Sturgeon conservation genomics: SNP discovery and validation using RAD sequencing

Caviar‐producing sturgeons belonging to the genus Acipenser are considered to be one of the most endangered species groups in the world. Continued overfishing in spite of increasing legislation, zero catch quotas and extensive aquaculture production have led to the collapse of wild stocks across Eur...

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Bibliographic Details
Published in:Molecular ecology 2013-06, Vol.22 (11), p.3112-3123
Main Authors: Ogden, R., Gharbi, K., Mugue, N., Martinsohn, J., Senn, H., Davey, J. W., Pourkazemi, M., McEwing, R., Eland, C., Vidotto, M., Sergeev, A., Congiu, L.
Format: Article
Language:English
Subjects:
Acipenser
Animals
Base Sequence
caviar
DNA
Endangered Species
fisheries
Fishes - classification
Fishes - genetics
Genetic Markers
Genomics
Genotype
Genotype & phenotype
High-Throughput Nucleotide Sequencing
Marine conservation
Microsatellite Repeats
Polymorphism
Polymorphism, Single Nucleotide - genetics
Sequence Analysis, DNA
Sturgeon
traceability
wildlife forensics
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Summary:Caviar‐producing sturgeons belonging to the genus Acipenser are considered to be one of the most endangered species groups in the world. Continued overfishing 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 sturgeons 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 characterize single nucleotide polymorphism (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 individual samples 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 sturgeons, representing an important advance in our ability to manage these cryptic species. The results highlight the challenges of genotyping‐by‐sequencing in polyploid taxa, while establishing the potential genetic resources for developing a new range of caviar traceability and enforcement tools.
ISSN:0962-1083
1365-294X
DOI:10.1111/mec.12234