Shrinkage estimation of the genomic relationship matrix can improve genomic estimated breeding values in the training set

TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik
Dominik MüllerAlbrecht E Melchinger

Abstract

We evaluated several methods for computing shrinkage estimates of the genomic relationship matrix and demonstrated their potential to enhance the reliability of genomic estimated breeding values of training set individuals. In genomic prediction in plant breeding, the training set constitutes a large fraction of the total number of genotypes assayed and is itself subject to selection. The objective of our study was to investigate whether genomic estimated breeding values (GEBVs) of individuals in the training set can be enhanced by shrinkage estimation of the genomic relationship matrix. We simulated two different population types: a diversity panel of unrelated individuals and a biparental family of doubled haploid lines. For different training set sizes (50, 100, 200), number of markers (50, 100, 200, 500, 2,500) and heritabilities (0.25, 0.5, 0.75), shrinkage coefficients were computed by four different methods. Two of these methods are novel and based on measures of LD, the other two were previously described in the literature, one of which was extended by us. Our results showed that shrinkage estimation of the genomic relationship matrix can significantly improve the reliability of the GEBVs of training set individuals, es...Continue Reading

References

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Citations

Nov 9, 2016·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Sebastian MichelHermann Buerstmayr
May 5, 2017·Evolutionary Bioinformatics Online·Bongsong Kim, William D Beavis
Feb 28, 2019·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Sebastian MichelHermann Bürstmayr
Jun 28, 2019·Journal of Animal Breeding and Genetics = Zeitschrift Für Tierzüchtung Und Züchtungsbiologie·Daniel J TolhurstBrian R Cullis
Aug 11, 2017·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·R RincentL Moreau
Aug 20, 2017·Scientific Reports·Venea Dara DaygonMelissa A Fitzgerald

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