Transferability of heterologous microsatellite primers in Leiarius marmoratus
DOI:
https://doi.org/10.5433/1679-0359.2020v41n5supl1p2297Keywords:
Aquaculture, Amazonian Jundiá, Cross-amplification, Genetic conservation, SSR.Abstract
The Amazonian Jundiá (Leiarius marmoratus) (Siluliformes: Pimelodidae) is a species of catfish with social and economic importance in some South American countries such as Brazil and Colombia. Genetic evaluation of this species is limited due to the lack of specific molecular markers, hindering studies on genetic diversity and structure in animals under captive conditions or in natural populations. The objective of the present study was to evaluate the transferability of heterologous microsatellite markers in Leiarius marmoratus. Thirty-two heterologous primers were tested in L. marmoratus. The primers that presented the best standards were applied to 20 specimens, and the number of alleles (Na), number of effective alleles (Ne), gene diversity per Locus (GdL) and percentage of amplification failure (Md) were calculated. Eleven primers demonstrated satisfactory transferability patterns, all from the fish of the Pimelodidae family, of which, seven were monomorphic and four polymorphic. The eleven markers presented low percentage of Md (mean was 5.9% samples per locus). Na varied from one to two alleles per locus, revealing low polymorphism in the evaluated samples. The mean Ne and GdL numbers were 1.77 and 0.32, respectively. The transferability of the heterologous microsatellite loci in L. marmoratus was shown to be possible. However, further tests are needed to apply these markers in population genetic studies.Downloads
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References
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Batista, J. S. (2010). Caracterização genética da dourada - Brachyplatystoma rousseauxii, Castelnau, 1855 (Siluriformes: Pimelodidae) na Amazônia por meio de marcadores moleculares mitocondriais e microssatélites: subsídios para conservação e manejo. Manaus: Instituto Nacional de Pesquisas da Amazônia 2010. Recuperado de https://bdtd.inpa.gov.br/handle/tede/721
Calcagnotto, D., Russello, M., & DeSalle, R. (2001). Isolation and characterization of microsatellite loci in Piaractus mesopotamicus and their applicability in other Serrasalminae fish. Molecular Ecology Notes, 1(4), 245-247. doi: 10.1046/j.1471-8278.2001.00091.x
Carmo, F. M. S., Polo, É. M., Silva, M. A., & Yazbeck, G. M. (2015). Optimization of heterologous microsatellites in Piracanjuba. Pesquisa Agropecuária Brasileira, 50(12), 1236-1239. doi: 10.1590/ S0100-204X2015001200015
Carvalho Lima, T. P., Egito, A. A., Feijó, G. L. D., Arruda Mauro, R., & Ferraz, A. L. J. (2017). Molecular identification and phylogenetic analysis of Siluriformes from the Paraguay River basin, Brazil. Mitochondrial DNA Part A, 28(4), 536-543. doi: 10.3109/24701394.2016.1149825
Castro, P. L., Ribeiro, R. P., Santos, S. C. A., Goes, E. S. R., Souza, F. P., Poveda-Parra, A. R., Lopera-Barrero, N. M. (2017). Cross-amplification of heterologous microsatellite markers in Piracanjuba. Ciência Rural, 47(12), 1-6. doi: 10.1590/0103-8478cr20170374
Cruz-Casallas, N. E., Marciales-Caro, L., Díaz-Olarte, J. J., & Cruz-Casallas, P. E. (2010). Desempeño productivo del yaque (Leiarius marmoratus Gill, 1870) bajo diferentes densidades de siembra en estanques en tierra. Revista Colombiana de Ciencias Pecuárias, 23(3), 325-335.
Esquer-Garrigos, Y., Hugueny, B., Ibañez, C., Zepita, C., Koerner, K., Lambourdière, J., Couloux A., & Gaubert, P. (2015). Detecting natural hybridization between two vulnerable Andean pupfishes (Orestias agassizii and O. luteus) representative of the Altiplano endemic fisheries. Conservation Genetics, 16(3), 717-727. doi: 10.1007/s10592-015-0695-3
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Food and Agriculture Organization (2018). The State of World Fisheries and Aquaculture 2018 - Meeting the sustainable development goals (Vol. 35). Rome: FAO.
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Hashimoto, D. T., Prado, F. D., Foresti, F., & Porto-Foresti, F. (2016). Molecular identification of intergenus crosses involving catfish hybrids: risks for aquaculture production. Neotropical Ichthyology, 14(2), 1-8. doi: 10.1590/1982-0224-20150139
Hashimoto, D. T., Senhorini, J. A., Foresti, F., Martínez, P., & Porto-Foresti, F. (2014). Genetic identification of F1 and Post-F1 serrasalmid juvenile hybrids in brazilian aquaculture. PLoS One, 9(3), 1-8. doi: 10.1371/journal.pone.0089902
Lima, J. S., Telles, M. P. C., Resende, L. V., Gouveia, F. O., Boni, T. A., & Sanches, A. C. (2008). Amplificação cruzada e padronização de marcadores microssatélites em Colossoma macropomum (tambaqui). Revista de Biologia Neotropical, 5(2), 41-49. doi: 10.5216/rbn.v5i2.9821
Lopera-Barrero, N. M., Ribeiro, R. P., Povh, J. A., Mendes, L. D. V. & Poveda-Parra, A. R. (2011). Produção de organismos aquáticos: Uma visão geral do Brasil e no Mundo. Guaíba, RS: Editora Agrolivros.
Lopera-Barrero, N. M., Povh, J. A., Ribeiro, R, P., Gomes, P. C., Jacometo, C. B., & Lopes, T. S. (2008). Comparación de protocolos de extracción de ADN con muestras de aleta y larva de peces: extracción modificada con cloruro de sodio. Ciencia e Investigación Agraria, 35(1), 15-24. doi: 10.4067/S0718-16202008000100008
Lopera-Barrero, N. M., Tanamati, F., Rodriguez-Rodriguez, M. P., Povh, J. A., Poveda-Parra, A. R., Otonel, R. A. A.,... Ribeiro, R. P. (2016). Cross-amplification of heterologous microsatellite markers in Rhamdia quelen and Leporinus elongatus. Semina: Ciências Agrarias, 37(1), 517-524. doi: 10.5433/ 1679-0359.2016v37n1p517
Nei, M. (1978). Estimation of average heterozygosity and genetic distance from a small number of individuals. Genetics, 89(3), 583-590.
Oliveira, E. J., Pádua, J. G., Zucchi, M. I., Vencovsky, R., & Vieira, M. L. C. (2006). Origin, evolution and genome distribution of microsatellites. Genetics and Molecular Biology, 29(2), 294-307. doi: 10.1590/ S1415-47572006000200018
Parveen, S., Abbas, K., Afzal, M., & Hussain, M. (2018). Prediction of potential hybridization between three major carps in ravi river (Punjab, Pakistan) basin by using microsatellite markers. Turkish Journal of Fisheries and Aquatic Sciences, 18(1), 27-35. doi: 10.4194/1303-2712-v18_1_04.
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/bts 460
Petersen, R. L., Garcia, J. E., Mello, G., Liedke, A. M. R., Sincero, T. C. M., & Grisard, E. C. (2012). Análise da diversidade genética de tilápias cultivadas no estado de Santa Catarina (Brasil) utilizando marcadores microssatélites. Boletim do Instituto de Pesca, 38(4), 313-321.
Prado, F. D., Pardo, B. G., Guerra-Varela, J., Senhorini, J. A., Martínez, P., Foresti, F., & Porto-Foresti, F. (2014). Development and characterization of 16 microsatellites for the Neotropical catfish Pseudoplatystoma reticulatum and cross species analysis. Conservation Genetics Resources, 6(3), 679-681. doi: 10.1007/s12686-014-0180-1
Ramírez-Gil, H., & Ajiaco-Martínez, R. (1997). Aspectos preliminares de la biologia pesquera del Yaque, Leiarius marmoratus (Guii, 1870) (pisces: siluriformes: pimelodidae) en la parte alta del rio Meta (Orinoquia colombiana). Boletín Científico INPA 1997. Recuperado de https://www.worldcat.org/title/ aspectos-preliminares-de-la-biologia-pesquera-del-yaque-leiarius-marmoratus-guii-1870-pisces-siluriformes-pimelodidae-en-la-parte-alta-del-rio-meta-orinoquia-colombiana/oclc/819847273
Revaldaves, E., Pereira, L. H. G., Foresti, F., & Oliveira, C. (2005). Isolation and characterization of microsatellite loci in Pseudoplatystoma corruscans (Siluriformes: Pimelodidae) and cross-species amplification. Molecular Ecology Notes, 5(3), 463-465. doi: 10.1111/j.1471-8286.2005.00883.x
Rodrigues, M. D. N., Moreira, C. G. A., Gutierrez, H. J. P., Almeida, D. B., Junoir, D. S., & Moreira, H. L. M. (2015). Development of microsatellite markers for use in breeding catfish, Rhamdia sp. African Journal of Biotechnology, 14(5), 400-411. doi: 10.5897/AJB2014.14116
Sanches, A., & Galetti, P. M. (2006). Microsatellites loci isolated in the freshwater fish Brycon hilarii. Molecular Ecology Notes, 6(4), 1045-1046. doi: 10.1111/j.1471-8286.2006.01427.x
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
Saulo-Machado, A. C., Formiga, K. M., Ortiz, M. F., Sousa, A. C. B., Alves-Gomes, J. A., & Batista, J. S. (2011). Polymorphic microsatellite DNA markers for the Amazonian catfish Pseudoplatystoma punctifer (Siluriformes: Pimelodidae). Conservation Genetics Resources, 3(2), 307-310. doi: 10.1007/ s12686-010-9349-4
Souza, F. P., Lima, E. C. S., Leite, N. G., Urrea-Rojas, A. M., Yamachita, A. L., Pandolfi, V. C. F., & Lopera-Barrero, N. M. (2018a). Transferability of heterologous microsatellite primers in Brycon gouldingi. Ciência Rural, 48(11), 1-6. doi: 10.1590/0103-8478cr20180412
Souza, F. P., Urrea-Rojas, A. M., Ruas, C. F., Povh, J. A., Ribeiro, R. P., Ruas, E. A.,... Lopera-Barrero, N. M. (2018b). Novel microsatellite markers for the endangered neotropical fish Brycon orbignyanus and cross-amplification in related species. Italian Journal of Animal Science, 17(4), 916-920. doi: 10.1080/ 1828051X.2018.1436008
Van Oosterhout, C., Hutchinson, W. F., Wills, D. P., & Shipley, P. (2004). MICRO CHECKER: software for identifying and correcting genotyping errors in microsatellite data. Molecular Ecology Notes, 4(3), 535-538. doi: 10.1111/j.1471-8286.2004.00684.x
Araújo, J. Ê. X. S., Streit, D. P, Jr., Ribeiro, J. S. A., Martins, E. F. F., Souza, F. N., Oliveira, C. A. L.,... Povh, J. A. (2014). Ovopel and carp pituitary extract as spawning inducers in males of the Amazon Catfish Leiarius marmoratus (Gill, 1970). Brazilian Archives of Biology and Technology, 7(6), 882-886. doi: 10.1590/S1516-8913201402469
Barbosa, A. C. D. R., Correa, T. C., Galzerani, F., Galetti, P. M., & Hatanaka, T. (2006). Thirteen polymorphic microsatellite loci in the Neotropical fish Prochilodus argenteus (Characiformes, Prochilodontidae). Molecular Ecology Notes, 6(3), 936-938. doi: 10.1111/j.1471-8286.2006.01406.x
Barroso, R. M., Hilsdorf, A. W. S., Moreira, H. L. M., Mello, A. M., Guimarães, S. E. F., Cabello, P. H., & Traub-Cseko, M. (2003). Identification and characterization of microsatellites loci in Brycon opalinus (Cuvier, 1819) (Characiforme, Characidae, Bryconiae). Molecular Ecology Notes, 3(2), 297-298. doi: 10.1046/j.1471-8286.2003.00435.x
Batista, J. S. (2010). Caracterização genética da dourada - Brachyplatystoma rousseauxii, Castelnau, 1855 (Siluriformes: Pimelodidae) na Amazônia por meio de marcadores moleculares mitocondriais e microssatélites: subsídios para conservação e manejo. Manaus: Instituto Nacional de Pesquisas da Amazônia 2010. Recuperado de https://bdtd.inpa.gov.br/handle/tede/721
Calcagnotto, D., Russello, M., & DeSalle, R. (2001). Isolation and characterization of microsatellite loci in Piaractus mesopotamicus and their applicability in other Serrasalminae fish. Molecular Ecology Notes, 1(4), 245-247. doi: 10.1046/j.1471-8278.2001.00091.x
Carmo, F. M. S., Polo, É. M., Silva, M. A., & Yazbeck, G. M. (2015). Optimization of heterologous microsatellites in Piracanjuba. Pesquisa Agropecuária Brasileira, 50(12), 1236-1239. doi: 10.1590/ S0100-204X2015001200015
Carvalho Lima, T. P., Egito, A. A., Feijó, G. L. D., Arruda Mauro, R., & Ferraz, A. L. J. (2017). Molecular identification and phylogenetic analysis of Siluriformes from the Paraguay River basin, Brazil. Mitochondrial DNA Part A, 28(4), 536-543. doi: 10.3109/24701394.2016.1149825
Castro, P. L., Ribeiro, R. P., Santos, S. C. A., Goes, E. S. R., Souza, F. P., Poveda-Parra, A. R., Lopera-Barrero, N. M. (2017). Cross-amplification of heterologous microsatellite markers in Piracanjuba. Ciência Rural, 47(12), 1-6. doi: 10.1590/0103-8478cr20170374
Cruz-Casallas, N. E., Marciales-Caro, L., Díaz-Olarte, J. J., & Cruz-Casallas, P. E. (2010). Desempeño productivo del yaque (Leiarius marmoratus Gill, 1870) bajo diferentes densidades de siembra en estanques en tierra. Revista Colombiana de Ciencias Pecuárias, 23(3), 325-335.
Esquer-Garrigos, Y., Hugueny, B., Ibañez, C., Zepita, C., Koerner, K., Lambourdière, J., Couloux A., & Gaubert, P. (2015). Detecting natural hybridization between two vulnerable Andean pupfishes (Orestias agassizii and O. luteus) representative of the Altiplano endemic fisheries. Conservation Genetics, 16(3), 717-727. doi: 10.1007/s10592-015-0695-3
Ferraris, C. J. (2007). Checklist of catfishes, recent and fossil (Osteichthyes: Siluriformes), and catalogue of siluriform primary types. Zootaxa, 1418(1), 1-628. doi: 10.11646/zootaxa.1418.1.1
Food and Agriculture Organization (2018). The State of World Fisheries and Aquaculture 2018 - Meeting the sustainable development goals (Vol. 35). Rome: FAO.
Goudet, J. (2001). FSTAT: A program to estimate and test gene diversities and fixation indices (version 2.9.3.2). Retrieved from https://www.scienceopen.com/document?vid=79097bb4-ec3c-47c3-94a1-47085d721e6b
Hashimoto, D. T., Prado, F. D., Foresti, F., & Porto-Foresti, F. (2016). Molecular identification of intergenus crosses involving catfish hybrids: risks for aquaculture production. Neotropical Ichthyology, 14(2), 1-8. doi: 10.1590/1982-0224-20150139
Hashimoto, D. T., Senhorini, J. A., Foresti, F., Martínez, P., & Porto-Foresti, F. (2014). Genetic identification of F1 and Post-F1 serrasalmid juvenile hybrids in brazilian aquaculture. PLoS One, 9(3), 1-8. doi: 10.1371/journal.pone.0089902
Lima, J. S., Telles, M. P. C., Resende, L. V., Gouveia, F. O., Boni, T. A., & Sanches, A. C. (2008). Amplificação cruzada e padronização de marcadores microssatélites em Colossoma macropomum (tambaqui). Revista de Biologia Neotropical, 5(2), 41-49. doi: 10.5216/rbn.v5i2.9821
Lopera-Barrero, N. M., Ribeiro, R. P., Povh, J. A., Mendes, L. D. V. & Poveda-Parra, A. R. (2011). Produção de organismos aquáticos: Uma visão geral do Brasil e no Mundo. Guaíba, RS: Editora Agrolivros.
Lopera-Barrero, N. M., Povh, J. A., Ribeiro, R, P., Gomes, P. C., Jacometo, C. B., & Lopes, T. S. (2008). Comparación de protocolos de extracción de ADN con muestras de aleta y larva de peces: extracción modificada con cloruro de sodio. Ciencia e Investigación Agraria, 35(1), 15-24. doi: 10.4067/S0718-16202008000100008
Lopera-Barrero, N. M., Tanamati, F., Rodriguez-Rodriguez, M. P., Povh, J. A., Poveda-Parra, A. R., Otonel, R. A. A.,... Ribeiro, R. P. (2016). Cross-amplification of heterologous microsatellite markers in Rhamdia quelen and Leporinus elongatus. Semina: Ciências Agrarias, 37(1), 517-524. doi: 10.5433/ 1679-0359.2016v37n1p517
Nei, M. (1978). Estimation of average heterozygosity and genetic distance from a small number of individuals. Genetics, 89(3), 583-590.
Oliveira, E. J., Pádua, J. G., Zucchi, M. I., Vencovsky, R., & Vieira, M. L. C. (2006). Origin, evolution and genome distribution of microsatellites. Genetics and Molecular Biology, 29(2), 294-307. doi: 10.1590/ S1415-47572006000200018
Parveen, S., Abbas, K., Afzal, M., & Hussain, M. (2018). Prediction of potential hybridization between three major carps in ravi river (Punjab, Pakistan) basin by using microsatellite markers. Turkish Journal of Fisheries and Aquatic Sciences, 18(1), 27-35. doi: 10.4194/1303-2712-v18_1_04.
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/bts 460
Petersen, R. L., Garcia, J. E., Mello, G., Liedke, A. M. R., Sincero, T. C. M., & Grisard, E. C. (2012). Análise da diversidade genética de tilápias cultivadas no estado de Santa Catarina (Brasil) utilizando marcadores microssatélites. Boletim do Instituto de Pesca, 38(4), 313-321.
Prado, F. D., Pardo, B. G., Guerra-Varela, J., Senhorini, J. A., Martínez, P., Foresti, F., & Porto-Foresti, F. (2014). Development and characterization of 16 microsatellites for the Neotropical catfish Pseudoplatystoma reticulatum and cross species analysis. Conservation Genetics Resources, 6(3), 679-681. doi: 10.1007/s12686-014-0180-1
Ramírez-Gil, H., & Ajiaco-Martínez, R. (1997). Aspectos preliminares de la biologia pesquera del Yaque, Leiarius marmoratus (Guii, 1870) (pisces: siluriformes: pimelodidae) en la parte alta del rio Meta (Orinoquia colombiana). Boletín Científico INPA 1997. Recuperado de https://www.worldcat.org/title/ aspectos-preliminares-de-la-biologia-pesquera-del-yaque-leiarius-marmoratus-guii-1870-pisces-siluriformes-pimelodidae-en-la-parte-alta-del-rio-meta-orinoquia-colombiana/oclc/819847273
Revaldaves, E., Pereira, L. H. G., Foresti, F., & Oliveira, C. (2005). Isolation and characterization of microsatellite loci in Pseudoplatystoma corruscans (Siluriformes: Pimelodidae) and cross-species amplification. Molecular Ecology Notes, 5(3), 463-465. doi: 10.1111/j.1471-8286.2005.00883.x
Rodrigues, M. D. N., Moreira, C. G. A., Gutierrez, H. J. P., Almeida, D. B., Junoir, D. S., & Moreira, H. L. M. (2015). Development of microsatellite markers for use in breeding catfish, Rhamdia sp. African Journal of Biotechnology, 14(5), 400-411. doi: 10.5897/AJB2014.14116
Sanches, A., & Galetti, P. M. (2006). Microsatellites loci isolated in the freshwater fish Brycon hilarii. Molecular Ecology Notes, 6(4), 1045-1046. doi: 10.1111/j.1471-8286.2006.01427.x
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
Saulo-Machado, A. C., Formiga, K. M., Ortiz, M. F., Sousa, A. C. B., Alves-Gomes, J. A., & Batista, J. S. (2011). Polymorphic microsatellite DNA markers for the Amazonian catfish Pseudoplatystoma punctifer (Siluriformes: Pimelodidae). Conservation Genetics Resources, 3(2), 307-310. doi: 10.1007/ s12686-010-9349-4
Souza, F. P., Lima, E. C. S., Leite, N. G., Urrea-Rojas, A. M., Yamachita, A. L., Pandolfi, V. C. F., & Lopera-Barrero, N. M. (2018a). Transferability of heterologous microsatellite primers in Brycon gouldingi. Ciência Rural, 48(11), 1-6. doi: 10.1590/0103-8478cr20180412
Souza, F. P., Urrea-Rojas, A. M., Ruas, C. F., Povh, J. A., Ribeiro, R. P., Ruas, E. A.,... Lopera-Barrero, N. M. (2018b). Novel microsatellite markers for the endangered neotropical fish Brycon orbignyanus and cross-amplification in related species. Italian Journal of Animal Science, 17(4), 916-920. doi: 10.1080/ 1828051X.2018.1436008
Van Oosterhout, C., Hutchinson, W. F., Wills, D. P., & Shipley, P. (2004). MICRO CHECKER: software for identifying and correcting genotyping errors in microsatellite data. Molecular Ecology Notes, 4(3), 535-538. doi: 10.1111/j.1471-8286.2004.00684.x
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2020-08-07
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Pandolfi, V. C. F., Yamachita, A. L., Souza, F. P. de, Lima, E. C. S. de, Ayres, D. R., Bignardi, A. B., … Lopera-Barrero, N. M. (2020). Transferability of heterologous microsatellite primers in Leiarius marmoratus. Semina: Ciências Agrárias, 41(5supl1), 2297–2306. https://doi.org/10.5433/1679-0359.2020v41n5supl1p2297
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