An amplicon panel for high-throughput and low-cost genotyping of Pacific oyster

Abstract

Maintaining genetic diversity in cultured shellfish can be challenging due to high variance in individual reproductive success, founder effects, and rapid genetic drift, but is important to retain adaptive potential and avoid inbreeding depression. To support broodstock management and selective breeding in cultured Pacific oysters (Crassostrea (Magallana) gigas), we developed an amplicon panel targeting 592 genomic regions and SNP variants with an average of 50 amplicons per chromosome. Target SNPs were selected based on elevated observed heterozygosity or differentiation in Pacific oyster populations in British Columbia (BC), Canada. The use of the panel for parentage applications was evaluated by genotyping three generations of oysters from a breeding program in BC (n = 181) and a set of families that were selected for Ostreid herpesvirus-1 (OSHV-1) resistance from the Molluscan Broodstock Program, a Pacific oyster breeding program in Oregon, USA (n = 136). Population characterization was evaluated using collections of wild, naturalized, farmed, or hatchery oysters sampled throughout the Northern Hemisphere (n = 190). Technical replicate samples showed high genotype concordance (97.5%; n = 68 replicates). Initial parentage analysis found instances of suspected pedigree and sample handling errors, demonstrating the panels value for quality control in breeding programs. Suspected null alleles were identified in parentage datasets and were found to reduce assignment success. Null alleles were largely population dependent, suggesting population-specific variation impacts target amplification. By taking an iterative approach, null alleles were identified using existing data without the need for pedigree information, and once null alleles were removed, assignments increased to 93.0% and 86.0% of possible assignments in the two breeding program datasets. A pipeline for analyzing the amplicon sequence data from sequencer output, amplitools, is also provided.