Construction and evaluation of a high-density SNP array for the Pacific oyster (Crassostrea gigas)

Abstract

Single nucleotide polymorphisms (SNPs) are widely used in genetics and genomics research. The Pacific oyster (Crassostrea gigas) is an economically and ecologically important marine bivalve, and it possesses one of the highest levels of genomic DNA variation among animal species. Pacific oyster SNPs have been extensively investigated; however, the mechanisms by which these SNPs may be used in a high-throughput, transferable, and economical manner remain to be elucidated. Here, we constructed an oyster 190K SNP array using Affymetrix Axiom genotyping technology. We designed 190,420 SNPs on the chip; these SNPs were selected from 54 million SNPs identified through re-sequencing of 472 Pacific oysters collected in China, Japan, Korea, and Canada. Our genotyping results indicated that 133,984 (70.4%) SNPs were polymorphic and successfully converted on the chip. The SNPs were distributed evenly throughout the oyster genome, located in 3,595 scaffolds with a length of ~509.4 million; the average interval spacing was 4,210 bp. In addition, 111,158 SNPs were distributed in 21,050 coding genes, with an average of 5.3 SNPs per gene. In comparison with genotypes obtained through re-sequencing, ~69% of the converted SNPs had a concordance rate of >0.971; the mean concordance rate was 0.966. Evaluation based on genotypes of full-sib family individuals revealed that the average genotyping accuracy rate was 0.975. Carrying 133 K polymorphic SNPs, our oyster 190K SNP array is the first commercially available high-density SNP chip for mollusks, with the highest throughput. It represents a valuable tool for oyster genome-wide association studies, fine linkage mapping, and population genetics.

Potential of genomic selection for improvement of resistance to ostreid herpesvirus in Pacific oyster (Crassostrea gigas)

“…Accordingly, SNP arrays have been developed for many important finfish aquaculture species such as Atlantic salmon, rainbow trout, catfish and carp, among others (Houston et al ; Liu et al ; Xu et al ; Palti et al ; Yáñez et al ). In addition, two SNP arrays have recently been developed for Pacific oyster ( Crassostrea gigas ): a combined‐species medium‐density array for Pacific oyster and European flat oyster ( Ostrea edulis Gutierrez et al ) and a high‐density array for Pacific oyster (Qi et al ). Moreover, a high‐density linkage map containing ~20 000 SNPs has recently been created and aligned with the physical reference genome assembly (Zhang et al ; Gutierrez et al ).…”

Genomic Selection for Growth Traits in Pacific Oyster (Crassostrea gigas): Potential of Low-Density Marker Panels for Breeding Value Prediction

“…In recent years, substantial effort has been put toward the development of genomic resources for Pacific oyster, which include a reference genome assembly ( Zhang et al, 2012 ), genetic marker databases including microsatellites ( Li et al, 2003 ; Sekino et al, 2003 ) and SNPs ( Sauvage et al, 2007 ; Fleury et al, 2009 ; Wang J. et al, 2015 ) and low density linkage maps, containing both microsatellites and SNPs ( Hubert and Hedgecock, 2004 ; Hedgecock et al, 2015 ). The recent development of two oyster SNP arrays; a combined-species medium density array for Pacific oyster and European flat oyster ( O. edulis) ( Gutierrez et al, 2017 ) and a high density array for Pacific oyster ( Qi et al, 2017 ); raises the opportunity of rapidly collecting genotype data for many 1000s of SNP markers dispersed throughout the genome. Moreover, a high density linkage map containing ∼20 K SNPs has recently been created and aligned with the physical reference genome assembly ( Gutierrez et al, 2018 ).…”

A genome-wide association study for host resistance to Ostreid Herpesvirus in Pacific oysters (Crassostrea gigas)

“…Importantly, the recent development of medium and high density SNP arrays for oysters (Gutierrez et al . 2017; Qi et al . 2017) raises the possibility of rapidly collecting genotype data for many thousands of SNP markers dispersed throughout the genome.…”