Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

    Full text documents are added when available. The database is updated daily and currently holds about 240,000 items, of which 72,000 in open access.

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Record number 478164
Title High Imputation Accuracy in Layer Chicken from Sequence Data on a Few Key Ancestors
Author(s) Heidaritabar, M.; Calus, M.P.L.; Vereijken, A.; Groenen, M.A.M.; Bastiaansen, J.W.M.
Source In: Proceedings, 10th World Congress of Genetics Applied to Livestock Production. - - p. 660 - 660.
Event 10th WCGALP, Vancouver, Canada, 2014-08-17/2014-08-22
Department(s) Animal Breeding and Genomics
Animal Breeding & Genomics
WIAS
Publication type Contribution in proceedings
Publication year 2014
Abstract We assessed a scenario designed to mimic the imputation of full genome sequence data in White layer chickens, genotyped at medium (60K) density. Factors affecting accuracy were the size of the reference population, the level of the relationship between the reference and test populations and minor allele frequency of the SNP being imputed. Genotype imputation based on 22 or 62 carefully selected reference animals resulted in accuracies between 0.78 and 0.87. So, a very small reference population already provided satisfactory results. These results suggest that full genome SNP imputation is possible in layer chicken when a suitable pool of key ancestors is sequenced. SNPs with low MAF were more difficult to impute. Accuracies did not reduce when test populations were 1, 2, or 3 generations away from the reference animals
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