Development of a Medium Density Combined-Species SNP Array for Pacific and European Oysters ( Crassostrea gigas and Ostrea edulis )
SNP arrays are enabling tools for high-resolution studies of the genetic basis of complex traits in farmed and wild animals. Oysters are of critical importance in many regions from both an ecological and economic perspective, and oyster aquaculture forms a key component of global food security. The...
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Published in | G3 : genes - genomes - genetics Vol. 7; no. 7; pp. 2209 - 2218 |
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Main Authors | , , , , , , , , , |
Format | Journal Article |
Language | English |
Published |
England
Genetics Society of America
01.07.2017
Oxford University Press |
Subjects | |
Online Access | Get full text |
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Summary: | SNP arrays are enabling tools for high-resolution studies of the genetic basis of complex traits in farmed and wild animals. Oysters are of critical importance in many regions from both an ecological and economic perspective, and oyster aquaculture forms a key component of global food security. The aim of our study was to design a combined-species, medium density SNP array for Pacific oyster (
) and European flat oyster (
), and to test the performance of this array on farmed and wild populations from multiple locations, with a focus on European populations. SNP discovery was carried out by whole-genome sequencing (WGS) of pooled genomic DNA samples from eight
populations, and restriction site-associated DNA sequencing (RAD-Seq) of 11 geographically diverse
populations. Nearly 12 million candidate SNPs were discovered and filtered based on several criteria, including preference for SNPs segregating in multiple populations and SNPs with monomorphic flanking regions. An Affymetrix Axiom Custom Array was created and tested on a diverse set of samples (
= 219) showing ∼27 K high quality SNPs for
and ∼11 K high quality SNPs for
segregating in these populations. A high proportion of SNPs were segregating in each of the populations, and the array was used to detect population structure and levels of linkage disequilibrium (LD). Further testing of the array on three
nuclear families (
= 165) revealed that the array can be used to clearly distinguish between both families based on identity-by-state (IBS) clustering parental assignment software. This medium density, combined-species array will be publicly available through Affymetrix, and will be applied for genome-wide association and evolutionary genetic studies, and for genomic selection in oyster breeding programs. |
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Bibliography: | ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23 This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
ISSN: | 2160-1836 2160-1836 |
DOI: | 10.1534/g3.117.041780 |