Optimizing Low-Cost Genotyping and Imputation Strategies for Genomic Selection in Atlantic Salmon
Abstract Genomic selection enables cumulative genetic gains in key production traits such as disease resistance, playing an important role in the economic and environmental sustainability of aquaculture production. However, it requires genome-wide genetic marker data on large populations, which can...
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Online Access: | http://dx.doi.org/10.1534/g3.119.400800 http://academic.oup.com/g3journal/article-pdf/10/2/581/40634029/g3journal0581.pdf |
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croxfordunivpr:10.1534/g3.119.400800 2024-09-30T14:32:24+00:00 Optimizing Low-Cost Genotyping and Imputation Strategies for Genomic Selection in Atlantic Salmon Tsairidou, Smaragda Hamilton, Alastair Robledo, Diego Bron, James E Houston, Ross D 2020 http://dx.doi.org/10.1534/g3.119.400800 http://academic.oup.com/g3journal/article-pdf/10/2/581/40634029/g3journal0581.pdf en eng Oxford University Press (OUP) https://academic.oup.com/journals/pages/open_access/funder_policies/chorus/standard_publication_model G3 Genes|Genomes|Genetics volume 10, issue 2, page 581-590 ISSN 2160-1836 journal-article 2020 croxfordunivpr https://doi.org/10.1534/g3.119.400800 2024-09-10T04:13:15Z Abstract Genomic selection enables cumulative genetic gains in key production traits such as disease resistance, playing an important role in the economic and environmental sustainability of aquaculture production. However, it requires genome-wide genetic marker data on large populations, which can be prohibitively expensive. Genotype imputation is a cost-effective method for obtaining high-density genotypes, but its value in aquaculture breeding programs which are characterized by large full-sibling families has yet to be fully assessed. The aim of this study was to optimize the use of low-density genotypes and evaluate genotype imputation strategies for cost-effective genomic prediction. Phenotypes and genotypes (78,362 SNPs) were obtained for 610 individuals from a Scottish Atlantic salmon breeding program population (Landcatch, UK) challenged with sea lice, Lepeophtheirus salmonis. The genomic prediction accuracy of genomic selection was calculated using GBLUP approaches and compared across SNP panels of varying densities and composition, with and without imputation. Imputation was tested when parents were genotyped for the optimal SNP panel, and offspring were genotyped for a range of lower density imputation panels. Reducing SNP density had little impact on prediction accuracy until 5,000 SNPs, below which the accuracy dropped. Imputation accuracy increased with increasing imputation panel density. Genomic prediction accuracy when offspring were genotyped for just 200 SNPs, and parents for 5,000 SNPs, was 0.53. This accuracy was similar to the full high density and optimal density dataset, and markedly higher than using 200 SNPs without imputation. These results suggest that imputation from very low to medium density can be a cost-effective tool for genomic selection in Atlantic salmon breeding programs. Article in Journal/Newspaper Atlantic salmon Oxford University Press G3 Genes|Genomes|Genetics 10 2 581 590 |
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Oxford University Press |
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croxfordunivpr |
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English |
description |
Abstract Genomic selection enables cumulative genetic gains in key production traits such as disease resistance, playing an important role in the economic and environmental sustainability of aquaculture production. However, it requires genome-wide genetic marker data on large populations, which can be prohibitively expensive. Genotype imputation is a cost-effective method for obtaining high-density genotypes, but its value in aquaculture breeding programs which are characterized by large full-sibling families has yet to be fully assessed. The aim of this study was to optimize the use of low-density genotypes and evaluate genotype imputation strategies for cost-effective genomic prediction. Phenotypes and genotypes (78,362 SNPs) were obtained for 610 individuals from a Scottish Atlantic salmon breeding program population (Landcatch, UK) challenged with sea lice, Lepeophtheirus salmonis. The genomic prediction accuracy of genomic selection was calculated using GBLUP approaches and compared across SNP panels of varying densities and composition, with and without imputation. Imputation was tested when parents were genotyped for the optimal SNP panel, and offspring were genotyped for a range of lower density imputation panels. Reducing SNP density had little impact on prediction accuracy until 5,000 SNPs, below which the accuracy dropped. Imputation accuracy increased with increasing imputation panel density. Genomic prediction accuracy when offspring were genotyped for just 200 SNPs, and parents for 5,000 SNPs, was 0.53. This accuracy was similar to the full high density and optimal density dataset, and markedly higher than using 200 SNPs without imputation. These results suggest that imputation from very low to medium density can be a cost-effective tool for genomic selection in Atlantic salmon breeding programs. |
format |
Article in Journal/Newspaper |
author |
Tsairidou, Smaragda Hamilton, Alastair Robledo, Diego Bron, James E Houston, Ross D |
spellingShingle |
Tsairidou, Smaragda Hamilton, Alastair Robledo, Diego Bron, James E Houston, Ross D Optimizing Low-Cost Genotyping and Imputation Strategies for Genomic Selection in Atlantic Salmon |
author_facet |
Tsairidou, Smaragda Hamilton, Alastair Robledo, Diego Bron, James E Houston, Ross D |
author_sort |
Tsairidou, Smaragda |
title |
Optimizing Low-Cost Genotyping and Imputation Strategies for Genomic Selection in Atlantic Salmon |
title_short |
Optimizing Low-Cost Genotyping and Imputation Strategies for Genomic Selection in Atlantic Salmon |
title_full |
Optimizing Low-Cost Genotyping and Imputation Strategies for Genomic Selection in Atlantic Salmon |
title_fullStr |
Optimizing Low-Cost Genotyping and Imputation Strategies for Genomic Selection in Atlantic Salmon |
title_full_unstemmed |
Optimizing Low-Cost Genotyping and Imputation Strategies for Genomic Selection in Atlantic Salmon |
title_sort |
optimizing low-cost genotyping and imputation strategies for genomic selection in atlantic salmon |
publisher |
Oxford University Press (OUP) |
publishDate |
2020 |
url |
http://dx.doi.org/10.1534/g3.119.400800 http://academic.oup.com/g3journal/article-pdf/10/2/581/40634029/g3journal0581.pdf |
genre |
Atlantic salmon |
genre_facet |
Atlantic salmon |
op_source |
G3 Genes|Genomes|Genetics volume 10, issue 2, page 581-590 ISSN 2160-1836 |
op_rights |
https://academic.oup.com/journals/pages/open_access/funder_policies/chorus/standard_publication_model |
op_doi |
https://doi.org/10.1534/g3.119.400800 |
container_title |
G3 Genes|Genomes|Genetics |
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10 |
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2 |
container_start_page |
581 |
op_container_end_page |
590 |
_version_ |
1811636577986674688 |