have we lost the plot? Journal of Heredity, 106(1), 1-19. doi: 10.1093/jhered/esu062
Wright, S. (1978). Evolution and genetics of populations. Variability within and among natural populations (p. 590, v. 4). Chicago: University of Chicago.
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2020-11-06
How to Cite
Urrea-Rojas, A. M., Souza, F. P. de, Lima, E. C. S. de, Yamachita, A. L., Pandolfi, V. C. F., Godoy, S. M. de, … Lopera-Barrero, N. M. (2020). Genetic diversity of Tambaqui (Teleostei - Characidae) broodstocks from Northern region of Brazil using microsatellite markers. Semina: Ciências Agrárias, 41(6Supl2), 3249–3258. https://doi.org/10.5433/1679-0359.2020v41n6Supl2p3249
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