We describe the development and characterization of the first high-density single nucleotide polymorphism (SNP) genotyping array for the European sea bass (Dicentrarchus labrax). This Axiom® sea bass Genotyping Array includes 56730 markers and is available in 384 format. To design this array, SNPs were selected from ~2.6 million SNPs identified through whole-genome resequencing of 8 parents-offspring trios generated by experimental crossing of wild sea bass by Duranton et al. 2018. From this database, only SNPs located more than 30bp away from another known variant were selected in order to ensure a high probe specificity. The final set of variants were chosen to cover the whole genome (including ungrouped scaffolds), but with a variable density of SNPs depending on the estimated local nucleotide diversity (π) reported by Tine et al. (2014). This strategy aimed at increasing the density of SNPs within chromosome regions displaying a higher recombination rate. A genetic map was created with LepMap3 (Rastas, 2017). ThermoFisher AxiomTM Sea Bass 57k SNP DlabChip genotypes of 4 backcross families (including 378, 454, 291 and 211 individuals) were merged with another sea bass dataset composed of 880 individuals from 94 sires mated with 39 dams in three partial factorial designs. The resulting data set included 2232 individuals genotyped for 51179 markers. We ran the recommended procedure of LepMap3 with custom settings: 1% segregation distortion for Filtering2, a LOD score of 50 as well as a subset of 25% of the markers for SeparateChromosomes2, and LOD score of 30 for JoinSingles2All. We obtained a genetic map with 50001 markers mapped on 24 linkage groups (LG) inferred as 24 chromosomes.

Four experimental backcross full-sib families (378, 454, 291 and 211 individuals) were produced by in vitro fertilization at Ifremer (Palavas-les-Flots, France). All 1334 individuals were genotyped with a ThermoFisher AxiomTM Sea Bass 57k SNP DlabChip at the genotyping platform Gentyane (INRAE, Clermont-Ferrand, France). SNP calling was done using ThermoFisher software AxiomAnalysisSuiteTM. Preliminary quality controls were applied with threshold values of 95% for SNP call rate and 90% for sample call rate.