Allele frequency data for SNPs on a combined-species SNP array for European seabass and gilthead seabream
Description
SNP arrays are enabling tools for high-resolution studies of the genetic basis of complex traits, and for incorporating genetic markers to expedite genetic gain in selective breeding programmes. The European seabass (Dicentrarchus labrax) and the gilthead seabream (Sparus aurata) are two primary fish species of importance for Mediterranean aquaculture. The aim of our study was to design a combined-species, 60K SNP array for the European seabass and the gilthead seabream, and to test its performance on farmed and wild populations from multiple locations throughout the Mediterranean. The data presented here are part of the validation process of the abovementioned platform and represents the allele frequencies of the SNPs on the array that were genotyped across 23 European seabass and 26 gilthead seabream populations sampled mainly from the Mediterranean Sea. The data comprises two text files, one for each fish species. Each file contains seven tab separated columns that indicate: chromosome/scaffold ID (1st column), position of the SNP (2nd column), SNP ID (3rd column), reference allele (4th column), alternate allele (5th column), the number of individuals successfully genotyped (6th column) and the average allele frequency of the SNP (7th column). The data shows that the majority of the SNPs on the platform are highly polymorphic across the sampled European seabass and gilthead seabream populations. The allele frequency information can be used to generate low-density panels to perform genetic research in both fish species.
Files
Steps to reproduce
Fish DNA samples were genotyped with the platform. CEL files were imported into the Axiom Analysis Suite software v 2.0.035 and genotypes were called at default parameter values for diploid species (call rate (CR) > 97; dish QC (DQC) >0.82) in the gilthead seabream samples. However, for the European seabass samples the CR threshold was reduced to 93 due to overall lower sample quality.