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Development and validation of a combined species SNP array for the European seabass (Dicentrarchus labrax) and gilthead seabream (Sparus aurata)

View ORCID ProfileC. Peñaloza, View ORCID ProfileT. Manousaki, R. Franch, A. Tsakogiannis, A. Sonesson, M. L. Aslam, F. Allal, View ORCID ProfileL. Bargelloni, View ORCID ProfileR. D. Houston, View ORCID ProfileC. S. Tsigenopoulos
doi: https://doi.org/10.1101/2020.12.17.423305
C. Peñaloza
1The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian EH25 9RG, UK
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  • ORCID record for C. Peñaloza
T. Manousaki
2Hellenic Centre for Marine Research, Thalassocosmos Gournes Pediados, 71500 Irakleio, Crete, Greece
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R. Franch
3University of Padova, Via Ugo Bassi, 58yB I-35131 Padova, Italy
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A. Tsakogiannis
2Hellenic Centre for Marine Research, Thalassocosmos Gournes Pediados, 71500 Irakleio, Crete, Greece
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A. Sonesson
4Nofima, Norwegian institute of Food, Fisheries and Aquaculture research, PO Box 210, N-1432 Ås, Norway
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M. L. Aslam
4Nofima, Norwegian institute of Food, Fisheries and Aquaculture research, PO Box 210, N-1432 Ås, Norway
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F. Allal
5MARBEC, University of Montpellier, Ifremer, CNRS, IRD, 34250 Palavas-les-Flots, France
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L. Bargelloni
3University of Padova, Via Ugo Bassi, 58yB I-35131 Padova, Italy
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R. D. Houston
1The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian EH25 9RG, UK
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  • For correspondence: ross.houston@roslin.ed.ac.uk tsigeno@hcmr.gr
C. S. Tsigenopoulos
2Hellenic Centre for Marine Research, Thalassocosmos Gournes Pediados, 71500 Irakleio, Crete, Greece
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  • For correspondence: ross.houston@roslin.ed.ac.uk tsigeno@hcmr.gr
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Abstract

SNP arrays are powerful tools for high-resolution studies of the genetic basis of complex traits, facilitating both population genomic and selective breeding research. The European seabass (Dicentrarchus labrax) and the gilthead seabream (Sparus aurata) are the two most important fish species for Mediterranean aquaculture. While selective breeding programmes increasingly underpin stocky supply for this industry, genomic selection is not yet widespread. Genomic selection has major potential to expedite genetic gain, in particular for traits practically impossible to measure on selection candidates, such as disease resistance and fillet yield. The aim of our study was to design a combined-species 60K SNP array for both European seabass and gilthead seabream, and to validate its performance on farmed and wild populations from numerous locations throughout the species range. To achieve this, high coverage Illumina whole genome sequencing of pooled samples was performed for 24 populations of European seabass and 27 populations of gilthead seabream. This resulted in a database of ~20 million SNPs per species, which were then filtered to identify high-quality variants and create the final set for the development of the ‘MedFish’ SNP array. The array was then tested by genotyping a subset of the discovery populations and demonstrated a high conversion rate to functioning polymorphic assays on the array (92% in seabass: 89% in seabream) and repeatability (99.4 - 99.7%). The platform interrogates ~30K markers in each fish species, includes features such as SNPs previously shown to be associated with performance traits, and is enriched for SNPs predicted to alter protein function. The array was demonstrated to be effective at detecting population structure across a wide range of fish populations from diverse geographical origins, and to examine the extent of haplotype sharing among Mediterranean fish farms. Therefore, the MedFish array enables efficient and accurate high-throughput genotyping for genome-wide distributed SNPs on each fish species, and will facilitate stock management, population genomics approaches, and acceleration of selective breeding through genomic selection.

Competing Interest Statement

The authors have declared no competing interest.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Development and validation of a combined species SNP array for the European seabass (Dicentrarchus labrax) and gilthead seabream (Sparus aurata)
C. Peñaloza, T. Manousaki, R. Franch, A. Tsakogiannis, A. Sonesson, M. L. Aslam, F. Allal, L. Bargelloni, R. D. Houston, C. S. Tsigenopoulos
bioRxiv 2020.12.17.423305; doi: https://doi.org/10.1101/2020.12.17.423305
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Development and validation of a combined species SNP array for the European seabass (Dicentrarchus labrax) and gilthead seabream (Sparus aurata)
C. Peñaloza, T. Manousaki, R. Franch, A. Tsakogiannis, A. Sonesson, M. L. Aslam, F. Allal, L. Bargelloni, R. D. Houston, C. S. Tsigenopoulos
bioRxiv 2020.12.17.423305; doi: https://doi.org/10.1101/2020.12.17.423305

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