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Genotype Imputation to Improve the Cost-Efficiency of Genomic Selection in Farmed Atlantic Salmon

journal contribution
posted on 2022-01-19, 23:37 authored by Hsin-Yuan Tsai, Oswald Matika, Stefan McKinnon Edwards, Roberto Antolín–Sánchez, Alastair Hamilton, Derrick R Guy, Alan E Tinch, Karim Gharbi, Michael StearMichael Stear, John B Taggart, James E Bron, John M Hickey, Ross D Houston
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 SNP data for genomic prediction in Atlantic salmon. Genotype imputation approaches are likely to form a critical component of cost-efficient genomic selection programs to improve economically important traits in aquaculture.


J.E.B. and J.B.T. were partly supported by the Marine Alliance for Science and Technology pooling initiative, funded by the Scottish Funding Council (grant reference HR09011) and contributing institutions. This research was supported by Biotechnology and Biological Sciences Research Council (BBSRC) grants (BB/N024044/1, BB/H022007/1, BB/M028321/1), and by BBSRC Institute Strategic Funding Grants to The Roslin Institute (BB/J004235/1, BB/J004324/1, BB/J004243/1).


Publication Date



G3: Genes, Genomes, Genetics






7p. (p. 1377-1383)


Genetics Society of America



Rights Statement

© 2017 Tsai et al. This article is published in G3 Genes|Genomes|Genetics on an exclusive licence or copyright assignment basis, and reuse rights are retained and controlled by OUP. It is distributed via the journal under the terms of the Oxford University Press, Standard Journals Publication Model (

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