Pedigree-based genome-wide imputation using a low-density amplicon panel for the highly polymorphic Pacific oyster Crassostrea ( Magallana ) gigas

High-density genomic data are instrumental for selective breeding, but the high costs associated with these approaches can hinder progress, as is the case for most aquaculture species. A strategy to reduce genotyping costs is to genotype a few select animals at high-density (e.g., parents, grandparents), and large numbers of other animals at low density (e.g., offspring), then impute genotypes. This has been demonstrated in silico for Pacific oyster Crassostrea ( Magallana ) gigas but was particularly challenging relative to other species and has never been empirically tested. Here, four families of Pacific oysters, bred via marker-assisted selection for variation at a locus for ostreid herpesvirus 1 (OsHV-1) survivorship, were exposed to OsHV-1 then genotyped using a low-density amplicon panel (n = 240). Parents were genotyped with the amplicon panel and whole-genome resequencing data. Offspring genotypes were imputed, and accuracy was characterized against a hold-out dataset. Imputation reduced minor allele frequencies and enriched homozygosity. An in silico three-generation analysis was used to investigate the effect of deepening the pedigree, which generated superior results (genotype concordance = 84.5%, allelic dosage r = 0.73), although the two-generation imputation is likely sufficient for selection decisions (GC = 75.3%; r = 0.63). Genome-wide associations to OsHV-1 survivorship with imputed data identified major effect loci on the expected chromosome 8, but in a different region than expected, pointing to a potentially more complex genetic architecture for the trait. These methods demonstrate the empirical utility of amplicon panel-based genome-wide imputation in shellfish, and thus enable low-cost selective breeding techniques.