An amplicon panel for high-throughput and low-cost genotyping of Pacific oyster.
Maintaining genetic diversity in cultured shellfish can be challenging due to high variance in individual reproductive success, founder effects, and rapid genetic drift, but is important to retain adaptive potential and avoid inbreeding depression. To support broodstock management and selective bree...
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Online Access: | https://doi.org/10.1093/g3journal/jkae125 https://pubmed.ncbi.nlm.nih.gov/38869232 |
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ftpubmed:38869232 2024-06-23T07:56:00+00:00 An amplicon panel for high-throughput and low-cost genotyping of Pacific oyster. Sutherland, Ben J G Thompson, Neil F Surry, Liam B Gujjula, Krishna Reddy Carrasco, Claudio D Chadaram, Srinivas Lunda, Spencer L Langdon, Christopher J Chan, Amy M Suttle, Curtis A Green, Timothy J 2024 Jun 13 https://doi.org/10.1093/g3journal/jkae125 https://pubmed.ncbi.nlm.nih.gov/38869232 eng eng Silverchair Information Systems https://doi.org/10.1093/g3journal/jkae125 https://pubmed.ncbi.nlm.nih.gov/38869232 © The Author(s) 2024. Published by Oxford University Press on behalf of The Genetics Society of America. G3 (Bethesda) ISSN:2160-1836 Crassostrea (Magallana) gigas Pacific oyster amplicon panel aquaculture genetic diversity parentage assignment Journal Article 2024 ftpubmed https://doi.org/10.1093/g3journal/jkae125 2024-06-13T16:02:00Z Maintaining genetic diversity in cultured shellfish can be challenging due to high variance in individual reproductive success, founder effects, and rapid genetic drift, but is important to retain adaptive potential and avoid inbreeding depression. To support broodstock management and selective breeding in cultured Pacific oysters (Crassostrea (Magallana) gigas), we developed an amplicon panel targeting 592 genomic regions and SNP variants with an average of 50 amplicons per chromosome. Target SNPs were selected based on elevated observed heterozygosity or differentiation in Pacific oyster populations in British Columbia, Canada. The use of the panel for parentage applications was evaluated using multiple generations of oysters from a breeding program on Vancouver Island, Canada (n = 181) and families selected for Ostreid herpesvirus-1 resistance from the Molluscan Broodstock Program in Oregon, USA (n = 136). Population characterization was evaluated using wild, naturalized, farmed, or hatchery oysters sampled throughout the Northern Hemisphere (n = 190). Technical replicates showed high genotype concordance (97.5%; n = 68 replicates). Parentage analysis found suspected pedigree and sample handling errors, demonstrating the panel's value for quality control in breeding programs. Suspected null alleles were identified and found to be largely population dependent, suggesting population-specific variation impacting target amplification. Null alleles were identified using existing data without the need for pedigree information, and once they were removed, assignment rates increased to 93.0% and 86.0% of possible assignments in the two breeding program datasets. A pipeline for analyzing the amplicon sequence data from sequencer output, amplitools, is also provided. Article in Journal/Newspaper Pacific oyster PubMed Central (PMC) British Columbia ENVELOPE(-125.003,-125.003,54.000,54.000) Canada Pacific G3: Genes, Genomes, Genetics |
institution |
Open Polar |
collection |
PubMed Central (PMC) |
op_collection_id |
ftpubmed |
language |
English |
topic |
Crassostrea (Magallana) gigas Pacific oyster amplicon panel aquaculture genetic diversity parentage assignment |
spellingShingle |
Crassostrea (Magallana) gigas Pacific oyster amplicon panel aquaculture genetic diversity parentage assignment Sutherland, Ben J G Thompson, Neil F Surry, Liam B Gujjula, Krishna Reddy Carrasco, Claudio D Chadaram, Srinivas Lunda, Spencer L Langdon, Christopher J Chan, Amy M Suttle, Curtis A Green, Timothy J An amplicon panel for high-throughput and low-cost genotyping of Pacific oyster. |
topic_facet |
Crassostrea (Magallana) gigas Pacific oyster amplicon panel aquaculture genetic diversity parentage assignment |
description |
Maintaining genetic diversity in cultured shellfish can be challenging due to high variance in individual reproductive success, founder effects, and rapid genetic drift, but is important to retain adaptive potential and avoid inbreeding depression. To support broodstock management and selective breeding in cultured Pacific oysters (Crassostrea (Magallana) gigas), we developed an amplicon panel targeting 592 genomic regions and SNP variants with an average of 50 amplicons per chromosome. Target SNPs were selected based on elevated observed heterozygosity or differentiation in Pacific oyster populations in British Columbia, Canada. The use of the panel for parentage applications was evaluated using multiple generations of oysters from a breeding program on Vancouver Island, Canada (n = 181) and families selected for Ostreid herpesvirus-1 resistance from the Molluscan Broodstock Program in Oregon, USA (n = 136). Population characterization was evaluated using wild, naturalized, farmed, or hatchery oysters sampled throughout the Northern Hemisphere (n = 190). Technical replicates showed high genotype concordance (97.5%; n = 68 replicates). Parentage analysis found suspected pedigree and sample handling errors, demonstrating the panel's value for quality control in breeding programs. Suspected null alleles were identified and found to be largely population dependent, suggesting population-specific variation impacting target amplification. Null alleles were identified using existing data without the need for pedigree information, and once they were removed, assignment rates increased to 93.0% and 86.0% of possible assignments in the two breeding program datasets. A pipeline for analyzing the amplicon sequence data from sequencer output, amplitools, is also provided. |
format |
Article in Journal/Newspaper |
author |
Sutherland, Ben J G Thompson, Neil F Surry, Liam B Gujjula, Krishna Reddy Carrasco, Claudio D Chadaram, Srinivas Lunda, Spencer L Langdon, Christopher J Chan, Amy M Suttle, Curtis A Green, Timothy J |
author_facet |
Sutherland, Ben J G Thompson, Neil F Surry, Liam B Gujjula, Krishna Reddy Carrasco, Claudio D Chadaram, Srinivas Lunda, Spencer L Langdon, Christopher J Chan, Amy M Suttle, Curtis A Green, Timothy J |
author_sort |
Sutherland, Ben J G |
title |
An amplicon panel for high-throughput and low-cost genotyping of Pacific oyster. |
title_short |
An amplicon panel for high-throughput and low-cost genotyping of Pacific oyster. |
title_full |
An amplicon panel for high-throughput and low-cost genotyping of Pacific oyster. |
title_fullStr |
An amplicon panel for high-throughput and low-cost genotyping of Pacific oyster. |
title_full_unstemmed |
An amplicon panel for high-throughput and low-cost genotyping of Pacific oyster. |
title_sort |
amplicon panel for high-throughput and low-cost genotyping of pacific oyster. |
publisher |
Silverchair Information Systems |
publishDate |
2024 |
url |
https://doi.org/10.1093/g3journal/jkae125 https://pubmed.ncbi.nlm.nih.gov/38869232 |
long_lat |
ENVELOPE(-125.003,-125.003,54.000,54.000) |
geographic |
British Columbia Canada Pacific |
geographic_facet |
British Columbia Canada Pacific |
genre |
Pacific oyster |
genre_facet |
Pacific oyster |
op_source |
G3 (Bethesda) ISSN:2160-1836 |
op_relation |
https://doi.org/10.1093/g3journal/jkae125 https://pubmed.ncbi.nlm.nih.gov/38869232 |
op_rights |
© The Author(s) 2024. Published by Oxford University Press on behalf of The Genetics Society of America. |
op_doi |
https://doi.org/10.1093/g3journal/jkae125 |
container_title |
G3: Genes, Genomes, Genetics |
_version_ |
1802648824476336128 |