Design and validation of a high-density SNP array for the Eastern oyster (Crassostrea virginica)

Abstract

Abstract Dense single nucleotide polymorphism (SNP) arrays are an essential tool for rapid high-throughput genotyping for many genetic analyses, including genomic selection and high-resolution population genomic assessments. We present a high-density (200K) SNP array developed for the Canadian Eastern oyster (Crassostrea virginica), which is a species of significant aquaculture production and restoration efforts throughout its native range. SNP discovery was performed using low-coverage whole-genome sequencing of 435 F1 oysters from families from 11 founder populations in New Brunswick, Canada. An Affymetrix Axiom Custom array was created with 219,447 SNPs meeting stringent selection criteria and validated by genotyping more than 4000 oysters across two generations. In total, 144,570 SNPs had a call rate >90%, most of which (96%) were polymorphic and were distributed across the Eastern oyster reference genome, with similar levels of genetic diversity observed in both generations. Linkage disequilibrium (LD) was low (maximum r2 ∼0.32) and decayed moderately with increasing distance between SNP pairs. Taking advantage of our intergenerational dataset, we quantified Mendelian inheritance errors (MIEs) to validate SNP selection. Although most of SNPs exhibited low MIE rates overall, with 72% of called SNPs having an error rate of <1%, many loci had elevated MIE rates, potentially indicating the presence of null alleles. This SNP panel provides a necessary tool to enable routine application of genomic approaches, including genomic selection, in C. virginica selective breeding programs. As demand for production increases, this resource will be essential for accelerating production and sustaining the Canadian oyster aquaculture industry.