Obtaining microsatellite markers for Pseudoplatystoma reticulatum using heterologous primers
DOI:
https://doi.org/10.5433/1679-0359.2021v42n3p1323Keywords:
Brachyplatystoma rousseauxi, Cachara, Genetic variability, Heterologous markers, Population genetics, Pseudoplatystoma punctifer.Abstract
Studies on genetic composition in fish populations contribute to conservationist practices and inbreeding control in fish stocks. To this end, molecular tools such as microsatellite markers (SSRs) are often used, but they are expensive and time-consuming to develop. A species-specific heterologous marker emerges as an alternative, which can be used in taxonomically related species in a fast way. Our goal was to test SSRs markers of Brachyplatystoma rousseauxi and Pseudoplatystoma punctifer in P. reticulatum in an unprecedented way. For this purpose, DNA was extracted from fragments of the caudal fin of 222 P. reticulatum adults, using a NaCl-based method. Then, DNA samples were amplified by Polymerase Chain Reaction (PCR) using six markers, four from B. rousseauxi (BR38, 47, 51, and 61) and two from P. punctifer (PPU13 and PPU15). Two primers showed non-specific amplification and were disregarded (BR38 and PPU13). In the remaining four primers, the number of alleles per locus varied between two (BR47) to sixteen (BR51), and the average size of alleles was between 142 and 400 bp. Mean effective number of alleles per locus ranged from 10,650 (BR51) to 1,784 (BR47), with null or low-frequency alleles in all studied loci. Observed heterozygosity ranged from 0.299 (BR47) to 0.640 (BR51) and was always lower than the expected heterozygosity. Hardy-Weinberg balance was significant (p < 0.05) in all loci, and inbreeding coefficient (FIS) was always positive. Polymorphic Information Content (PIC) confirmed the efficiency of the markers since they had moderate (BR47) to high levels of information (BR51, BR61, and PPU15). Transferability test showed that the heterologous microsatellite molecular markers, originally for B. rousseauxi and P. punctifer, were efficient in P. reticulatum, producing three primers with high information content. Therefore, these markers can be safely used in future population studies of this species.References
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Castro, P. L., Ribeiro, R. P., Alves, S. C., Goes, E. S., Souza, F. P., Poveda-Parra, A. R.,... Lopera-Barrero, N. M. (2017). Cross-amplification of heterologous microsatellite markers in Piracanjuba. Ciência Rural, 47(12), e20170374. doi: 10.1590/0103-8478cr20170374
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Maduna, S. N., Rossouw, C., Roodt-Wilding, R., & Merwe, A. E. B. (2014). Microsatellite cross-species amplification and utility in southern African elasmobranchs: a valuable resource for fisheries management and conservation. BMC Research Notes, 7(352), 1-12. doi: 10.1186/1756-0500-7-352
Mantovani, L. S. C. (2018). Diversidade genética em estoques de jundiá da Amazônia (Leirarius marmoratus). Dissertação de mestrado, Universidade Estadual de Maringá, Maringá, Paraná, Brasil. Recuperado de http://repositorio.uem.br:8080/jspui/handle/1/4715
Ochoa, L. E., Pereira, L. H. G., Costa-Silva, G. J., Roxo, F. F., Batista, J. S., Formiga, K.,... Oliveira, C. (2015). Genetic structure and historical diversification of catfish Brachyplatystoma platynemum (Siluriformes: Pimelodidae) in the Amazon basin with implications for its conservation. Phylogeography of B. platynemum. Ecology and Evolution, 5(10), 2005-2020. doi: 10.1002/ece3.1486
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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 Genetic Resource, 6(1), 679-681. doi: 10.1007/s12686-014-0180-1.
Povh, J. A., Ribeiro, R. P., Sirol, R. N., Streit, D. P., Jr., Moreira, H. L. M., Siewerdt, F.,... Vargas, L. (2010). Microsatellite analysis of the parental contribution of Piaractus mesopotamicus to the production of offspring in the semi-natural system of reproduction. Brazilian Archives of Biology and Technology, 53(2), 389-396. doi: 10.1590/S1516-89132010000200018
Ribeiro, R. P., Rodriguez-Rodriguez, M. P., Resende, E. K., Pinheiro, F. S., Povh, J. A., Poveda-Parra, A. R.,… Lopera-Barrero, N. M. (2016). Caracterização genética de estoques de Tambaqui do Estado de Rondônia (Brasil): implicações na produção e na conservação. Semina: Ciências Agrárias, 37(4), 2375-2385. doi: 10.5433/1679-0359.2016v37n4Supl1p2375
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 Genetic Resource, 3(2), 307-310. doi: 10.1007/s12 686-010-9349-4
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. (2018). Transferability of heterologous microsatellite primers in Brycon gouldingi. Ciência Rural, 48(11), 1-6. doi: 10.1590/0103-8478cr20180412
Sudheer, P. D. V., Mastan, N. S. G., Rahman, H., Ravi Prakash, C., Singh, S., & Reddy, M. P. (2011). Cross species amplification ability of novel microsatellites isolated from Jatropha curcas and genetic relationship with sister taxa: cross species amplification and genetic relationship of Jatropha using novel microsatellites. Molecular Biology Reports, 38(2), 1383-1388. doi: 10.1007/s11033-010-0241-9
Sun, D. Q., Li, H. Y., Xu, T. J., & Wang, R. X. (2012). Development of microsatellite markers for the small yellow croaker Larimichthys polyactis (Sciaenidae) by cross-species amplification. Genetics and Molecular Research, 11(2), 1469-1474. doi: 10.4238/2012
Virmond, M., Conceição, D., Amaral, H., Jr., & Petersen, R. L. (2017). Genetic variability of captive populations of Rhamdia quelen (Teleostei: Pimelodidae) using microsatellite markers. Biotemas, 30(4), 51-58. doi: 10.5007/2175-7925.2017v30n4p51
Abdul-Muneer, P. M. (2014). Application of microsatellite markers in conservation genetics and fisheries management: recent advances in population structure analysis and conservation strategies: review article. Genetics Research International, 2014(6), 1-11. doi: 10.1155/2014/691759
Albuquerque, D. M., Oliveira, A. L., Rodriguez Rodriguez, M. D., & Ribeiro, R. P. (2020). Variabilidade genética de Pseudoplatystoma reticulatum de um programa de melhoramento genético no Brasil. Revista Ciência Agronômica, 51(1), e20164786. doi: 10.5935/1806-6690.20200007
Bassam, B. J., Caetano-Anollés, G., & Gresshoff, P. M. (1991). Fast and sensitive silver staining of DNA in polyacrylamide gels. Analytical Biochemistry, 196(1), 80-83. doi: 10.1016/0003-2697(91)90120-i
Batista, J. S., Farias, I. P., Formiga-Aquino, K., Sousa, A. C. B., & Alves-Gomes, J. A. (2010). DNA microsatellite markers for ‘‘dourada’’ (Brachyplatystoma rousseauxii, Siluriformes: Pimelodidae), a migratory catfish of utmost importance for fisheries in the Amazon: development, characterization and inter-specific amplification. Conservation Genetic Resources, 2(1), 5-10. doi: 10.1007/s12686-009-91 17-5
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.
Brazilian Association of Fish Farming (2020). Anuário peixe BR da piscicultura. São Paulo, SP: Autor.
Calcagnotto, D., & DeSalle, R. (2009). Population genetic structuring in pacu (Piaractus mesopotamicus) across the Paraná-Paraguay basin: evidence from microsatellites. Neotropical Ichthyology, 7(4), 607-616. doi: 10.1590/S1679-62252009000400008
Campos, J. L. (2010). O cultivo do pintado (Pseudoplatystoma corruscans, Spix; Agassiz, 1829), outras espécies do gênero Pseudoplatystoma e seus híbridos. In B. Baldisserotto, & L. C. Gomes (Eds.), Espécies nativas para piscicultura no Brasil (pp. 335-361). Santa Maria, RS: Ed. da UFSM.
Carvalho, D. C., Seerig, A. S., Brasil, B. S. A. F., Crepaldi, D. V., & Oliveria, D. A. A. (2013). Molecular identification of the hybrid between the catfish species Pseudoplatystoma corruscans and Pseudoplatystoma reticulatum using a set of eight microsatellite markers. Journal of Fish Biology, 83(3), 671-676. doi: 10.1111/jfb.12194
Castro, P. L., Ribeiro, R. P., Alves, S. C., Goes, E. S., Souza, F. P., Poveda-Parra, A. R.,... Lopera-Barrero, N. M. (2017). Cross-amplification of heterologous microsatellite markers in Piracanjuba. Ciência Rural, 47(12), e20170374. doi: 10.1590/0103-8478cr20170374
Kalinowski, S. T., Taper, M. L., & Marshall, T. C. (2007). Revising how the computer program CERVUS accommodates genotyping error increases success in paternity assignment. Molecular Ecology, 16(5), 1099-1106. doi: 10.1111/j.1365-294X.2007.03089.x
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 com muestras de aleta y larva de peces: extracción modificada con sal (NaCl). Ciencia e Investigación Agraria, 35(1), 15-24. doi: 10.4067/S0718-162020 08000100008
Lopera-Barrero, N. M., Povh, J. A., Sirol, R. N., Rodriguez-Rodriguez, M. P., Lima, E. C. S., Poveda-Parra, A. R.,… Ribeiro, R. P. (2016). Genetic diversity of pacu and piapara broodstocks in restocking programs in the rivers Paraná and Paranapanema (Brazil). Semina: Ciências Agrárias, 37(4), 2365-2374. doi: 10.5433/1679-0359.2016v37n4Supl1p2365
Maduna, S. N., Rossouw, C., Roodt-Wilding, R., & Merwe, A. E. B. (2014). Microsatellite cross-species amplification and utility in southern African elasmobranchs: a valuable resource for fisheries management and conservation. BMC Research Notes, 7(352), 1-12. doi: 10.1186/1756-0500-7-352
Mantovani, L. S. C. (2018). Diversidade genética em estoques de jundiá da Amazônia (Leirarius marmoratus). Dissertação de mestrado, Universidade Estadual de Maringá, Maringá, Paraná, Brasil. Recuperado de http://repositorio.uem.br:8080/jspui/handle/1/4715
Ochoa, L. E., Pereira, L. H. G., Costa-Silva, G. J., Roxo, F. F., Batista, J. S., Formiga, K.,... Oliveira, C. (2015). Genetic structure and historical diversification of catfish Brachyplatystoma platynemum (Siluriformes: Pimelodidae) in the Amazon basin with implications for its conservation. Phylogeography of B. platynemum. Ecology and Evolution, 5(10), 2005-2020. doi: 10.1002/ece3.1486
Oosterhout, C. V., Hutchinson, W. F., Wills, D. P. M., & Peter, S. (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.ISSN 1365-294X
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
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 Genetic Resource, 6(1), 679-681. doi: 10.1007/s12686-014-0180-1.
Povh, J. A., Ribeiro, R. P., Sirol, R. N., Streit, D. P., Jr., Moreira, H. L. M., Siewerdt, F.,... Vargas, L. (2010). Microsatellite analysis of the parental contribution of Piaractus mesopotamicus to the production of offspring in the semi-natural system of reproduction. Brazilian Archives of Biology and Technology, 53(2), 389-396. doi: 10.1590/S1516-89132010000200018
Ribeiro, R. P., Rodriguez-Rodriguez, M. P., Resende, E. K., Pinheiro, F. S., Povh, J. A., Poveda-Parra, A. R.,… Lopera-Barrero, N. M. (2016). Caracterização genética de estoques de Tambaqui do Estado de Rondônia (Brasil): implicações na produção e na conservação. Semina: Ciências Agrárias, 37(4), 2375-2385. doi: 10.5433/1679-0359.2016v37n4Supl1p2375
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 Genetic Resource, 3(2), 307-310. doi: 10.1007/s12 686-010-9349-4
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. (2018). Transferability of heterologous microsatellite primers in Brycon gouldingi. Ciência Rural, 48(11), 1-6. doi: 10.1590/0103-8478cr20180412
Sudheer, P. D. V., Mastan, N. S. G., Rahman, H., Ravi Prakash, C., Singh, S., & Reddy, M. P. (2011). Cross species amplification ability of novel microsatellites isolated from Jatropha curcas and genetic relationship with sister taxa: cross species amplification and genetic relationship of Jatropha using novel microsatellites. Molecular Biology Reports, 38(2), 1383-1388. doi: 10.1007/s11033-010-0241-9
Sun, D. Q., Li, H. Y., Xu, T. J., & Wang, R. X. (2012). Development of microsatellite markers for the small yellow croaker Larimichthys polyactis (Sciaenidae) by cross-species amplification. Genetics and Molecular Research, 11(2), 1469-1474. doi: 10.4238/2012
Virmond, M., Conceição, D., Amaral, H., Jr., & Petersen, R. L. (2017). Genetic variability of captive populations of Rhamdia quelen (Teleostei: Pimelodidae) using microsatellite markers. Biotemas, 30(4), 51-58. doi: 10.5007/2175-7925.2017v30n4p51
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2021-03-19
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Penafort, J. M., Mantovani, L. S. C., Granzoto, G. H., Castro, P. L. de, Alves, L. F. de S., Souza, F. P. de, … Ribeiro, R. P. (2021). Obtaining microsatellite markers for Pseudoplatystoma reticulatum using heterologous primers. Semina: Ciências Agrárias, 42(3), 1323–1334. https://doi.org/10.5433/1679-0359.2021v42n3p1323
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