Integrative Transcriptome, Genome and Quantitative Trait Loci Resources Identify Single Nucleotide Polymorphisms in Candidate Genes for Growth Traits in Turbot

Autores
Robledo, Diego; Fernández, Carlos; Hermida, Miguel; Sciara, Andres Angel; Álvarez Dios, José Antonio; Cabaleiro, Santiago; Caamaño, Rubén; Martínez, Paulino; Bouza, Carmen
Año de publicación
2016
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
Growth traits represent a main goal in aquaculture breeding programs and may be related to adaptive variation in wild fisheries. Integrating quantitative trait loci (QTL) mapping and next generation sequencing can greatly help to identify variation in candidate genes, which can result in marker-assisted selection and better genetic structure information. Turbot is a commercially important flatfish in Europe and China, with available genomic information on QTLs and genome mapping. Muscle and liver RNA-seq from 18 individuals was carried out to obtain gene sequences and markers functionally related to growth, resulting in a total of 20,447 genes and 85,344 single nucleotide polymorphisms (SNPs). Many growth-related genes and SNPs were identified and placed in the turbot genome and genetic map to explore their co-localization with growth-QTL markers. Forty-five SNPs on growth-related genes were selected based on QTL co-localization and relevant function for growth traits. Forty-three SNPs were technically feasible and validated in a wild Atlantic population, where 91% were polymorphic. The integration of functional and structural genomic resources in turbot provides a practical approach for QTL mining in this species. Validated SNPs represent a useful set of growth-related gene markers for future association, functional and population studies in this flatfish species.
Fil: Robledo, Diego. Universidad de Santiago de Compostela; España
Fil: Fernández, Carlos. Universidad de Santiago de Compostela; España
Fil: Hermida, Miguel. Universidad de Santiago de Compostela; España
Fil: Sciara, Andres Angel. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Rosario. Instituto de Biología Molecular y Celular de Rosario. Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas. Instituto de Biología Molecular y Celular de Rosario; Argentina
Fil: Álvarez Dios, José Antonio. Universidad de Santiago de Compostela; España
Fil: Cabaleiro, Santiago. Centro Tecnológico del Cluster de la Acuicultura de Galicia; España
Fil: Caamaño, Rubén. Centro Tecnológico del Cluster de la Acuicultura de Galicia; España
Fil: Martínez, Paulino. Universidad de Santiago de Compostela; España
Fil: Bouza, Carmen. Universidad de Santiago de Compostela; España
Materia
CANDIDATE GENES
GROWTH
INTEGRATIVE GENOMICS
RNA-SEQ
SCOPHTHALMUSMAXIMUS
SNP
TURBOT
Nivel de accesibilidad
acceso abierto
Condiciones de uso
https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
Repositorio
CONICET Digital (CONICET)
Institución
Consejo Nacional de Investigaciones Científicas y Técnicas
OAI Identificador
oai:ri.conicet.gov.ar:11336/50377
Acceder
id CONICETDig_7b938654b1ab7e06592edbe08f8c211b
oai_identifier_str oai:ri.conicet.gov.ar:11336/50377
network_acronym_str CONICETDig
repository_id_str 3498
network_name_str CONICET Digital (CONICET)
spelling Integrative Transcriptome, Genome and Quantitative Trait Loci Resources Identify Single Nucleotide Polymorphisms in Candidate Genes for Growth Traits in TurbotRobledo, DiegoFernández, CarlosHermida, MiguelSciara, Andres AngelÁlvarez Dios, José AntonioCabaleiro, SantiagoCaamaño, RubénMartínez, PaulinoBouza, CarmenCANDIDATE GENESGROWTHINTEGRATIVE GENOMICSRNA-SEQSCOPHTHALMUSMAXIMUSSNPTURBOThttps://purl.org/becyt/ford/1.6https://purl.org/becyt/ford/1Growth traits represent a main goal in aquaculture breeding programs and may be related to adaptive variation in wild fisheries. Integrating quantitative trait loci (QTL) mapping and next generation sequencing can greatly help to identify variation in candidate genes, which can result in marker-assisted selection and better genetic structure information. Turbot is a commercially important flatfish in Europe and China, with available genomic information on QTLs and genome mapping. Muscle and liver RNA-seq from 18 individuals was carried out to obtain gene sequences and markers functionally related to growth, resulting in a total of 20,447 genes and 85,344 single nucleotide polymorphisms (SNPs). Many growth-related genes and SNPs were identified and placed in the turbot genome and genetic map to explore their co-localization with growth-QTL markers. Forty-five SNPs on growth-related genes were selected based on QTL co-localization and relevant function for growth traits. Forty-three SNPs were technically feasible and validated in a wild Atlantic population, where 91% were polymorphic. The integration of functional and structural genomic resources in turbot provides a practical approach for QTL mining in this species. Validated SNPs represent a useful set of growth-related gene markers for future association, functional and population studies in this flatfish species.Fil: Robledo, Diego. Universidad de Santiago de Compostela; EspañaFil: Fernández, Carlos. Universidad de Santiago de Compostela; EspañaFil: Hermida, Miguel. Universidad de Santiago de Compostela; EspañaFil: Sciara, Andres Angel. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Rosario. Instituto de Biología Molecular y Celular de Rosario. Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas. Instituto de Biología Molecular y Celular de Rosario; ArgentinaFil: Álvarez Dios, José Antonio. Universidad de Santiago de Compostela; EspañaFil: Cabaleiro, Santiago. Centro Tecnológico del Cluster de la Acuicultura de Galicia; EspañaFil: Caamaño, Rubén. Centro Tecnológico del Cluster de la Acuicultura de Galicia; EspañaFil: Martínez, Paulino. Universidad de Santiago de Compostela; EspañaFil: Bouza, Carmen. Universidad de Santiago de Compostela; EspañaMDPI2016-02info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfapplication/pdfhttp://hdl.handle.net/11336/50377Robledo, Diego; Fernández, Carlos; Hermida, Miguel; Sciara, Andres Angel; Álvarez Dios, José Antonio; et al.; Integrative Transcriptome, Genome and Quantitative Trait Loci Resources Identify Single Nucleotide Polymorphisms in Candidate Genes for Growth Traits in Turbot ; MDPI; International Journal of Molecular Sciences; 17; 2; 2-2016; 1-171422-0067CONICET DigitalCONICETenginfo:eu-repo/semantics/altIdentifier/doi/10.3390/ijms17020243info:eu-repo/semantics/altIdentifier/url/http://www.mdpi.com/1422-0067/17/2/243info:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by-nc-sa/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2025-09-03T09:43:33Zoai:ri.conicet.gov.ar:11336/50377instacron:CONICETInstitucionalhttp://ri.conicet.gov.ar/Organismo científico-tecnológicoNo correspondehttp://ri.conicet.gov.ar/oai/requestdasensio@conicet.gov.ar; lcarlino@conicet.gov.arArgentinaNo correspondeNo correspondeNo correspondeopendoar:34982025-09-03 09:43:34.2CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse
dc.title.none.fl_str_mv Integrative Transcriptome, Genome and Quantitative Trait Loci Resources Identify Single Nucleotide Polymorphisms in Candidate Genes for Growth Traits in Turbot
title Integrative Transcriptome, Genome and Quantitative Trait Loci Resources Identify Single Nucleotide Polymorphisms in Candidate Genes for Growth Traits in Turbot
spellingShingle Integrative Transcriptome, Genome and Quantitative Trait Loci Resources Identify Single Nucleotide Polymorphisms in Candidate Genes for Growth Traits in Turbot
Robledo, Diego
CANDIDATE GENES
GROWTH
INTEGRATIVE GENOMICS
RNA-SEQ
SCOPHTHALMUSMAXIMUS
SNP
TURBOT
title_short Integrative Transcriptome, Genome and Quantitative Trait Loci Resources Identify Single Nucleotide Polymorphisms in Candidate Genes for Growth Traits in Turbot
title_full Integrative Transcriptome, Genome and Quantitative Trait Loci Resources Identify Single Nucleotide Polymorphisms in Candidate Genes for Growth Traits in Turbot
title_fullStr Integrative Transcriptome, Genome and Quantitative Trait Loci Resources Identify Single Nucleotide Polymorphisms in Candidate Genes for Growth Traits in Turbot
title_full_unstemmed Integrative Transcriptome, Genome and Quantitative Trait Loci Resources Identify Single Nucleotide Polymorphisms in Candidate Genes for Growth Traits in Turbot
title_sort Integrative Transcriptome, Genome and Quantitative Trait Loci Resources Identify Single Nucleotide Polymorphisms in Candidate Genes for Growth Traits in Turbot
dc.creator.none.fl_str_mv Robledo, Diego
Fernández, Carlos
Hermida, Miguel
Sciara, Andres Angel
Álvarez Dios, José Antonio
Cabaleiro, Santiago
Caamaño, Rubén
Martínez, Paulino
Bouza, Carmen
author Robledo, Diego
author_facet Robledo, Diego
Fernández, Carlos
Hermida, Miguel
Sciara, Andres Angel
Álvarez Dios, José Antonio
Cabaleiro, Santiago
Caamaño, Rubén
Martínez, Paulino
Bouza, Carmen
author_role author
author2 Fernández, Carlos
Hermida, Miguel
Sciara, Andres Angel
Álvarez Dios, José Antonio
Cabaleiro, Santiago
Caamaño, Rubén
Martínez, Paulino
Bouza, Carmen
author2_role author
author
author
author
author
author
author
author
dc.subject.none.fl_str_mv CANDIDATE GENES
GROWTH
INTEGRATIVE GENOMICS
RNA-SEQ
SCOPHTHALMUSMAXIMUS
SNP
TURBOT
topic CANDIDATE GENES
GROWTH
INTEGRATIVE GENOMICS
RNA-SEQ
SCOPHTHALMUSMAXIMUS
SNP
TURBOT
purl_subject.fl_str_mv https://purl.org/becyt/ford/1.6
https://purl.org/becyt/ford/1
dc.description.none.fl_txt_mv Growth traits represent a main goal in aquaculture breeding programs and may be related to adaptive variation in wild fisheries. Integrating quantitative trait loci (QTL) mapping and next generation sequencing can greatly help to identify variation in candidate genes, which can result in marker-assisted selection and better genetic structure information. Turbot is a commercially important flatfish in Europe and China, with available genomic information on QTLs and genome mapping. Muscle and liver RNA-seq from 18 individuals was carried out to obtain gene sequences and markers functionally related to growth, resulting in a total of 20,447 genes and 85,344 single nucleotide polymorphisms (SNPs). Many growth-related genes and SNPs were identified and placed in the turbot genome and genetic map to explore their co-localization with growth-QTL markers. Forty-five SNPs on growth-related genes were selected based on QTL co-localization and relevant function for growth traits. Forty-three SNPs were technically feasible and validated in a wild Atlantic population, where 91% were polymorphic. The integration of functional and structural genomic resources in turbot provides a practical approach for QTL mining in this species. Validated SNPs represent a useful set of growth-related gene markers for future association, functional and population studies in this flatfish species.
Fil: Robledo, Diego. Universidad de Santiago de Compostela; España
Fil: Fernández, Carlos. Universidad de Santiago de Compostela; España
Fil: Hermida, Miguel. Universidad de Santiago de Compostela; España
Fil: Sciara, Andres Angel. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Rosario. Instituto de Biología Molecular y Celular de Rosario. Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas. Instituto de Biología Molecular y Celular de Rosario; Argentina
Fil: Álvarez Dios, José Antonio. Universidad de Santiago de Compostela; España
Fil: Cabaleiro, Santiago. Centro Tecnológico del Cluster de la Acuicultura de Galicia; España
Fil: Caamaño, Rubén. Centro Tecnológico del Cluster de la Acuicultura de Galicia; España
Fil: Martínez, Paulino. Universidad de Santiago de Compostela; España
Fil: Bouza, Carmen. Universidad de Santiago de Compostela; España
description Growth traits represent a main goal in aquaculture breeding programs and may be related to adaptive variation in wild fisheries. Integrating quantitative trait loci (QTL) mapping and next generation sequencing can greatly help to identify variation in candidate genes, which can result in marker-assisted selection and better genetic structure information. Turbot is a commercially important flatfish in Europe and China, with available genomic information on QTLs and genome mapping. Muscle and liver RNA-seq from 18 individuals was carried out to obtain gene sequences and markers functionally related to growth, resulting in a total of 20,447 genes and 85,344 single nucleotide polymorphisms (SNPs). Many growth-related genes and SNPs were identified and placed in the turbot genome and genetic map to explore their co-localization with growth-QTL markers. Forty-five SNPs on growth-related genes were selected based on QTL co-localization and relevant function for growth traits. Forty-three SNPs were technically feasible and validated in a wild Atlantic population, where 91% were polymorphic. The integration of functional and structural genomic resources in turbot provides a practical approach for QTL mining in this species. Validated SNPs represent a useful set of growth-related gene markers for future association, functional and population studies in this flatfish species.
publishDate 2016
dc.date.none.fl_str_mv 2016-02
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
http://purl.org/coar/resource_type/c_6501
info:ar-repo/semantics/articulo
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/11336/50377
Robledo, Diego; Fernández, Carlos; Hermida, Miguel; Sciara, Andres Angel; Álvarez Dios, José Antonio; et al.; Integrative Transcriptome, Genome and Quantitative Trait Loci Resources Identify Single Nucleotide Polymorphisms in Candidate Genes for Growth Traits in Turbot ; MDPI; International Journal of Molecular Sciences; 17; 2; 2-2016; 1-17
1422-0067
CONICET Digital
CONICET
url http://hdl.handle.net/11336/50377
identifier_str_mv Robledo, Diego; Fernández, Carlos; Hermida, Miguel; Sciara, Andres Angel; Álvarez Dios, José Antonio; et al.; Integrative Transcriptome, Genome and Quantitative Trait Loci Resources Identify Single Nucleotide Polymorphisms in Candidate Genes for Growth Traits in Turbot ; MDPI; International Journal of Molecular Sciences; 17; 2; 2-2016; 1-17
1422-0067
CONICET Digital
CONICET
dc.language.none.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv info:eu-repo/semantics/altIdentifier/doi/10.3390/ijms17020243
info:eu-repo/semantics/altIdentifier/url/http://www.mdpi.com/1422-0067/17/2/243
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
eu_rights_str_mv openAccess
rights_invalid_str_mv https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
dc.format.none.fl_str_mv application/pdf
application/pdf
dc.publisher.none.fl_str_mv MDPI
publisher.none.fl_str_mv MDPI
dc.source.none.fl_str_mv reponame:CONICET Digital (CONICET)
instname:Consejo Nacional de Investigaciones Científicas y Técnicas
reponame_str CONICET Digital (CONICET)
collection CONICET Digital (CONICET)
instname_str Consejo Nacional de Investigaciones Científicas y Técnicas
repository.name.fl_str_mv CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicas
repository.mail.fl_str_mv dasensio@conicet.gov.ar; lcarlino@conicet.gov.ar
_version_ 1842268610194571264
score 13.13397

Publicaciones similares