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.

Highlights

  • IntroductionOysters (phylum Mollusca, class Bivalvia) constitute an essential component of many aquatic ecosystems and are economically important in the fisheries and aquaculture industries [1]

  • Oysters constitute an essential component of many aquatic ecosystems and are economically important in the fisheries and aquaculture industries [1]

  • After aligning the reads to oyster genome reference sequences through BurrowsWheeler Aligner (BWA), we identified 54 million high-quality SNPs using Samtools and Genome Analysis Toolkit (GATK) software; these SNPs may constitute the largest available oyster SNP dataset with broad representation of oyster resources

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Summary

Introduction

Oysters (phylum Mollusca, class Bivalvia) constitute an essential component of many aquatic ecosystems and are economically important in the fisheries and aquaculture industries [1]. The Pacific cupped oyster Crassostrea gigas (Thunberg 1793) originated in northeastern Asia, and is natively distributed along the coasts of China, Japan, and Korea. It was introduced into Europe [2], Australia [3], and America [4] during the 20th century and has since established naturalized populations in most countries where it has been introduced for aquaculture purposes. On the basis of its rapid growth rate, high disease resistance, and adaptability to different environments, the Pacific oyster is one of the most economically important bivalves worldwide

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