Utility of whole-genome sequence data for across-breed genomic prediction

Genetics, Selection, Evolution : GSE
Biaty RaymondRoel F Veerkamp

Abstract

Genomic prediction (GP) across breeds has so far resulted in low accuracies of the predicted genomic breeding values. Our objective was to evaluate whether using whole-genome sequence (WGS) instead of low-density markers can improve GP across breeds, especially when markers are pre-selected from a genome-wide association study (GWAS), and to test our hypothesis that many non-causal markers in WGS data have a diluting effect on accuracy of across-breed prediction. Estimated breeding values for stature and bovine high-density (HD) genotypes were available for 595 Jersey bulls from New Zealand, 957 Holstein bulls from New Zealand and 5553 Holstein bulls from the Netherlands. BovineHD genotypes for all bulls were imputed to WGS using Beagle4 and Minimac2. Genomic prediction across the three populations was performed with ASReml4, with each population used as single reference and as single validation sets. In addition to the 50k, HD and WGS, markers that were significantly associated with stature in a large meta-GWAS analysis were selected and used for prediction, resulting in 10 prediction scenarios. Furthermore, we estimated the proportion of genetic variance captured by markers in each scenario. Across breeds, 50k, HD and WGS mar...Continue Reading

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Citations

May 17, 2019·Genetics, Selection, Evolution : GSE·Danang CrysnantoHubert Pausch
Sep 21, 2019·Journal of Animal Science·Yvette SteynIgnacy Misztal
Dec 21, 2019·G3 : Genes - Genomes - Genetics·Pascal DuenkJulius H J van der Werf
Apr 7, 2020·Genetics, Selection, Evolution : GSE·Roger Ros-FreixedesJohn M Hickey
Apr 7, 2020·Genetics, Selection, Evolution : GSE·Roger Ros-FreixedesJohn M Hickey
Oct 14, 2018·Genetics, Selection, Evolution : GSE·Biaty RaymondRoel F Veerkamp
Dec 7, 2018·Annual Review of Animal Biosciences·Ben J Hayes, Hans D Daetwyler
Dec 7, 2019·Genetics, Selection, Evolution : GSE·Nasir MoghaddarIona M MacLeod
Jan 27, 2019·Genetics, Selection, Evolution : GSE·Sanne van den BergRoel F Veerkamp
Oct 1, 2020·Genetics, Selection, Evolution : GSE·Sara de Las Heras-SaldanaJulius H J van der Werf
May 28, 2020·G3 : Genes - Genomes - Genetics·Marcus O OlatoyeAlexander E Lipka
Dec 4, 2019·G3 : Genes - Genomes - Genetics·Sai Krishna ArojjuMarty J Faville
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May 14, 2021·BMC Genomics·Johannes GeibelHenner Simianer
Jun 2, 2021·Genetics, Selection, Evolution : GSE·Emre KaramanMogens S Lund
Aug 11, 2021·Journal of Animal Breeding and Genetics = Zeitschrift Für Tierzüchtung Und Züchtungsbiologie·Nasir MoghaddarJulius H van der Werf
Aug 24, 2021·Frontiers in Plant Science·Lance F MerrickArron H Carter

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Methods Mentioned

BETA
chip

Software Mentioned

BayesB
grm
GCTA
calc
GREML
BEAGLE
MINIMAC2
ASReml

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