Genomic selection signatures in farmed Colossoma macropomum from tropical and subtropical regions in South America
Autor(a) principal: | |
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Data de Publicação: | 2022 |
Outros Autores: | , , , , , , , , , |
Tipo de documento: | Artigo |
Idioma: | eng |
Título da fonte: | Repositório Institucional da UNESP |
Texto Completo: | http://dx.doi.org/10.1111/eva.13351 http://hdl.handle.net/11449/230531 |
Resumo: | Tambaqui or cachama (Colossoma macropomum) is one of the most important neotropical freshwater fish used for aquaculture in South America, and its production is concentrated at low latitudes (close to the Equator, 0°), where the water temperature is warm. Therefore, understanding how selection shapes genetic variations and structure in farmed populations is of paramount importance in evolutionary biology. High-throughput sequencing to generate genome-wide data for fish species allows for elucidating the genomic basis of adaptation to local or farmed conditions and uncovering genes that control the phenotypes of interest. The present study aimed to detect genomic selection signatures and analyze the genetic variability in farmed populations of tambaqui in South America using single-nucleotide polymorphism (SNP) markers obtained with double-digest restriction site-associated DNA sequencing. Initially, 199 samples of tambaqui farmed populations from different locations (located in Brazil, Colombia, and Peru), a wild population (Amazon River, Brazil), and the base population of a breeding program (Aquaculture Center, CAUNESP, Jaboticabal, SP, Brazil) were genotyped. Observed and expected heterozygosity was 0.231–0.350 and 0.288–0.360, respectively. Significant genetic differentiation was observed using global FST analyses of SNP loci (FST = 0.064, p < 0.050). Farmed populations from Colombia and Peru that differentiated from the Brazilian populations formed distinct groups. Several regions, particularly those harboring the genes of significance to aquaculture, were identified to be under positive selection, suggesting local adaptation to stress under different farming conditions and management practices. Studies aimed at improving the knowledge of genomics of tambaqui farmed populations are essential for aquaculture to gain deeper insights into the evolutionary history of these fish and provide resources for the establishment of breeding programs. |
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Genomic selection signatures in farmed Colossoma macropomum from tropical and subtropical regions in South Americagenetic structureneotropical fishserrasalmidaesignatures of selectionSouth American Aquaculturestress in aquacultureTambaqui or cachama (Colossoma macropomum) is one of the most important neotropical freshwater fish used for aquaculture in South America, and its production is concentrated at low latitudes (close to the Equator, 0°), where the water temperature is warm. Therefore, understanding how selection shapes genetic variations and structure in farmed populations is of paramount importance in evolutionary biology. High-throughput sequencing to generate genome-wide data for fish species allows for elucidating the genomic basis of adaptation to local or farmed conditions and uncovering genes that control the phenotypes of interest. The present study aimed to detect genomic selection signatures and analyze the genetic variability in farmed populations of tambaqui in South America using single-nucleotide polymorphism (SNP) markers obtained with double-digest restriction site-associated DNA sequencing. Initially, 199 samples of tambaqui farmed populations from different locations (located in Brazil, Colombia, and Peru), a wild population (Amazon River, Brazil), and the base population of a breeding program (Aquaculture Center, CAUNESP, Jaboticabal, SP, Brazil) were genotyped. Observed and expected heterozygosity was 0.231–0.350 and 0.288–0.360, respectively. Significant genetic differentiation was observed using global FST analyses of SNP loci (FST = 0.064, p < 0.050). Farmed populations from Colombia and Peru that differentiated from the Brazilian populations formed distinct groups. Several regions, particularly those harboring the genes of significance to aquaculture, were identified to be under positive selection, suggesting local adaptation to stress under different farming conditions and management practices. Studies aimed at improving the knowledge of genomics of tambaqui farmed populations are essential for aquaculture to gain deeper insights into the evolutionary history of these fish and provide resources for the establishment of breeding programs.Aquaculture Center of UNESP São Paulo State University (UNESP)Facultad de Ciencias Agrarias Universidad de AntioquiaFacultad de Veterinaria Universidad de Santiago de Compostela (USC)Facultad de Zootecnia Universidad Nacional Agraria de la SelvaAquaculture Center of UNESP São Paulo State University (UNESP)Universidade Estadual Paulista (UNESP)Universidad de AntioquiaUniversidad de Santiago de Compostela (USC)Universidad Nacional Agraria de la SelvaAgudelo, John Fredy Gómez [UNESP]Mastrochirico-Filho, Vito Antonio [UNESP]Borges, Carolina Heloisa de Souza [UNESP]Ariede, Raquel Belini [UNESP]Lira, Lieschen Valeria Guerra [UNESP]Neto, Rubens Ricardo de Oliveira [UNESP]de Freitas, Milena Vieira [UNESP]Sucerquia, Gustavo Adolfo LenisVera, ManuelBerrocal, Milthon Honorio MuñozHashimoto, Diogo Teruo [UNESP]2022-04-29T08:40:39Z2022-04-29T08:40:39Z2022-01-01info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articlehttp://dx.doi.org/10.1111/eva.13351Evolutionary Applications.1752-45711752-4563http://hdl.handle.net/11449/23053110.1111/eva.133512-s2.0-85125923810Scopusreponame:Repositório Institucional da UNESPinstname:Universidade Estadual Paulista (UNESP)instacron:UNESPengEvolutionary Applicationsinfo:eu-repo/semantics/openAccess2024-04-09T15:43:44Zoai:repositorio.unesp.br:11449/230531Repositório InstitucionalPUBhttp://repositorio.unesp.br/oai/requestopendoar:29462024-08-05T23:49:27.907097Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP)false |
dc.title.none.fl_str_mv |
Genomic selection signatures in farmed Colossoma macropomum from tropical and subtropical regions in South America |
title |
Genomic selection signatures in farmed Colossoma macropomum from tropical and subtropical regions in South America |
spellingShingle |
Genomic selection signatures in farmed Colossoma macropomum from tropical and subtropical regions in South America Agudelo, John Fredy Gómez [UNESP] genetic structure neotropical fish serrasalmidae signatures of selection South American Aquaculture stress in aquaculture |
title_short |
Genomic selection signatures in farmed Colossoma macropomum from tropical and subtropical regions in South America |
title_full |
Genomic selection signatures in farmed Colossoma macropomum from tropical and subtropical regions in South America |
title_fullStr |
Genomic selection signatures in farmed Colossoma macropomum from tropical and subtropical regions in South America |
title_full_unstemmed |
Genomic selection signatures in farmed Colossoma macropomum from tropical and subtropical regions in South America |
title_sort |
Genomic selection signatures in farmed Colossoma macropomum from tropical and subtropical regions in South America |
author |
Agudelo, John Fredy Gómez [UNESP] |
author_facet |
Agudelo, John Fredy Gómez [UNESP] Mastrochirico-Filho, Vito Antonio [UNESP] Borges, Carolina Heloisa de Souza [UNESP] Ariede, Raquel Belini [UNESP] Lira, Lieschen Valeria Guerra [UNESP] Neto, Rubens Ricardo de Oliveira [UNESP] de Freitas, Milena Vieira [UNESP] Sucerquia, Gustavo Adolfo Lenis Vera, Manuel Berrocal, Milthon Honorio Muñoz Hashimoto, Diogo Teruo [UNESP] |
author_role |
author |
author2 |
Mastrochirico-Filho, Vito Antonio [UNESP] Borges, Carolina Heloisa de Souza [UNESP] Ariede, Raquel Belini [UNESP] Lira, Lieschen Valeria Guerra [UNESP] Neto, Rubens Ricardo de Oliveira [UNESP] de Freitas, Milena Vieira [UNESP] Sucerquia, Gustavo Adolfo Lenis Vera, Manuel Berrocal, Milthon Honorio Muñoz Hashimoto, Diogo Teruo [UNESP] |
author2_role |
author author author author author author author author author author |
dc.contributor.none.fl_str_mv |
Universidade Estadual Paulista (UNESP) Universidad de Antioquia Universidad de Santiago de Compostela (USC) Universidad Nacional Agraria de la Selva |
dc.contributor.author.fl_str_mv |
Agudelo, John Fredy Gómez [UNESP] Mastrochirico-Filho, Vito Antonio [UNESP] Borges, Carolina Heloisa de Souza [UNESP] Ariede, Raquel Belini [UNESP] Lira, Lieschen Valeria Guerra [UNESP] Neto, Rubens Ricardo de Oliveira [UNESP] de Freitas, Milena Vieira [UNESP] Sucerquia, Gustavo Adolfo Lenis Vera, Manuel Berrocal, Milthon Honorio Muñoz Hashimoto, Diogo Teruo [UNESP] |
dc.subject.por.fl_str_mv |
genetic structure neotropical fish serrasalmidae signatures of selection South American Aquaculture stress in aquaculture |
topic |
genetic structure neotropical fish serrasalmidae signatures of selection South American Aquaculture stress in aquaculture |
description |
Tambaqui or cachama (Colossoma macropomum) is one of the most important neotropical freshwater fish used for aquaculture in South America, and its production is concentrated at low latitudes (close to the Equator, 0°), where the water temperature is warm. Therefore, understanding how selection shapes genetic variations and structure in farmed populations is of paramount importance in evolutionary biology. High-throughput sequencing to generate genome-wide data for fish species allows for elucidating the genomic basis of adaptation to local or farmed conditions and uncovering genes that control the phenotypes of interest. The present study aimed to detect genomic selection signatures and analyze the genetic variability in farmed populations of tambaqui in South America using single-nucleotide polymorphism (SNP) markers obtained with double-digest restriction site-associated DNA sequencing. Initially, 199 samples of tambaqui farmed populations from different locations (located in Brazil, Colombia, and Peru), a wild population (Amazon River, Brazil), and the base population of a breeding program (Aquaculture Center, CAUNESP, Jaboticabal, SP, Brazil) were genotyped. Observed and expected heterozygosity was 0.231–0.350 and 0.288–0.360, respectively. Significant genetic differentiation was observed using global FST analyses of SNP loci (FST = 0.064, p < 0.050). Farmed populations from Colombia and Peru that differentiated from the Brazilian populations formed distinct groups. Several regions, particularly those harboring the genes of significance to aquaculture, were identified to be under positive selection, suggesting local adaptation to stress under different farming conditions and management practices. Studies aimed at improving the knowledge of genomics of tambaqui farmed populations are essential for aquaculture to gain deeper insights into the evolutionary history of these fish and provide resources for the establishment of breeding programs. |
publishDate |
2022 |
dc.date.none.fl_str_mv |
2022-04-29T08:40:39Z 2022-04-29T08:40:39Z 2022-01-01 |
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/10.1111/eva.13351 Evolutionary Applications. 1752-4571 1752-4563 http://hdl.handle.net/11449/230531 10.1111/eva.13351 2-s2.0-85125923810 |
url |
http://dx.doi.org/10.1111/eva.13351 http://hdl.handle.net/11449/230531 |
identifier_str_mv |
Evolutionary Applications. 1752-4571 1752-4563 10.1111/eva.13351 2-s2.0-85125923810 |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.relation.none.fl_str_mv |
Evolutionary Applications |
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 |
|
_version_ |
1808129556521943040 |