Design and validation of a high-density single nucleotide polymorphism array for the Eastern oyster (Crassostrea virginica).

ABSTRACT: Dense single nucleotide polymorphism (SNP) arrays are essential tools for rapid high-throughput genotyping for many genetic analyses, including genomic selection and high-resolution population genomic assessments. We present a high-density (200 K) SNP array developed for the 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 4,000 oysters across 2 generations. In total, 144,570 SNPs had a call rate >90%

SUBMITTER: Xuereb A 

PROVIDER: S-EPMC10234413 | biostudies-literature | 2023 Jun

REPOSITORIES: biostudies-literature