Development and Application of a High Density SNP Array for Oysters

Single nucleotide polymorphism (SNP) arrays have enabled high resolution genetic studies and the application of genomic selection in breeding programs for several livestock and aquaculture species. Pacific oyster (C. gigas) is one of the most important aquaculture species worldwide, with a production in 2014 of > 625 K tonnes. The European flat oyster (O. edulis) is farmed in smaller volumes, but is an important native species in several countries. Extensive genomic resources exist for oysters, but no high density SNP array is available. The goal of the current study was to create and characterize a high-density SNP array for these two oyster species. SNPs were discovered by whole genome sequencing of pooled samples from eight diverse C. gigas populations, and RAD Sequencing of 11 diverse O. edulis populations. Tens of millions of candidate SNPs were filtered to favour those with intermediate allele frequency, high coverage across populations, monomorphic flanking regions, even distribution across the genome, and SNP conversion probability score. The final array was tested on the SNP discovery samples (n=384), showing 25K validated SNPs for C.gigas and 11K validated SNPs for O.edulis; these being informative SNPs with high call rate and clear cluster separation. The first application of this combined-species oyster array is to map genes affecting resistance to Oyster Herpes Virus (OsHV-1 µvar) from a large-scale challenge of commercial C. gigas oyster families.