Development of a multi-species SNP array for serrasalmid fish Colossoma macropomum and Piaractus mesopotamicus
Autor(a) principal: | |
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Data de Publicação: | 2021 |
Outros Autores: | , , , , , , , , , , , |
Tipo de documento: | Artigo |
Idioma: | eng |
Título da fonte: | Repositório Institucional da UNESP |
Texto Completo: | http://dx.doi.org/10.1038/s41598-021-98885-x http://hdl.handle.net/11449/229638 |
Resumo: | Scarce genomic resources have limited the development of breeding programs for serrasalmid fish Colossoma macropomum (tambaqui) and Piaractus mesopotamicus (pacu), the key native freshwater fish species produced in South America. The main objectives of this study were to design a dense SNP array for this fish group and to validate its performance on farmed populations from several locations in South America. Using multiple approaches based on different populations of tambaqui and pacu, a final list of 29,575 and 29,612 putative SNPs was selected, respectively, to print an Axiom AFFYMETRIX (THERMOFISHER) SerraSNP array. After validation, 74.17% (n = 21,963) and 71.25% (n = 21,072) of SNPs were classified as polymorphic variants in pacu and tambaqui, respectively. Most of the SNPs segregated within each population ranging from 14,199 to 19,856 in pacu; and from 15,075 to 20,380 in tambaqui. Our results indicate high levels of genetic diversity and clustered samples according to their hatchery origin. The developed SerraSNP array represents a valuable genomic tool approaching in-depth genetic studies for these species. |
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Development of a multi-species SNP array for serrasalmid fish Colossoma macropomum and Piaractus mesopotamicusScarce genomic resources have limited the development of breeding programs for serrasalmid fish Colossoma macropomum (tambaqui) and Piaractus mesopotamicus (pacu), the key native freshwater fish species produced in South America. The main objectives of this study were to design a dense SNP array for this fish group and to validate its performance on farmed populations from several locations in South America. Using multiple approaches based on different populations of tambaqui and pacu, a final list of 29,575 and 29,612 putative SNPs was selected, respectively, to print an Axiom AFFYMETRIX (THERMOFISHER) SerraSNP array. After validation, 74.17% (n = 21,963) and 71.25% (n = 21,072) of SNPs were classified as polymorphic variants in pacu and tambaqui, respectively. Most of the SNPs segregated within each population ranging from 14,199 to 19,856 in pacu; and from 15,075 to 20,380 in tambaqui. Our results indicate high levels of genetic diversity and clustered samples according to their hatchery origin. The developed SerraSNP array represents a valuable genomic tool approaching in-depth genetic studies for these species.Comisión Nacional de Investigación Científica y TecnológicaConselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)São Paulo State University (Unesp) Aquaculture Center of UnespFacultad de Ciencias Veterinarias y Pecuarias Universidad de ChileFacultad de Zootecnia Universidad Nacional Agraria de la SelvaFacultad de Ciencias Agrarias Universidad de AntioquiaSão Paulo State University (Unesp) Aquaculture Center of UnespCNPq: 140740/2016–3FAPESP: 2016/18294–9FAPESP: 2016/21011–9FAPESP: 2017/19717-3CNPq: 311559/2018–2Universidade Estadual Paulista (UNESP)Universidad de ChileUniversidad Nacional Agraria de la SelvaUniversidad de AntioquiaMastrochirico-Filho, Vito A. [UNESP]Ariede, Raquel B. [UNESP]Freitas, Milena V. [UNESP]Borges, Carolina H. S. [UNESP]Lira, Lieschen V. G. [UNESP]Mendes, Natália J. [UNESP]Agudelo, John F. G. [UNESP]Cáceres, PabloBerrocal, Milthon H. M.Sucerquia, Gustavo A. L.Porto-Foresti, Fabio [UNESP]Yáñez, José M.Hashimoto, Diogo T. [UNESP]2022-04-29T08:34:55Z2022-04-29T08:34:55Z2021-12-01info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articlehttp://dx.doi.org/10.1038/s41598-021-98885-xScientific Reports, v. 11, n. 1, 2021.2045-2322http://hdl.handle.net/11449/22963810.1038/s41598-021-98885-x2-s2.0-85116350058Scopusreponame:Repositório Institucional da UNESPinstname:Universidade Estadual Paulista (UNESP)instacron:UNESPengScientific Reportsinfo:eu-repo/semantics/openAccess2024-04-09T15:36:43Zoai:repositorio.unesp.br:11449/229638Repositório InstitucionalPUBhttp://repositorio.unesp.br/oai/requestopendoar:29462024-08-05T19:26:08.334287Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP)false |
dc.title.none.fl_str_mv |
Development of a multi-species SNP array for serrasalmid fish Colossoma macropomum and Piaractus mesopotamicus |
title |
Development of a multi-species SNP array for serrasalmid fish Colossoma macropomum and Piaractus mesopotamicus |
spellingShingle |
Development of a multi-species SNP array for serrasalmid fish Colossoma macropomum and Piaractus mesopotamicus Mastrochirico-Filho, Vito A. [UNESP] |
title_short |
Development of a multi-species SNP array for serrasalmid fish Colossoma macropomum and Piaractus mesopotamicus |
title_full |
Development of a multi-species SNP array for serrasalmid fish Colossoma macropomum and Piaractus mesopotamicus |
title_fullStr |
Development of a multi-species SNP array for serrasalmid fish Colossoma macropomum and Piaractus mesopotamicus |
title_full_unstemmed |
Development of a multi-species SNP array for serrasalmid fish Colossoma macropomum and Piaractus mesopotamicus |
title_sort |
Development of a multi-species SNP array for serrasalmid fish Colossoma macropomum and Piaractus mesopotamicus |
author |
Mastrochirico-Filho, Vito A. [UNESP] |
author_facet |
Mastrochirico-Filho, Vito A. [UNESP] Ariede, Raquel B. [UNESP] Freitas, Milena V. [UNESP] Borges, Carolina H. S. [UNESP] Lira, Lieschen V. G. [UNESP] Mendes, Natália J. [UNESP] Agudelo, John F. G. [UNESP] Cáceres, Pablo Berrocal, Milthon H. M. Sucerquia, Gustavo A. L. Porto-Foresti, Fabio [UNESP] Yáñez, José M. Hashimoto, Diogo T. [UNESP] |
author_role |
author |
author2 |
Ariede, Raquel B. [UNESP] Freitas, Milena V. [UNESP] Borges, Carolina H. S. [UNESP] Lira, Lieschen V. G. [UNESP] Mendes, Natália J. [UNESP] Agudelo, John F. G. [UNESP] Cáceres, Pablo Berrocal, Milthon H. M. Sucerquia, Gustavo A. L. Porto-Foresti, Fabio [UNESP] Yáñez, José M. Hashimoto, Diogo T. [UNESP] |
author2_role |
author author author author author author author author author author author author |
dc.contributor.none.fl_str_mv |
Universidade Estadual Paulista (UNESP) Universidad de Chile Universidad Nacional Agraria de la Selva Universidad de Antioquia |
dc.contributor.author.fl_str_mv |
Mastrochirico-Filho, Vito A. [UNESP] Ariede, Raquel B. [UNESP] Freitas, Milena V. [UNESP] Borges, Carolina H. S. [UNESP] Lira, Lieschen V. G. [UNESP] Mendes, Natália J. [UNESP] Agudelo, John F. G. [UNESP] Cáceres, Pablo Berrocal, Milthon H. M. Sucerquia, Gustavo A. L. Porto-Foresti, Fabio [UNESP] Yáñez, José M. Hashimoto, Diogo T. [UNESP] |
description |
Scarce genomic resources have limited the development of breeding programs for serrasalmid fish Colossoma macropomum (tambaqui) and Piaractus mesopotamicus (pacu), the key native freshwater fish species produced in South America. The main objectives of this study were to design a dense SNP array for this fish group and to validate its performance on farmed populations from several locations in South America. Using multiple approaches based on different populations of tambaqui and pacu, a final list of 29,575 and 29,612 putative SNPs was selected, respectively, to print an Axiom AFFYMETRIX (THERMOFISHER) SerraSNP array. After validation, 74.17% (n = 21,963) and 71.25% (n = 21,072) of SNPs were classified as polymorphic variants in pacu and tambaqui, respectively. Most of the SNPs segregated within each population ranging from 14,199 to 19,856 in pacu; and from 15,075 to 20,380 in tambaqui. Our results indicate high levels of genetic diversity and clustered samples according to their hatchery origin. The developed SerraSNP array represents a valuable genomic tool approaching in-depth genetic studies for these species. |
publishDate |
2021 |
dc.date.none.fl_str_mv |
2021-12-01 2022-04-29T08:34:55Z 2022-04-29T08:34:55Z |
dc.type.status.fl_str_mv |
info:eu-repo/semantics/publishedVersion |
dc.type.driver.fl_str_mv |
info:eu-repo/semantics/article |
format |
article |
status_str |
publishedVersion |
dc.identifier.uri.fl_str_mv |
http://dx.doi.org/10.1038/s41598-021-98885-x Scientific Reports, v. 11, n. 1, 2021. 2045-2322 http://hdl.handle.net/11449/229638 10.1038/s41598-021-98885-x 2-s2.0-85116350058 |
url |
http://dx.doi.org/10.1038/s41598-021-98885-x http://hdl.handle.net/11449/229638 |
identifier_str_mv |
Scientific Reports, v. 11, n. 1, 2021. 2045-2322 10.1038/s41598-021-98885-x 2-s2.0-85116350058 |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.relation.none.fl_str_mv |
Scientific Reports |
dc.rights.driver.fl_str_mv |
info:eu-repo/semantics/openAccess |
eu_rights_str_mv |
openAccess |
dc.source.none.fl_str_mv |
Scopus reponame:Repositório Institucional da UNESP instname:Universidade Estadual Paulista (UNESP) instacron:UNESP |
instname_str |
Universidade Estadual Paulista (UNESP) |
instacron_str |
UNESP |
institution |
UNESP |
reponame_str |
Repositório Institucional da UNESP |
collection |
Repositório Institucional da UNESP |
repository.name.fl_str_mv |
Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP) |
repository.mail.fl_str_mv |
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1808129068635258880 |