Highly accurate sequence imputation enables precise QTL mapping in Brown Swiss cattle

BMC Genomics
Mirjam FrischknechtBirgit Gredler-Grandl

Abstract

Within the last few years a large amount of genomic information has become available in cattle. Densities of genomic information vary from a few thousand variants up to whole genome sequence information. In order to combine genomic information from different sources and infer genotypes for a common set of variants, genotype imputation is required. In this study we evaluated the accuracy of imputation from high density chips to whole genome sequence data in Brown Swiss cattle. Using four popular imputation programs (Beagle, FImpute, Impute2, Minimac) and various compositions of reference panels, the accuracy of the imputed sequence variant genotypes was high and differences between the programs and scenarios were small. We imputed sequence variant genotypes for more than 1600 Brown Swiss bulls and performed genome-wide association studies for milk fat percentage at two stages of lactation. We found one and three quantitative trait loci for early and late lactation fat content, respectively. Known causal variants that were imputed from the sequenced reference panel were among the most significantly associated variants of the genome-wide association study. Our study demonstrates that whole-genome sequence information can be impute...Continue Reading

References

Jun 1, 1992·Journal of Dairy Science·T L StantonS D Kachman
Mar 8, 2000·International Journal for Parasitology·I MollaretJ L Justine
Oct 24, 2008·Journal of Dairy Science·P M VanRaden
Feb 10, 2009·American Journal of Human Genetics·Brian L Browning, Sharon R Browning
Apr 25, 2009·PloS One·Lakshmi K MatukumalliCurtis P Van Tassell
Apr 28, 2009·Genome Biology·Aleksey V ZiminSteven L Salzberg
Jun 10, 2009·Bioinformatics·Heng LiUNKNOWN 1000 Genome Project Data Processing Subgroup
Dec 10, 2009·Nature Reviews. Genetics·Michael L Metzker
Jun 3, 2010·Nature Reviews. Genetics·Jonathan Marchini, Bryan Howie
Jun 10, 2011·Bioinformatics·Petr DanecekUNKNOWN 1000 Genomes Project Analysis Group
Jan 10, 2012·Animal Genetics·B J HayesJ H J van der Werf
Feb 15, 2013·Genetics, Selection, Evolution : GSE·Hubert PauschRuedi Fries
Sep 6, 2013·Genetics, Selection, Evolution : GSE·Chris HozéPascal Croiseau
Feb 6, 2014·Genetics, Selection, Evolution : GSE·Laura J CorbinJohn A Woolliams
Feb 13, 2014·BMC Genomics·Ezequiel Luis NicolazziAlessandra Stella
Jun 18, 2014·BMC Genomics·Mehdi SargolzaeiFlavio S Schenkel
Jul 16, 2014·Genetics, Selection, Evolution : GSE·Rianne van BinsbergenRoel F Veerkamp
Oct 24, 2014·Bioinformatics·Christian FuchsbergerDavid A Hinds
Dec 30, 2014·BMC Genetics·Mario L PiccoliFlávio S Schenkel
Feb 28, 2015·GigaScience·Christopher C ChangJames J Lee
Apr 1, 2015·Journal of Animal Breeding and Genetics = Zeitschrift Für Tierzüchtung Und Züchtungsbiologie·K E KemperM E Goddard
Apr 11, 2015·Frontiers in Genetics·Eva M StruckenGudrun A Brockmann
Jan 1, 2014·Genetics, Selection, Evolution : GSE·Mirjam FrischknechtStefan Rieder

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Citations

Apr 17, 2019·Frontiers in Genetics·Avhashoni A ZwaneJeremy F Taylor
Dec 7, 2018·Annual Review of Animal Biosciences·Ben J Hayes, Hans D Daetwyler
Dec 28, 2019·Genetics, Selection, Evolution : GSE·Troy N RowanJared E Decker
Mar 14, 2021·Genetics, Selection, Evolution : GSE·Gerardo A Fernandes JúniorLucia G de Albuquerque

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Methods Mentioned

BETA
chips
chip
genotyping
PCA

Software Mentioned

VCFtools
MEM
Simmental
IMPUTE2
samtools
FImpute
BEAGLE
EMMAX
Minimac
R princomp

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