Short communication: Accuracy of whole-genome sequence imputation in Angus cattle using within-breed and multi breed reference populations

Title
Short communication: Accuracy of whole-genome sequence imputation in Angus cattle using within-breed and multi breed reference populations
Publication Date
2024-03
Author(s)
Kamprasert, N
( author )
OrcID: https://orcid.org/0000-0001-5747-7043
Email: nkampras@myune.edu.au
UNE Id une-id:nkampras
Aliloo, H
( author )
OrcID: https://orcid.org/0000-0002-5587-6929
Email: haliloo@une.edu.au
UNE Id une-id:haliloo
Van Der Werf, J H J
( author )
OrcID: https://orcid.org/0000-0003-2512-1696
Email: jvanderw@une.edu.au
UNE Id une-id:jvanderw
Clark, S A
( author )
OrcID: https://orcid.org/0000-0001-8605-1738
Email: sclark37@une.edu.au
UNE Id une-id:sclark37
Type of document
Journal Article
Language
en
Entity Type
Publication
Publisher
Elsevier BV
Place of publication
United Kingdom
DOI
10.1016/j.animal.2024.101087
UNE publication id
une:1959.11/64517
Abstract

Genotype imputation is a standard approach used in the field of genetics. It can be used to fill in missing genotypes or to increase genotype density. Accurate imputed genotypes are required for downstream analyses. In this study, the accuracy of whole-genome sequence imputation for Angus beef cattle was examined using two different ways to form the reference panel, a within-breed reference population and a multi breed reference population. A stepwise imputation was conducted by imputing medium density (50k) genotypes to high-density, and then to the whole genome sequence (WGS). The reference population consisted of animals with WGS information from the 1,000 Bull Genomes project. The withinbreed reference panel comprised 396 Angus cattle, while an additional 2 380 Taurine cattle were added to the reference population for the multi breed reference scenario. Imputation accuracies were variant-wise average accuracies from a 10-fold cross-validation and expressed as concordance rates (CR) and Pearson’s correlations (PR). The two imputation scenarios achieved moderate to high imputation accuracies ranging from 0.896 to 0.966 for CR and from 0.779 to 0.834 for PR. The accuracies from two different scenarios were similar, except for PR from WGS imputation, where the within-breed scenario outperformed the multi breed scenario. The result indicated that including a large number of animals from other breeds in the reference panel to impute purebred Angus did not improve the accuracy and may negatively impact the results. In conclusion, the imputed WGS in Angus cattle can be obtained with high accuracy using a within-breed reference panel.

Link
Citation
Animal, v.18 (3)
ISSN
1751-732X
1751-7311
Rights
Attribution-NonCommercial-NoDerivatives 4.0 International

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