Development and Validation of Single Nucleotide Polymorphisms (SNPs) Markers from Two Transcriptome 454-Runs of Turbot (Scophthalmus maximus) Using High-Throughput Genotyping
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 dif...
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ftciteseerx:oai:CiteSeerX.psu:10.1.1.391.7841 2023-05-15T18:15:42+02:00 Development and Validation of Single Nucleotide Polymorphisms (SNPs) Markers from Two Transcriptome 454-Runs of Turbot (Scophthalmus maximus) Using High-Throughput Genotyping Manuel Vera Jose-antonio Alvarez-dios Carlos Fern Carmen Bouza Roman Vilas Paulino Martinez The Pennsylvania State University CiteSeerX Archives 2013 http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.391.7841 http://www.mdpi.com/1422-0067/14/3/5694/pdf/ en eng http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.391.7841 http://www.mdpi.com/1422-0067/14/3/5694/pdf/ Metadata may be used without restrictions as long as the oai identifier remains attached to it. http://www.mdpi.com/1422-0067/14/3/5694/pdf/ text 2013 ftciteseerx 2016-01-08T02:17:25Z 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 Text Scophthalmus maximus Turbot Unknown |
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ftciteseerx |
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English |
description |
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 |
author2 |
The Pennsylvania State University CiteSeerX Archives |
format |
Text |
author |
Manuel Vera Jose-antonio Alvarez-dios Carlos Fern Carmen Bouza Roman Vilas Paulino Martinez |
spellingShingle |
Manuel Vera Jose-antonio Alvarez-dios Carlos Fern Carmen Bouza Roman Vilas Paulino Martinez Development and Validation of Single Nucleotide Polymorphisms (SNPs) Markers from Two Transcriptome 454-Runs of Turbot (Scophthalmus maximus) Using High-Throughput Genotyping |
author_facet |
Manuel Vera Jose-antonio Alvarez-dios Carlos Fern Carmen Bouza Roman Vilas Paulino Martinez |
author_sort |
Manuel Vera |
title |
Development and Validation of Single Nucleotide Polymorphisms (SNPs) Markers from Two Transcriptome 454-Runs of Turbot (Scophthalmus maximus) Using High-Throughput Genotyping |
title_short |
Development and Validation of Single Nucleotide Polymorphisms (SNPs) Markers from Two Transcriptome 454-Runs of Turbot (Scophthalmus maximus) Using High-Throughput Genotyping |
title_full |
Development and Validation of Single Nucleotide Polymorphisms (SNPs) Markers from Two Transcriptome 454-Runs of Turbot (Scophthalmus maximus) Using High-Throughput Genotyping |
title_fullStr |
Development and Validation of Single Nucleotide Polymorphisms (SNPs) Markers from Two Transcriptome 454-Runs of Turbot (Scophthalmus maximus) Using High-Throughput Genotyping |
title_full_unstemmed |
Development and Validation of Single Nucleotide Polymorphisms (SNPs) Markers from Two Transcriptome 454-Runs of Turbot (Scophthalmus maximus) Using High-Throughput Genotyping |
title_sort |
development and validation of single nucleotide polymorphisms (snps) markers from two transcriptome 454-runs of turbot (scophthalmus maximus) using high-throughput genotyping |
publishDate |
2013 |
url |
http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.391.7841 http://www.mdpi.com/1422-0067/14/3/5694/pdf/ |
genre |
Scophthalmus maximus Turbot |
genre_facet |
Scophthalmus maximus Turbot |
op_source |
http://www.mdpi.com/1422-0067/14/3/5694/pdf/ |
op_relation |
http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.391.7841 http://www.mdpi.com/1422-0067/14/3/5694/pdf/ |
op_rights |
Metadata may be used without restrictions as long as the oai identifier remains attached to it. |
_version_ |
1766188884811579392 |