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

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.

Investigating Genetic Diversity and Genomic Signatures of Hatchery-Induced Evolution in Gilthead Seabream (Sparus aurata) Populations

“…The three reported robust outlier SNPs were found to be significant outliers in multiple genetic clusters of farmed fish populations when contrasted with different genetic clusters of wild populations. This finding supports a scenario of parallel signatures of adaptation of gilthead seabream to the farmed conditions, which remains to be investigated further, for instance, with the use of higher-density SNPs that have been recently developed for gilthead seabream [75]. We also reported on the biological role and function of multiple genes closely linked to the outlier SNPs that may explain the observed divergence, and provide targets for future research in the domestication of gilthead seabream.…”

“…The fact that we detected three candidate SNPs for domestication in gilthead seabream by screening a relatively low number of 1159 random genomic SNPs suggests potentially strong divergent selection for domestication that, for example, medium-to-high-density SNP screening approaches may be able to elucidate further. To this end, Peñaloza et al recently reported on the development of a 15K SNP chip for gilthead seabream that may be ideally suited for this purpose [75]. Our analysis of the semantic similarity of the genes within 20 Kbps from the three candidate SNPs also managed to recognize some common functional patterns (Figure 5).…”

Genetic Basis for Resistance Against Viral Nervous Necrosis: GWAS and Potential of Genomic Prediction Explored in Farmed European Sea Bass (Dicentrarchus labrax)

“…The availability of resources including reference genomes, linkage maps, genotyping arrays, etc., convenes the applicability of the GS along with genome-wide association studies. Not long ago, the reference genome of European sea bass became available (Tine et al, 2014), and very recently, the SNP genotyping Axiom arrays were also developed, which are a part of the public domain now (Griot et al, 2021;Peñaloza et al, 2021). There are several studies on different aquaculture species where quantitative trait loci (QTL) were detected for traits of economic and welfare importance using medium-to high-density SNP arrays.…”

MHC class I‐α population differentiation in a commercial fish, the European sea bass (Dicentrarchus labrax)

“…The difference in private alleles between the Celtic shelf and Portuguese uncovered population structuring not observed using neutral markers (Souche et al, 2015), and indicates the potential for MHC‐I to detect fine‐scale population variation. Markers in the MHC region can be particularly good for showing fine scale differentiation, as changes can accumulate relatively quickly and are affected by local selection (Consuegra et al, 2005), and genome‐wide high‐throughput methods (Griot et al, 2021; Penaloza et al, 2021) can help identify additional markers under selection (Carreras et al, 2017). Our study provides the first detailed analysis of MHC class I in seabass, a species that supports important commercial and sport fisheries, as well as aquaculture.…”