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dc.contributor.author
Da Costa Hermisdorff, Isis
dc.contributor.author
Costa, Raphael Bermal
dc.contributor.author
Galvão de Albuquerque, Lucia
dc.contributor.author
Pausch, Hubert
dc.contributor.author
Kadri, Naveen Kumar
dc.date.accessioned
2020-11-10T09:23:13Z
dc.date.available
2020-11-10T08:40:01Z
dc.date.available
2020-11-10T09:23:13Z
dc.date.issued
2020-11-10
dc.identifier.other
10.1186/s12864-020-07184-8
en_US
dc.identifier.uri
http://hdl.handle.net/20.500.11850/450471
dc.identifier.doi
10.3929/ethz-b-000450471
dc.description.abstract
Background Imputation accuracy among other things depends on the size of the reference panel, the marker’s minor allele frequency (MAF), and the correct placement of single nucleotide polymorphism (SNP) on the reference genome assembly. Using high-density genotypes of 3938 Nellore cattle from Brazil, we investigated the accuracy of imputation from 50 K to 777 K SNP density using Minimac3, when map positions were determined according to the bovine genome assemblies UMD3.1 and ARS-UCD1.2. We assessed the effect of reference and target panel sizes on the pre-phasing based imputation quality using ten-fold cross-validation. Further, we compared the reliability of the model-based imputation quality score (Rsq) from Minimac3 to the empirical imputation accuracy. Results The overall accuracy of imputation measured as the squared correlation between true and imputed allele dosages (R2dose) was almost identical using either the UMD3.1 or ARS-UCD1.2 genome assembly. When the size of the reference panel increased from 250 to 2000, R2dose increased from 0.845 to 0.917, and the number of polymorphic markers in the imputed data set increased from 586,701 to 618,660. Advantages in both accuracy and marker density were also observed when larger target panels were imputed, likely resulting from more accurate haplotype inference. Imputation accuracy increased from 0.903 to 0.913, and the marker density in the imputed data increased from 593,239 to 595,570 when haplotypes were inferred in 500 and 2900 target animals. The model-based imputation quality scores from Minimac3 (Rsq) were systematically higher than empirically estimated accuracies. However, both metrics were positively correlated and the correlation increased with the size of the reference panel and MAF of imputed variants. Conclusions Accurate imputation of BovineHD BeadChip markers is possible in Nellore cattle using the new bovine reference genome assembly ARS-UCD1.2. The use of large reference and target panels improves the accuracy of the imputed genotypes and provides genotypes for more markers segregating at low frequency for downstream genomic analyses. The model-based imputation quality score from Minimac3 (Rsq) can be used to detect poorly imputed variants but its reliability depends on the size of the reference panel and MAF of the imputed variants.
en_US
dc.format
application/pdf
en_US
dc.language.iso
en
en_US
dc.publisher
BioMed Central
en_US
dc.rights.uri
http://creativecommons.org/licenses/by/4.0/
dc.title
Investigating the accuracy of imputing autosomal variants in Nellore cattle using the ARS-UCD1.2 assembly of the bovine genome
en_US
dc.type
Journal Article
dc.rights.license
Creative Commons Attribution 4.0 International
ethz.journal.title
BMC Genomics
ethz.journal.volume
21
en_US
ethz.journal.issue
1
en_US
ethz.pages.start
772
en_US
ethz.size
12 p.
en_US
ethz.version.deposit
publishedVersion
en_US
ethz.identifier.wos
ethz.identifier.scopus
ethz.publication.place
London
en_US
ethz.publication.status
published
en_US
ethz.leitzahl
ETH Zürich::00002 - ETH Zürich::00012 - Lehre und Forschung::00007 - Departemente::02350 - Dep. Umweltsystemwissenschaften / Dep. of Environmental Systems Science::02703 - Institut für Agrarwissenschaften / Institute of Agricultural Sciences::09575 - Pausch, Hubert / Pausch, Hubert
en_US
ethz.leitzahl.certified
ETH Zürich::00002 - ETH Zürich::00012 - Lehre und Forschung::00007 - Departemente::02350 - Dep. Umweltsystemwissenschaften / Dep. of Environmental Systems Science::02703 - Institut für Agrarwissenschaften / Institute of Agricultural Sciences::09575 - Pausch, Hubert / Pausch, Hubert
en_US
ethz.date.deposited
2020-11-10T08:40:25Z
ethz.source
FORM
ethz.eth
yes
en_US
ethz.availability
Open access
en_US
ethz.rosetta.installDate
2020-11-10T09:23:24Z
ethz.rosetta.lastUpdated
2021-02-15T20:39:24Z
ethz.rosetta.versionExported
true
ethz.COinS
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