Int. J. Mol. Sci. 2013, 14(3), 5694-5711; doi:10.3390/ijms14035694
Abstract

Development and Validation of Single Nucleotide Polymorphisms (SNPs) Markers from Two Transcriptome 454-Runs of Turbot (Scophthalmus maximus) Using High-Throughput Genotyping

1 Laboratory of Genetics Ichthyology, Department of Biology, Faculty of Sciences, University of Girona, Campus of Montilivi s/n, Girona 17071, Spain 2 Department of Genetics, Faculty of Veterinary, University of Santiago de Compostela, Campus of Lugo, Lugo 27002, Spain 3 Department of Applied Mathematics, Faculty of Mathematics, University of Santiago de Compostela, Santiago de Compostela 15782, Spain
* Author to whom correspondence should be addressed.
Received: 3 December 2012; in revised form: 17 February 2013 / Accepted: 22 February 2013 / Published: 12 March 2013
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
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Abstract: The turbot (Scophthalmus maximus) is a commercially valuable flatfish and one of the most promising aquaculture species in Europe. Two transcriptome 454-pyrosequencing runs were used in order to detect Single Nucleotide Polymorphisms (SNPs) in genes related to immune response and gonad differentiation. A total of 866 true SNPs were detected in 140 different contigs representing 262,093 bp as a whole. Only one true SNP was analyzed in each contig. One hundred and thirteen SNPs out of the 140 analyzed were feasible (genotyped), while Ш were polymorphic in a wild population. Transition/transversion ratio (1.354) was similar to that observed in other fish studies. Unbiased gene diversity (He) estimates ranged from 0.060 to 0.510 (mean = 0.351), minimum allele frequency (MAF) from 0.030 to 0.500 (mean = 0.259) and all loci were in Hardy-Weinberg equilibrium after Bonferroni correction. A large number of SNPs (49) were located in the coding region, 33 representing synonymous and 16 non-synonymous changes. Most SNP-containing genes were related to immune response and gonad differentiation processes, and could be candidates for functional changes leading to phenotypic changes. These markers will be useful for population screening to look for adaptive variation in wild and domestic turbot.
Keywords: turbot; Scophthalmus maximus; SNP validation; EST database; non-synonymous substitution; high-throughput genotyping

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MDPI and ACS Style

Vera, M.; Alvarez-Dios, J.-A.; Fernandez, C.; Bouza, C.; Vilas, R.; Martinez, P. Development and Validation of Single Nucleotide Polymorphisms (SNPs) Markers from Two Transcriptome 454-Runs of Turbot (Scophthalmus maximus) Using High-Throughput Genotyping. Int. J. Mol. Sci. 2013, 14, 5694-5711.

AMA Style

Vera M, Alvarez-Dios J-A, Fernandez C, Bouza C, Vilas R, Martinez P. Development and Validation of Single Nucleotide Polymorphisms (SNPs) Markers from Two Transcriptome 454-Runs of Turbot (Scophthalmus maximus) Using High-Throughput Genotyping. International Journal of Molecular Sciences. 2013; 14(3):5694-5711.

Chicago/Turabian Style

Vera, Manuel; Alvarez-Dios, Jose-Antonio; Fernandez, Carlos; Bouza, Carmen; Vilas, Roman; Martinez, Paulino. 2013. "Development and Validation of Single Nucleotide Polymorphisms (SNPs) Markers from Two Transcriptome 454-Runs of Turbot (Scophthalmus maximus) Using High-Throughput Genotyping." Int. J. Mol. Sci. 14, no. 3: 5694-5711.

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