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...
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ftmdpi:oai:mdpi.com:/1422-0067/17/2/243/ 2023-08-20T04:09:40+02:00 Integrative Transcriptome, Genome and Quantitative Trait Loci Resources Identify Single Nucleotide Polymorphisms in Candidate Genes for Growth Traits in Turbot Diego Robledo Carlos Fernández Miguel Hermida Andrés Sciara José Álvarez-Dios Santiago Cabaleiro Rubén Caamaño Paulino Martínez Carmen Bouza agris 2016-02-17 application/pdf https://doi.org/10.3390/ijms17020243 EN eng Multidisciplinary Digital Publishing Institute Biochemistry https://dx.doi.org/10.3390/ijms17020243 https://creativecommons.org/licenses/by/4.0/ International Journal of Molecular Sciences; Volume 17; Issue 2; Pages: 243 Scophthalmus maximus turbot growth RNA-seq candidate genes SNP integrative genomics Text 2016 ftmdpi https://doi.org/10.3390/ijms17020243 2023-07-31T20:50:23Z 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. Text Scophthalmus maximus Turbot MDPI Open Access Publishing International Journal of Molecular Sciences 17 2 243 |
institution |
Open Polar |
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MDPI Open Access Publishing |
op_collection_id |
ftmdpi |
language |
English |
topic |
Scophthalmus maximus turbot growth RNA-seq candidate genes SNP integrative genomics |
spellingShingle |
Scophthalmus maximus turbot growth RNA-seq candidate genes SNP integrative genomics Diego Robledo Carlos Fernández Miguel Hermida Andrés Sciara José 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 |
topic_facet |
Scophthalmus maximus turbot growth RNA-seq candidate genes SNP integrative genomics |
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. |
format |
Text |
author |
Diego Robledo Carlos Fernández Miguel Hermida Andrés Sciara José Álvarez-Dios Santiago Cabaleiro Rubén Caamaño Paulino Martínez Carmen Bouza |
author_facet |
Diego Robledo Carlos Fernández Miguel Hermida Andrés Sciara José 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 |
Multidisciplinary Digital Publishing Institute |
publishDate |
2016 |
url |
https://doi.org/10.3390/ijms17020243 |
op_coverage |
agris |
genre |
Scophthalmus maximus Turbot |
genre_facet |
Scophthalmus maximus Turbot |
op_source |
International Journal of Molecular Sciences; Volume 17; Issue 2; Pages: 243 |
op_relation |
Biochemistry https://dx.doi.org/10.3390/ijms17020243 |
op_rights |
https://creativecommons.org/licenses/by/4.0/ |
op_doi |
https://doi.org/10.3390/ijms17020243 |
container_title |
International Journal of Molecular Sciences |
container_volume |
17 |
container_issue |
2 |
container_start_page |
243 |
_version_ |
1774723273582444544 |