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

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 differentiati...

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Bibliographic Details
Published in:International Journal of Molecular Sciences
Main Authors: Vera Rodríguez, Manuel, Álvarez Dios, José Antonio, Fernández López, Carlos, Bouza Fernández, María Carmen, Vilas Peleteiro, Román, Martínez Portela, Paulino
Other Authors: Universidade de Santiago de Compostela. Departamento de Zooloxía, Xenética e Antropoloxía Física, Universidade de Santiago de Compostela. Departamento de Matemática Aplicada
Format: Article in Journal/Newspaper
Language:English
Published: MDPI
Subjects:
Turbot
Scophthalmus maximus
SNP validation
EST database
Non-synonymous substitution
High-throughput genotyping
Online Access:http://hdl.handle.net/10347/21913
https://doi.org/10.3390/ijms14035694
Description
Summary: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. This study was supported by the Consolider Ingenio Aquagenomics (CSD200700002), the Science and Education Spanish Ministry (AGL2009-11782) and the Xunta de Galicia (09MMA011261PR) projects SI

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