Obtaining microsatellite markers for Pseudoplatystoma reticulatum using heterologous primers
Main Author: | |
---|---|
Publication Date: | 2021 |
Other Authors: | , , , , , , , |
Format: | Article |
Language: | eng |
Source: | Semina. Ciências Agrárias (Online) |
Download full: | https://ojs.uel.br/revistas/uel/index.php/semagrarias/article/view/41215 |
Summary: | 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. |
id |
UEL-11_7f97a8ba22f0de9ae9840cebad0d17e5 |
---|---|
oai_identifier_str |
oai:ojs.pkp.sfu.ca:article/41215 |
network_acronym_str |
UEL-11 |
network_name_str |
Semina. Ciências Agrárias (Online) |
repository_id_str |
|
spelling |
Obtaining microsatellite markers for Pseudoplatystoma reticulatum using heterologous primersObtenção de marcadores microssatélites para Pseudoplatystoma reticulatum a partir de primers heterólogosBrachyplatystoma rousseauxiCacharaGenetic variabilityHeterologous markersPopulation geneticsPseudoplatystoma punctifer.B. rousseauxiiCacharaGenetic variabilityHeterologous markersPopulation geneticsP. punctifer.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.Estudos acerca da composição genética de populações de peixes contribuem para a elaboração de práticas conservacionista, bem como para controle da consanguinidade em estoques de piscicultura. Neste sentido, ferramentas moleculares como os marcadores microssatélites (SSR’s) são comumente utilizados, contudo, seu desenvolvimento corresponde a um processo caro e demorado. Surge como alternativa a utilização dos marcadores heterólogos, originalmente desenvolvidos para uma espécie, mas que podem ser utilizados de maneira rápida em outras taxonomicamente relacionadas. O objetivo desta pesquisa foi testar de maneira inédita a utilização de marcadores SSR’s de Brachyplatystoma rousseauxi e Pseudoplatystoma punctifer em P. reticulatum. Para tanto, foram extraídas amostras de DNA a partir de fragmentos de nadadeira caudal de 222 indivíduos adultos de P. reticulatum por metodologia a base de NaCl. As amostras foram então amplificadas por Reação em Cadeia da Polimerase (PCR) utilizando-se seis marcadores, quatro de B. rousseauxi (BR38, 47, 51 e 61) e dois de P. punctifer (PPU13 e PPU15). Dois primers apresentaram amplificação inespecífica e foram desconsiderados (BR38 e PPU13). Entre os quatro restantes, o número de alelos por locus variou entre dois (BR47) a dezesseis (BR51), com tamanho médio de alelos entre 142 e 400 pb. O número efetivo médio de alelos por locus variou de 10,650 (BR51) à 1,784 (BR47), com alelos nulos ou de baixa frequência presentes em todos os loci estudados. Os valores de heterozigosidade observada variaram de 0,299 (BR47) à 0,640 (BR51), e foram sempre menores que os de heterozigosidade esperada. O Equilíbrio de Hardy-Weinberg foi significativo (P < 0,05) em todos os locus e o coeficiente de endogamia Fis sempre apresentou valores positivos. Os valores de Conteúdo de Informação Polimórfica (PIC) confirmaram a eficiência dos marcadores utilizados, já que possuíram de moderado (BR47) a alto nível de informação (BR51, BR61 e PPU15). O teste de transferibilidade de marcadores moleculares microssatélites heterólogos, originalmente desenvolvidos para B. rousseauxi e P. punctifer em P. reticulatum se mostrou eficiente, produzindo três primers com alto nível de informação, fato que garante sua utilização segura em estudos populacionais futuros voltados à esta espécie.UEL2021-03-19info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionPesquisa Científicaapplication/pdfhttps://ojs.uel.br/revistas/uel/index.php/semagrarias/article/view/4121510.5433/1679-0359.2021v42n3p1323Semina: Ciências Agrárias; Vol. 42 No. 3 (2021); 1323-1334Semina: Ciências Agrárias; v. 42 n. 3 (2021); 1323-13341679-03591676-546Xreponame:Semina. Ciências Agrárias (Online)instname:Universidade Estadual de Londrina (UEL)instacron:UELenghttps://ojs.uel.br/revistas/uel/index.php/semagrarias/article/view/41215/29175Copyright (c) 2021 Semina: Ciências Agráriashttp://creativecommons.org/licenses/by-nc/4.0info:eu-repo/semantics/openAccessPenafort, Jefferson MuriciMantovani, Laís Santana CelestinoGranzoto, Gabriela HernandesCastro, Pedro Luiz deAlves, Luiz Fernando de SouzaSouza, Felipe Pinheiro deLopera-Barrero, Nelson MaurícioOliveira, Carlos Antônio Lopes deRibeiro, Ricardo Pereira2022-10-04T13:09:08Zoai:ojs.pkp.sfu.ca:article/41215Revistahttp://www.uel.br/revistas/uel/index.php/semagrariasPUBhttps://ojs.uel.br/revistas/uel/index.php/semagrarias/oaisemina.agrarias@uel.br1679-03591676-546Xopendoar:2022-10-04T13:09:08Semina. Ciências Agrárias (Online) - Universidade Estadual de Londrina (UEL)false |
dc.title.none.fl_str_mv |
Obtaining microsatellite markers for Pseudoplatystoma reticulatum using heterologous primers Obtenção de marcadores microssatélites para Pseudoplatystoma reticulatum a partir de primers heterólogos |
title |
Obtaining microsatellite markers for Pseudoplatystoma reticulatum using heterologous primers |
spellingShingle |
Obtaining microsatellite markers for Pseudoplatystoma reticulatum using heterologous primers Penafort, Jefferson Murici Brachyplatystoma rousseauxi Cachara Genetic variability Heterologous markers Population genetics Pseudoplatystoma punctifer. B. rousseauxii Cachara Genetic variability Heterologous markers Population genetics P. punctifer. |
title_short |
Obtaining microsatellite markers for Pseudoplatystoma reticulatum using heterologous primers |
title_full |
Obtaining microsatellite markers for Pseudoplatystoma reticulatum using heterologous primers |
title_fullStr |
Obtaining microsatellite markers for Pseudoplatystoma reticulatum using heterologous primers |
title_full_unstemmed |
Obtaining microsatellite markers for Pseudoplatystoma reticulatum using heterologous primers |
title_sort |
Obtaining microsatellite markers for Pseudoplatystoma reticulatum using heterologous primers |
author |
Penafort, Jefferson Murici |
author_facet |
Penafort, Jefferson Murici Mantovani, Laís Santana Celestino Granzoto, Gabriela Hernandes Castro, Pedro Luiz de Alves, Luiz Fernando de Souza Souza, Felipe Pinheiro de Lopera-Barrero, Nelson Maurício Oliveira, Carlos Antônio Lopes de Ribeiro, Ricardo Pereira |
author_role |
author |
author2 |
Mantovani, Laís Santana Celestino Granzoto, Gabriela Hernandes Castro, Pedro Luiz de Alves, Luiz Fernando de Souza Souza, Felipe Pinheiro de Lopera-Barrero, Nelson Maurício Oliveira, Carlos Antônio Lopes de Ribeiro, Ricardo Pereira |
author2_role |
author author author author author author author author |
dc.contributor.author.fl_str_mv |
Penafort, Jefferson Murici Mantovani, Laís Santana Celestino Granzoto, Gabriela Hernandes Castro, Pedro Luiz de Alves, Luiz Fernando de Souza Souza, Felipe Pinheiro de Lopera-Barrero, Nelson Maurício Oliveira, Carlos Antônio Lopes de Ribeiro, Ricardo Pereira |
dc.subject.por.fl_str_mv |
Brachyplatystoma rousseauxi Cachara Genetic variability Heterologous markers Population genetics Pseudoplatystoma punctifer. B. rousseauxii Cachara Genetic variability Heterologous markers Population genetics P. punctifer. |
topic |
Brachyplatystoma rousseauxi Cachara Genetic variability Heterologous markers Population genetics Pseudoplatystoma punctifer. B. rousseauxii Cachara Genetic variability Heterologous markers Population genetics P. punctifer. |
description |
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. |
publishDate |
2021 |
dc.date.none.fl_str_mv |
2021-03-19 |
dc.type.driver.fl_str_mv |
info:eu-repo/semantics/article info:eu-repo/semantics/publishedVersion Pesquisa Científica |
format |
article |
status_str |
publishedVersion |
dc.identifier.uri.fl_str_mv |
https://ojs.uel.br/revistas/uel/index.php/semagrarias/article/view/41215 10.5433/1679-0359.2021v42n3p1323 |
url |
https://ojs.uel.br/revistas/uel/index.php/semagrarias/article/view/41215 |
identifier_str_mv |
10.5433/1679-0359.2021v42n3p1323 |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.relation.none.fl_str_mv |
https://ojs.uel.br/revistas/uel/index.php/semagrarias/article/view/41215/29175 |
dc.rights.driver.fl_str_mv |
Copyright (c) 2021 Semina: Ciências Agrárias http://creativecommons.org/licenses/by-nc/4.0 info:eu-repo/semantics/openAccess |
rights_invalid_str_mv |
Copyright (c) 2021 Semina: Ciências Agrárias http://creativecommons.org/licenses/by-nc/4.0 |
eu_rights_str_mv |
openAccess |
dc.format.none.fl_str_mv |
application/pdf |
dc.publisher.none.fl_str_mv |
UEL |
publisher.none.fl_str_mv |
UEL |
dc.source.none.fl_str_mv |
Semina: Ciências Agrárias; Vol. 42 No. 3 (2021); 1323-1334 Semina: Ciências Agrárias; v. 42 n. 3 (2021); 1323-1334 1679-0359 1676-546X reponame:Semina. Ciências Agrárias (Online) instname:Universidade Estadual de Londrina (UEL) instacron:UEL |
instname_str |
Universidade Estadual de Londrina (UEL) |
instacron_str |
UEL |
institution |
UEL |
reponame_str |
Semina. Ciências Agrárias (Online) |
collection |
Semina. Ciências Agrárias (Online) |
repository.name.fl_str_mv |
Semina. Ciências Agrárias (Online) - Universidade Estadual de Londrina (UEL) |
repository.mail.fl_str_mv |
semina.agrarias@uel.br |
_version_ |
1799306083551936512 |