Integrative Transcriptome, Genome and Quantitative Trait Loci Resources Identify Single Nucleotide Polymorphisms in Candidate Genes for Growth Traits in Turbot
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-assi...
Main Authors: | , , , , , , , , |
---|---|
Format: | Article |
Language: | English |
Published: |
MDPI AG
2016-02-01
|
Series: | International Journal of Molecular Sciences |
Subjects: | |
Online Access: | http://www.mdpi.com/1422-0067/17/2/243 |
id |
doaj-370fc63dc46b433b9ae963b3f716f160 |
---|---|
record_format |
Article |
spelling |
doaj-370fc63dc46b433b9ae963b3f716f1602020-11-25T00:59:52ZengMDPI AGInternational Journal of Molecular Sciences1422-00672016-02-0117224310.3390/ijms17020243ijms17020243Integrative Transcriptome, Genome and Quantitative Trait Loci Resources Identify Single Nucleotide Polymorphisms in Candidate Genes for Growth Traits in TurbotDiego Robledo0Carlos Fernández1Miguel Hermida2Andrés Sciara3José Antonio Álvarez-Dios4Santiago Cabaleiro5Rubén Caamaño6Paulino Martínez7Carmen Bouza8Departamento de Xenética, Facultade de Bioloxía (CIBUS), Universidade de Santiago de Compostela, Santiago de Compostela 15782, SpainDepartamento de Xenética, Facultade de Veterinaria, Universidade de Santiago de Compostela, Lugo 27002, SpainDepartamento de Xenética, Facultade de Veterinaria, Universidade de Santiago de Compostela, Lugo 27002, SpainInstituto de Biología Molecular y Celular de Rosario (IBR-CONICET), Rosario S2002LRK, ArgentinaDepartamento de Matemática Aplicada, Facultade de Matemáticas, Universidade de Santiago de Compostela, Santiago de Compostela 15782, SpainCluster de Acuicultura de Galicia (Punta do Couso), Aguiño-Ribeira 15695, SpainCluster de Acuicultura de Galicia (Punta do Couso), Aguiño-Ribeira 15695, SpainDepartamento de Xenética, Facultade de Veterinaria, Universidade de Santiago de Compostela, Lugo 27002, SpainDepartamento de Xenética, Facultade de Veterinaria, Universidade de Santiago de Compostela, Lugo 27002, SpainGrowth 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.http://www.mdpi.com/1422-0067/17/2/243Scophthalmus maximusturbotgrowthRNA-seqcandidate genesSNPintegrative genomics |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Diego Robledo Carlos Fernández Miguel Hermida Andrés Sciara José Antonio Álvarez-Dios Santiago Cabaleiro Rubén Caamaño Paulino Martínez Carmen Bouza |
spellingShingle |
Diego Robledo Carlos Fernández Miguel Hermida Andrés Sciara José Antonio Álvarez-Dios Santiago Cabaleiro Rubén Caamaño Paulino Martínez Carmen Bouza Integrative Transcriptome, Genome and Quantitative Trait Loci Resources Identify Single Nucleotide Polymorphisms in Candidate Genes for Growth Traits in Turbot International Journal of Molecular Sciences Scophthalmus maximus turbot growth RNA-seq candidate genes SNP integrative genomics |
author_facet |
Diego Robledo Carlos Fernández Miguel Hermida Andrés Sciara José Antonio Álvarez-Dios Santiago Cabaleiro Rubén Caamaño Paulino Martínez Carmen Bouza |
author_sort |
Diego Robledo |
title |
Integrative Transcriptome, Genome and Quantitative Trait Loci Resources Identify Single Nucleotide Polymorphisms in Candidate Genes for Growth Traits in 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 |
publisher |
MDPI AG |
series |
International Journal of Molecular Sciences |
issn |
1422-0067 |
publishDate |
2016-02-01 |
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. |
topic |
Scophthalmus maximus turbot growth RNA-seq candidate genes SNP integrative genomics |
url |
http://www.mdpi.com/1422-0067/17/2/243 |
work_keys_str_mv |
AT diegorobledo integrativetranscriptomegenomeandquantitativetraitlociresourcesidentifysinglenucleotidepolymorphismsincandidategenesforgrowthtraitsinturbot AT carlosfernandez integrativetranscriptomegenomeandquantitativetraitlociresourcesidentifysinglenucleotidepolymorphismsincandidategenesforgrowthtraitsinturbot AT miguelhermida integrativetranscriptomegenomeandquantitativetraitlociresourcesidentifysinglenucleotidepolymorphismsincandidategenesforgrowthtraitsinturbot AT andressciara integrativetranscriptomegenomeandquantitativetraitlociresourcesidentifysinglenucleotidepolymorphismsincandidategenesforgrowthtraitsinturbot AT joseantonioalvarezdios integrativetranscriptomegenomeandquantitativetraitlociresourcesidentifysinglenucleotidepolymorphismsincandidategenesforgrowthtraitsinturbot AT santiagocabaleiro integrativetranscriptomegenomeandquantitativetraitlociresourcesidentifysinglenucleotidepolymorphismsincandidategenesforgrowthtraitsinturbot AT rubencaamano integrativetranscriptomegenomeandquantitativetraitlociresourcesidentifysinglenucleotidepolymorphismsincandidategenesforgrowthtraitsinturbot AT paulinomartinez integrativetranscriptomegenomeandquantitativetraitlociresourcesidentifysinglenucleotidepolymorphismsincandidategenesforgrowthtraitsinturbot AT carmenbouza integrativetranscriptomegenomeandquantitativetraitlociresourcesidentifysinglenucleotidepolymorphismsincandidategenesforgrowthtraitsinturbot |
_version_ |
1725215600435789824 |