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...
Published in: | G3 Genes|Genomes|Genetics |
---|---|
Main Authors: | , , , , , , , , , |
Other Authors: | , , , , |
Format: | Article in Journal/Newspaper |
Language: | English |
Published: |
Genetics Society of America
2017
|
Subjects: | |
Online Access: | http://hdl.handle.net/1893/32076 https://doi.org/10.1534/g3.117.041780 http://dspace.stir.ac.uk/bitstream/1893/32076/1/2209.full.pdf |
id |
ftunivstirling:oai:dspace.stir.ac.uk:1893/32076 |
---|---|
record_format |
openpolar |
spelling |
ftunivstirling:oai:dspace.stir.ac.uk:1893/32076 2023-05-15T15:58:29+02:00 Development of a Medium Density Combined-Species SNP Array for Pacific and European Oysters (Crassostrea gigas and Ostrea edulis) Gutierrez, Alejandro P Turner, Frances Gharbi, Karim Talbot, Richard Lowe, Natalie R Peñaloza, Carolina McCullough, Mark Prodöhl, Paulo A Bean, Tim P Houston, Ross D Biotechnology and Biological Sciences Research Council Roslin Institute University of Edinburgh Queen's University Belfast CEFAS - Centre for Environment, Fisheries and Aquaculture Science 2017-07 application/pdf http://hdl.handle.net/1893/32076 https://doi.org/10.1534/g3.117.041780 http://dspace.stir.ac.uk/bitstream/1893/32076/1/2209.full.pdf en eng Genetics Society of America Gutierrez AP, Turner F, Gharbi K, Talbot R, Lowe NR, Peñaloza C, McCullough M, Prodöhl PA, Bean TP & Houston RD (2017) Development of a Medium Density Combined-Species SNP Array for Pacific and European Oysters (Crassostrea gigas and Ostrea edulis). G3: Genes%7CGenomes%7CGenetics, 7 (7), pp. 2209-2218. https://doi.org/10.1534/g3.117.041780 http://hdl.handle.net/1893/32076 doi:10.1534/g3.117.041780 28533337 WOS:000404991600018 2-s2.0-85021834364 1685010 http://dspace.stir.ac.uk/bitstream/1893/32076/1/2209.full.pdf Copyright © 2017 Gutierrez et al. 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. http://creativecommons.org/licenses/by/4.0/ CC-BY Pacific Oyster Flat Oyster Single Nucleotide Polymorphism (SNP) Array Aquaculture Journal Article VoR - Version of Record 2017 ftunivstirling https://doi.org/10.1534/g3.117.041780 2022-06-13T18:42:05Z 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 (Crassostrea gigas) and European flat oyster (Ostrea edulis), 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 C. gigas populations, and restriction site-associated DNA sequencing (RAD-Seq) of 11 geographically diverse O. edulis 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 (n = 219) showing ∼27 K high quality SNPs for C. gigas and ∼11 K high quality SNPs for O. edulis 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 C. gigas nuclear families (n = 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. Article in Journal/Newspaper Crassostrea gigas Pacific oyster University of Stirling: Stirling Digital Research Repository Pacific G3 Genes|Genomes|Genetics 7 7 2209 2218 |
institution |
Open Polar |
collection |
University of Stirling: Stirling Digital Research Repository |
op_collection_id |
ftunivstirling |
language |
English |
topic |
Pacific Oyster Flat Oyster Single Nucleotide Polymorphism (SNP) Array Aquaculture |
spellingShingle |
Pacific Oyster Flat Oyster Single Nucleotide Polymorphism (SNP) Array Aquaculture Gutierrez, Alejandro P Turner, Frances Gharbi, Karim Talbot, Richard Lowe, Natalie R Peñaloza, Carolina McCullough, Mark Prodöhl, Paulo A Bean, Tim P Houston, Ross D Development of a Medium Density Combined-Species SNP Array for Pacific and European Oysters (Crassostrea gigas and Ostrea edulis) |
topic_facet |
Pacific Oyster Flat Oyster Single Nucleotide Polymorphism (SNP) Array Aquaculture |
description |
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 (Crassostrea gigas) and European flat oyster (Ostrea edulis), 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 C. gigas populations, and restriction site-associated DNA sequencing (RAD-Seq) of 11 geographically diverse O. edulis 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 (n = 219) showing ∼27 K high quality SNPs for C. gigas and ∼11 K high quality SNPs for O. edulis 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 C. gigas nuclear families (n = 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. |
author2 |
Biotechnology and Biological Sciences Research Council Roslin Institute University of Edinburgh Queen's University Belfast CEFAS - Centre for Environment, Fisheries and Aquaculture Science |
format |
Article in Journal/Newspaper |
author |
Gutierrez, Alejandro P Turner, Frances Gharbi, Karim Talbot, Richard Lowe, Natalie R Peñaloza, Carolina McCullough, Mark Prodöhl, Paulo A Bean, Tim P Houston, Ross D |
author_facet |
Gutierrez, Alejandro P Turner, Frances Gharbi, Karim Talbot, Richard Lowe, Natalie R Peñaloza, Carolina McCullough, Mark Prodöhl, Paulo A Bean, Tim P Houston, Ross D |
author_sort |
Gutierrez, Alejandro P |
title |
Development of a Medium Density Combined-Species SNP Array for Pacific and European Oysters (Crassostrea gigas and Ostrea edulis) |
title_short |
Development of a Medium Density Combined-Species SNP Array for Pacific and European Oysters (Crassostrea gigas and Ostrea edulis) |
title_full |
Development of a Medium Density Combined-Species SNP Array for Pacific and European Oysters (Crassostrea gigas and Ostrea edulis) |
title_fullStr |
Development of a Medium Density Combined-Species SNP Array for Pacific and European Oysters (Crassostrea gigas and Ostrea edulis) |
title_full_unstemmed |
Development of a Medium Density Combined-Species SNP Array for Pacific and European Oysters (Crassostrea gigas and Ostrea edulis) |
title_sort |
development of a medium density combined-species snp array for pacific and european oysters (crassostrea gigas and ostrea edulis) |
publisher |
Genetics Society of America |
publishDate |
2017 |
url |
http://hdl.handle.net/1893/32076 https://doi.org/10.1534/g3.117.041780 http://dspace.stir.ac.uk/bitstream/1893/32076/1/2209.full.pdf |
geographic |
Pacific |
geographic_facet |
Pacific |
genre |
Crassostrea gigas Pacific oyster |
genre_facet |
Crassostrea gigas Pacific oyster |
op_relation |
Gutierrez AP, Turner F, Gharbi K, Talbot R, Lowe NR, Peñaloza C, McCullough M, Prodöhl PA, Bean TP & Houston RD (2017) Development of a Medium Density Combined-Species SNP Array for Pacific and European Oysters (Crassostrea gigas and Ostrea edulis). G3: Genes%7CGenomes%7CGenetics, 7 (7), pp. 2209-2218. https://doi.org/10.1534/g3.117.041780 http://hdl.handle.net/1893/32076 doi:10.1534/g3.117.041780 28533337 WOS:000404991600018 2-s2.0-85021834364 1685010 http://dspace.stir.ac.uk/bitstream/1893/32076/1/2209.full.pdf |
op_rights |
Copyright © 2017 Gutierrez et al. 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. http://creativecommons.org/licenses/by/4.0/ |
op_rightsnorm |
CC-BY |
op_doi |
https://doi.org/10.1534/g3.117.041780 |
container_title |
G3 Genes|Genomes|Genetics |
container_volume |
7 |
container_issue |
7 |
container_start_page |
2209 |
op_container_end_page |
2218 |
_version_ |
1766394227895304192 |