Do stronger measures of genomic connectedness enhance prediction accuracies across management units?

Journal of Animal Science
Haipeng YuGota Morota

Abstract

Genetic connectedness assesses the extent to which estimated breeding values can be fairly compared across management units. Ranking of individuals across units based on best linear unbiased prediction (BLUP) is reliable when there is a sufficient level of connectedness due to a better disentangling of genetic signal from noise. Connectedness arises from genetic relationships among individuals. Although a recent study showed that genomic relatedness strengthens the estimates of connectedness across management units compared with that of pedigree, the relationship between connectedness measures and prediction accuracies only has been explored to a limited extent. In this study, we examined whether increased measures of connectedness led to higher prediction accuracies evaluated by a cross-validation (CV) based on computer simulations. We applied prediction error variance of the difference, coefficient of determination (CD), and BLUP-type prediction models to data simulated under various scenarios. We found that a greater extent of connectedness enhanced accuracy of whole-genome prediction. The impact of genomics was more marked when large numbers of markers were used to infer connectedness and evaluate prediction accuracy. Conne...Continue Reading

References

Sep 1, 1993·Journal of Animal Science·B W Kennedy, D Trus
Dec 13, 2007·Journal of Animal Science·L A KuehnR M Lewis
Oct 24, 2008·Journal of Dairy Science·P M VanRaden
Jan 30, 2009·Bioinformatics·Mehdi Sargolzaei, Flavio S Schenkel
Apr 22, 2010·Genetics·Hans D DaetwylerJohn A Woolliams
Sep 30, 2010·Nature Reviews. Genetics·Joseph E PowellMichael E Goddard
Jul 11, 2014·Genetics·Paulino Pérez, Gustavo de los Campos
Nov 2, 2014·Frontiers in Genetics·Gota Morota, Daniel Gianola
Nov 5, 2014·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Julio IsidroMark E Sorrells
Sep 2, 2017·G3 : Genes - Genomes - Genetics·Haipeng YuGota Morota
Dec 22, 2017·Genetics, Selection, Evolution : GSE·Gota Morota

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Citations

Sep 19, 2018·Genetics, Selection, Evolution : GSE·Mehdi Momen, Gota Morota

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Methods Mentioned

BETA
genotyping

Software Mentioned

BGLR R
QMSim
GBLUP

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