A function accounting for training set size and marker density to model the average accuracy of genomic prediction

PloS One
M ErbeHenner Simianer

Abstract

Prediction of genomic breeding values is of major practical relevance in dairy cattle breeding. Deterministic equations have been suggested to predict the accuracy of genomic breeding values in a given design which are based on training set size, reliability of phenotypes, and the number of independent chromosome segments ([Formula: see text]). The aim of our study was to find a general deterministic equation for the average accuracy of genomic breeding values that also accounts for marker density and can be fitted empirically. Two data sets of 5'698 Holstein Friesian bulls genotyped with 50 K SNPs and 1'332 Brown Swiss bulls genotyped with 50 K SNPs and imputed to ∼600 K SNPs were available. Different k-fold (k = 2-10, 15, 20) cross-validation scenarios (50 replicates, random assignment) were performed using a genomic BLUP approach. A maximum likelihood approach was used to estimate the parameters of different prediction equations. The highest likelihood was obtained when using a modified form of the deterministic equation of Daetwyler et al. (2010), augmented by a weighting factor (w) based on the assumption that the maximum achievable accuracy is [Formula: see text]. The proportion of genetic variance captured by the complet...Continue Reading

References

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Sep 2, 2008·Genetics·Andrés LegarraJean-Michel Elsen
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Citations

Jun 27, 2014·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Hans D DaetwylerBen J Hayes
Mar 14, 2016·Journal of Dairy Science·Ashley A MikshowskyKent A Weigel
Nov 8, 2014·Journal of Animal Breeding and Genetics = Zeitschrift Für Tierzüchtung Und Züchtungsbiologie·S Brard, A Ricard
Apr 18, 2015·Genetics, Selection, Evolution : GSE·Yvonne C J WientjesMario P L Calus
Nov 2, 2014·Frontiers in Genetics·Gota Morota, Daniel Gianola
Apr 1, 2017·Genetics, Selection, Evolution : GSE·Matti TaskinenIsmo Strandén
Dec 22, 2017·Genetics, Selection, Evolution : GSE·Gota Morota
Dec 29, 2017·Genetics, Selection, Evolution : GSE·Jean-Michel Elsen
Sep 13, 2017·Genetics·Hwasoon KimGustavo de Los Campos
Dec 3, 2016·The Plant Genome·Anthony T SlaterHans D Daetwyler
Mar 13, 2019·Frontiers in Genetics·Zhengcao LiHenner Simianer
May 17, 2017·Journal of Animal Breeding and Genetics = Zeitschrift Für Tierzüchtung Und Züchtungsbiologie·G NiM Erbe
Mar 16, 2019·Frontiers in Genetics·Solomon Antwi BoisonHooman K Moghadam
Oct 6, 2018·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Simon RioAlain Charcosset
Oct 12, 2020·Journal of Animal Breeding and Genetics = Zeitschrift Für Tierzüchtung Und Züchtungsbiologie·Jovana Marjanovic, Mario P L Calus
Dec 8, 2020·Frontiers in Genetics·Torsten PookHenner Simianer
Dec 15, 2020·PloS One·Gustavo de Los CamposAna I Vazquez
Jul 1, 2021·Genetics, Selection, Evolution : GSE·Jack C M DekkersJian Cheng

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Methods Mentioned

BETA
sequence-based
chip
genotyping

Software Mentioned

Beagle
FImpute
ASReml
POPREP
R

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