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 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.

A genotyping array for the globally invasive vector mosquito, Aedes albopictus

“…The technical replicates showed high concordance, with an average of 99.32% using the Axiom Suite or 99.46% using custom scripts (File S5, Table 3), which is similar for other SNP chips 7,54…”

Consequences of domestication in eastern oyster: Insights from whole genomic analyses

“…These functional genetic inferences are tentative because the high LD in oyster selected strains that we and others have documented (Xuereb et al., 2023 ) makes it unlikely that identified outliers are the direct target of selection. During a few generations of positive selection on small populations in early domestication, there is little opportunity for meiotic recombination to separate selection effects on target SNPs from surrounding polymorphisms.…”

A genotyping array for the globally invasive vector mosquito, Aedes albopictus

“…Technical replicates: The technical replicates showed high concordance, with an average of 99.32% using Axiom Analysis Suite or 99.46% using custom scripts (Additional file 5: File S5, Table 3), which is similar for other SNP chips [6,53]. Several factors can produce small differences among replicates, including DNA sample quality, chip manufacturing inconsistencies, hybridization conditions, software difficulties in interpreting raw signals of different intensities, especially when signal levels are low, and the possibility of potential errors during DNA sample handling, processing, or normalization.…”

“…Generally, if a SNP has a higher p-convert score, it is more likely to be correctly genotyped, while a lower score indicates potential inaccuracies in genotyping. The mean p-convert value for the probes in the Aealbo chip is 0.71 (Additional file 18 : File S18), which is relatively high compared to other chips [ 6 , 53 ].…”