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Int. J. Mol. Sci. 2016, 17(2), 243; doi:10.3390/ijms17020243

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

1
Departamento de Xenética, Facultade de Bioloxía (CIBUS), Universidade de Santiago de Compostela, Santiago de Compostela 15782, Spain
2
Departamento de Xenética, Facultade de Veterinaria, Universidade de Santiago de Compostela, Lugo 27002, Spain
3
Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET), Rosario S2002LRK, Argentina
4
Departamento de Matemática Aplicada, Facultade de Matemáticas, Universidade de Santiago de Compostela, Santiago de Compostela 15782, Spain
5
Cluster de Acuicultura de Galicia (Punta do Couso), Aguiño-Ribeira 15695, Spain
*
Author to whom correspondence should be addressed.
Academic Editor: Li Lin
Received: 13 January 2016 / Revised: 2 February 2016 / Accepted: 4 February 2016 / Published: 17 February 2016
(This article belongs to the Special Issue Fish Molecular Biology)
View Full-Text   |   Download PDF [1239 KB, uploaded 17 February 2016]   |  

Abstract

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. View Full-Text
Keywords: Scophthalmus maximus; turbot; growth; RNA-seq; candidate genes; SNP; integrative genomics Scophthalmus maximus; turbot; growth; RNA-seq; candidate genes; SNP; integrative genomics
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Robledo, D.; Fernández, C.; Hermida, M.; Sciara, A.; Álvarez-Dios, J.A.; Cabaleiro, S.; Caamaño, R.; Martínez, P.; Bouza, C. Integrative Transcriptome, Genome and Quantitative Trait Loci Resources Identify Single Nucleotide Polymorphisms in Candidate Genes for Growth Traits in Turbot. Int. J. Mol. Sci. 2016, 17, 243.

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