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

Authors
  • Peñaloza, C1
  • Manousaki, T2
  • Franch, R3
  • Tsakogiannis, A2
  • Sonesson, A K4
  • Aslam, M L4
  • Allal, F5
  • Bargelloni, L3
  • Houston, R D6
  • Tsigenopoulos, C S7
  • 1 The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian EH25 9RG, UK.
  • 2 Hellenic Centre for Marine Research, Thalassocosmos Gournes Pediados, 71500 Irakleio, Crete, Greece. , (Greece)
  • 3 Padova University, Via Ugo Bassi, 58yB, I-35131 Padova, Italy. , (Italy)
  • 4 Nofima, Norwegian Institute of Food, Fisheries and Aquaculture Research, PO Box 210, N-1432 Ås, Norway. , (Norway)
  • 5 MARBEC, University of Montpellier, Ifremer, CNRS, IRD, 34250 Palavas-les-Flots, France. , (France)
  • 6 The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian EH25 9RG, UK. Electronic address: [email protected]
  • 7 Hellenic Centre for Marine Research, Thalassocosmos Gournes Pediados, 71500 Irakleio, Crete, Greece. Electronic address: [email protected] , (Greece)
Type
Published Article
Journal
Genomics
Publisher
Elsevier
Publication Date
Apr 30, 2021
Volume
113
Issue
4
Pages
2096–2107
Identifiers
DOI: 10.1016/j.ygeno.2021.04.038
PMID: 33933591
Source
Medline
Keywords
Language
English
License
Unknown

Abstract

SNP arrays are powerful tools for high-resolution studies of the genetic basis of complex traits, facilitating both selective breeding and population genomic 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 stock supply for this industry, genomic selection is not yet widespread. Genomic selection has major potential to expedite genetic gain, particularly for traits practically impossible to measure on selection candidates, such as disease resistance and fillet characteristics. The aim of our study was to design a combined-species 60 K SNP array for European seabass and gilthead seabream, and to test 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, highlighting 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 ~30 K markers in each species, includes features such as SNPs previously shown to be associated with performance traits, and is enriched for SNPs predicted to have high functional effects on proteins. 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 farmed fish populations. In conclusion, the new MedFish array enables efficient and accurate high-throughput genotyping for genome-wide distributed SNPs for each fish species, and will facilitate stock management, population genomics approaches, and acceleration of selective breeding through genomic selection. Copyright © 2021 The Authors. Published by Elsevier Inc. All rights reserved.

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