Sturgeon conservation genomics: SNP discovery and validation using RAD sequencing
Caviar-producing sturgeon belonging to the genus Acipenser are considered to be one of the most endangered species groups in the world. Continued over-fishing in spite of increasing legislation, zero catch quotas and extensive aquaculture production, have led to the collapse of wild stocks across Eu...
Published in: | Molecular Ecology |
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WILEY-BLACKWELL
2013
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Online Access: | https://publications.jrc.ec.europa.eu/repository/handle/JRC76930 http://onlinelibrary.wiley.com/doi/10.1111/mec.12234/abstract https://doi.org/10.1111/mec.12234 |
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ftjrc:oai:publications.jrc.ec.europa.eu:JRC76930 2023-05-15T18:19:31+02:00 Sturgeon conservation genomics: SNP discovery and validation using RAD sequencing OGDEN Rob GHARBI Karim MUGUE Nicolai MARTINSOHN Jann SENN Helen DAVEY John POURKAZEMI Mohammad MCEWING Ross ELAND C VIDOTTO Michele CONGIU Leonardo SERGEEV Alexander 2013 Printed https://publications.jrc.ec.europa.eu/repository/handle/JRC76930 http://onlinelibrary.wiley.com/doi/10.1111/mec.12234/abstract https://doi.org/10.1111/mec.12234 ENG eng WILEY-BLACKWELL JRC76930 2013 ftjrc https://doi.org/10.1111/mec.12234 2022-05-01T08:17:54Z Caviar-producing sturgeon belonging to the genus Acipenser are considered to be one of the most endangered species groups in the world. Continued over-fishing in spite of increasing legislation, zero catch quotas and extensive aquaculture production, have led to the collapse of wild stocks across Europe and Asia. The evolutionary relationships among Adriatic, Russian, Persian and Siberian sturgeon are complex because of past introgression events and remain poorly understood. Conservation management, traceability and enforcement suffer a lack of appropriate DNA markers for the genetic identification of sturgeon at the species, population and individual level. This study employed RAD sequencing to discover and characterise SNP DNA markers for use in sturgeon conservation in these four tetraploid species over three biological levels, using a single sequencing lane. Four population meta-samples and eight individuals from one family were barcoded separately before sequencing. Analysis of 14.4 Gb of paired-end RAD data focused on the identification of SNPs in the paired-end contig, with subsequent in silico and empirical validation of candidate markers. Thousands of putatively-informative markers were identified including, for the first time, SNPs that show population-wide differentiation between Russian and Persian sturgeon, representing an important advance in our ability to manage these cryptic species. The results highlight the challenges of GBS in polyploid taxa, while establishing the potential genetic resources for developing a new range of caviar traceability and enforcement tools. JRC.G.4 - Maritime affairs Other/Unknown Material Siberian sturgeon Joint Research Centre, European Commission: JRC Publications Repository Molecular Ecology 22 11 3112 3123 |
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Open Polar |
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Joint Research Centre, European Commission: JRC Publications Repository |
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ftjrc |
language |
English |
description |
Caviar-producing sturgeon belonging to the genus Acipenser are considered to be one of the most endangered species groups in the world. Continued over-fishing in spite of increasing legislation, zero catch quotas and extensive aquaculture production, have led to the collapse of wild stocks across Europe and Asia. The evolutionary relationships among Adriatic, Russian, Persian and Siberian sturgeon are complex because of past introgression events and remain poorly understood. Conservation management, traceability and enforcement suffer a lack of appropriate DNA markers for the genetic identification of sturgeon at the species, population and individual level. This study employed RAD sequencing to discover and characterise SNP DNA markers for use in sturgeon conservation in these four tetraploid species over three biological levels, using a single sequencing lane. Four population meta-samples and eight individuals from one family were barcoded separately before sequencing. Analysis of 14.4 Gb of paired-end RAD data focused on the identification of SNPs in the paired-end contig, with subsequent in silico and empirical validation of candidate markers. Thousands of putatively-informative markers were identified including, for the first time, SNPs that show population-wide differentiation between Russian and Persian sturgeon, representing an important advance in our ability to manage these cryptic species. The results highlight the challenges of GBS in polyploid taxa, while establishing the potential genetic resources for developing a new range of caviar traceability and enforcement tools. JRC.G.4 - Maritime affairs |
author |
OGDEN Rob GHARBI Karim MUGUE Nicolai MARTINSOHN Jann SENN Helen DAVEY John POURKAZEMI Mohammad MCEWING Ross ELAND C VIDOTTO Michele CONGIU Leonardo SERGEEV Alexander |
spellingShingle |
OGDEN Rob GHARBI Karim MUGUE Nicolai MARTINSOHN Jann SENN Helen DAVEY John POURKAZEMI Mohammad MCEWING Ross ELAND C VIDOTTO Michele CONGIU Leonardo SERGEEV Alexander Sturgeon conservation genomics: SNP discovery and validation using RAD sequencing |
author_facet |
OGDEN Rob GHARBI Karim MUGUE Nicolai MARTINSOHN Jann SENN Helen DAVEY John POURKAZEMI Mohammad MCEWING Ross ELAND C VIDOTTO Michele CONGIU Leonardo SERGEEV Alexander |
author_sort |
OGDEN Rob |
title |
Sturgeon conservation genomics: SNP discovery and validation using RAD sequencing |
title_short |
Sturgeon conservation genomics: SNP discovery and validation using RAD sequencing |
title_full |
Sturgeon conservation genomics: SNP discovery and validation using RAD sequencing |
title_fullStr |
Sturgeon conservation genomics: SNP discovery and validation using RAD sequencing |
title_full_unstemmed |
Sturgeon conservation genomics: SNP discovery and validation using RAD sequencing |
title_sort |
sturgeon conservation genomics: snp discovery and validation using rad sequencing |
publisher |
WILEY-BLACKWELL |
publishDate |
2013 |
url |
https://publications.jrc.ec.europa.eu/repository/handle/JRC76930 http://onlinelibrary.wiley.com/doi/10.1111/mec.12234/abstract https://doi.org/10.1111/mec.12234 |
genre |
Siberian sturgeon |
genre_facet |
Siberian sturgeon |
op_relation |
JRC76930 |
op_doi |
https://doi.org/10.1111/mec.12234 |
container_title |
Molecular Ecology |
container_volume |
22 |
container_issue |
11 |
container_start_page |
3112 |
op_container_end_page |
3123 |
_version_ |
1766196607168020480 |