Genotype Imputation To Improve the Cost-Efficiency of Genomic Selection in Farmed Atlantic Salmon
Genomic selection uses genome-wide marker information to predict breeding values for traits of economic interest, and is more accurate than pedigree-based methods. The development of high density SNP arrays for Atlantic salmon has enabled genomic selection in selective breeding programs, alongside h...
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ftpubmed:oai:pubmedcentral.nih.gov:5386885 2023-05-15T15:32:01+02:00 Genotype Imputation To Improve the Cost-Efficiency of Genomic Selection in Farmed Atlantic Salmon Tsai, Hsin-Yuan Matika, Oswald Edwards, Stefan McKinnon Antolín–Sánchez, Roberto Hamilton, Alastair Guy, Derrick R. Tinch, Alan E. Gharbi, Karim Stear, Michael J. Taggart, John B. Bron, James E. Hickey, John M. Houston, Ross D. 2017-03-01 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5386885/ http://www.ncbi.nlm.nih.gov/pubmed/28250015 https://doi.org/10.1534/g3.117.040717 en eng Genetics Society of America http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5386885/ http://www.ncbi.nlm.nih.gov/pubmed/28250015 http://dx.doi.org/10.1534/g3.117.040717 Copyright © 2017 Tsai et al. http://creativecommons.org/licenses/by/4.0/ 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. CC-BY Genomic Selection Text 2017 ftpubmed https://doi.org/10.1534/g3.117.040717 2017-04-16T00:15:19Z Genomic selection uses genome-wide marker information to predict breeding values for traits of economic interest, and is more accurate than pedigree-based methods. The development of high density SNP arrays for Atlantic salmon has enabled genomic selection in selective breeding programs, alongside high-resolution association mapping of the genetic basis of complex traits. However, in sibling testing schemes typical of salmon breeding programs, trait records are available on many thousands of fish with close relationships to the selection candidates. Therefore, routine high density SNP genotyping may be prohibitively expensive. One means to reducing genotyping cost is the use of genotype imputation, where selected key animals (e.g., breeding program parents) are genotyped at high density, and the majority of individuals (e.g., performance tested fish and selection candidates) are genotyped at much lower density, followed by imputation to high density. The main objectives of the current study were to assess the feasibility and accuracy of genotype imputation in the context of a salmon breeding program. The specific aims were: (i) to measure the accuracy of genotype imputation using medium (25 K) and high (78 K) density mapped SNP panels, by masking varying proportions of the genotypes and assessing the correlation between the imputed genotypes and the true genotypes; and (ii) to assess the efficacy of imputed genotype data in genomic prediction of key performance traits (sea lice resistance and body weight). Imputation accuracies of up to 0.90 were observed using the simple two-generation pedigree dataset, and moderately high accuracy (0.83) was possible even with very low density SNP data (∼250 SNPs). The performance of genomic prediction using imputed genotype data was comparable to using true genotype data, and both were superior to pedigree-based prediction. These results demonstrate that the genotype imputation approach used in this study can provide a cost-effective method for generating robust genome-wide ... Text Atlantic salmon PubMed Central (PMC) G3 Genes|Genomes|Genetics 7 4 1377 1383 |
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PubMed Central (PMC) |
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English |
topic |
Genomic Selection |
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Genomic Selection Tsai, Hsin-Yuan Matika, Oswald Edwards, Stefan McKinnon Antolín–Sánchez, Roberto Hamilton, Alastair Guy, Derrick R. Tinch, Alan E. Gharbi, Karim Stear, Michael J. Taggart, John B. Bron, James E. Hickey, John M. Houston, Ross D. Genotype Imputation To Improve the Cost-Efficiency of Genomic Selection in Farmed Atlantic Salmon |
topic_facet |
Genomic Selection |
description |
Genomic selection uses genome-wide marker information to predict breeding values for traits of economic interest, and is more accurate than pedigree-based methods. The development of high density SNP arrays for Atlantic salmon has enabled genomic selection in selective breeding programs, alongside high-resolution association mapping of the genetic basis of complex traits. However, in sibling testing schemes typical of salmon breeding programs, trait records are available on many thousands of fish with close relationships to the selection candidates. Therefore, routine high density SNP genotyping may be prohibitively expensive. One means to reducing genotyping cost is the use of genotype imputation, where selected key animals (e.g., breeding program parents) are genotyped at high density, and the majority of individuals (e.g., performance tested fish and selection candidates) are genotyped at much lower density, followed by imputation to high density. The main objectives of the current study were to assess the feasibility and accuracy of genotype imputation in the context of a salmon breeding program. The specific aims were: (i) to measure the accuracy of genotype imputation using medium (25 K) and high (78 K) density mapped SNP panels, by masking varying proportions of the genotypes and assessing the correlation between the imputed genotypes and the true genotypes; and (ii) to assess the efficacy of imputed genotype data in genomic prediction of key performance traits (sea lice resistance and body weight). Imputation accuracies of up to 0.90 were observed using the simple two-generation pedigree dataset, and moderately high accuracy (0.83) was possible even with very low density SNP data (∼250 SNPs). The performance of genomic prediction using imputed genotype data was comparable to using true genotype data, and both were superior to pedigree-based prediction. These results demonstrate that the genotype imputation approach used in this study can provide a cost-effective method for generating robust genome-wide ... |
format |
Text |
author |
Tsai, Hsin-Yuan Matika, Oswald Edwards, Stefan McKinnon Antolín–Sánchez, Roberto Hamilton, Alastair Guy, Derrick R. Tinch, Alan E. Gharbi, Karim Stear, Michael J. Taggart, John B. Bron, James E. Hickey, John M. Houston, Ross D. |
author_facet |
Tsai, Hsin-Yuan Matika, Oswald Edwards, Stefan McKinnon Antolín–Sánchez, Roberto Hamilton, Alastair Guy, Derrick R. Tinch, Alan E. Gharbi, Karim Stear, Michael J. Taggart, John B. Bron, James E. Hickey, John M. Houston, Ross D. |
author_sort |
Tsai, Hsin-Yuan |
title |
Genotype Imputation To Improve the Cost-Efficiency of Genomic Selection in Farmed Atlantic Salmon |
title_short |
Genotype Imputation To Improve the Cost-Efficiency of Genomic Selection in Farmed Atlantic Salmon |
title_full |
Genotype Imputation To Improve the Cost-Efficiency of Genomic Selection in Farmed Atlantic Salmon |
title_fullStr |
Genotype Imputation To Improve the Cost-Efficiency of Genomic Selection in Farmed Atlantic Salmon |
title_full_unstemmed |
Genotype Imputation To Improve the Cost-Efficiency of Genomic Selection in Farmed Atlantic Salmon |
title_sort |
genotype imputation to improve the cost-efficiency of genomic selection in farmed atlantic salmon |
publisher |
Genetics Society of America |
publishDate |
2017 |
url |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5386885/ http://www.ncbi.nlm.nih.gov/pubmed/28250015 https://doi.org/10.1534/g3.117.040717 |
genre |
Atlantic salmon |
genre_facet |
Atlantic salmon |
op_relation |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5386885/ http://www.ncbi.nlm.nih.gov/pubmed/28250015 http://dx.doi.org/10.1534/g3.117.040717 |
op_rights |
Copyright © 2017 Tsai et al. http://creativecommons.org/licenses/by/4.0/ 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. |
op_rightsnorm |
CC-BY |
op_doi |
https://doi.org/10.1534/g3.117.040717 |
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7 |
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