Genomic-Enabled Prediction Kernel Models with Random Intercepts for Multi-environment Trials

G3 : Genes - Genomes - Genetics
Jaime CuevasJosé Crossa

Abstract

In this study, we compared the prediction accuracy of the main genotypic effect model (MM) without G×E interactions, the multi-environment single variance G×E deviation model (MDs), and the multi-environment environment-specific variance G×E deviation model (MDe) where the random genetic effects of the lines are modeled with the markers (or pedigree). With the objective of further modeling the genetic residual of the lines, we incorporated the random intercepts of the lines ([Formula: see text]) and generated another three models. Each of these 6 models were fitted with a linear kernel method (Genomic Best Linear Unbiased Predictor, GB) and a Gaussian Kernel (GK) method. We compared these 12 model-method combinations with another two multi-environment G×E interactions models with unstructured variance-covariances (MUC) using GB and GK kernels (4 model-method). Thus, we compared the genomic-enabled prediction accuracy of a total of 16 model-method combinations on two maize data sets with positive phenotypic correlations among environments, and on two wheat data sets with complex G×E that includes some negative and close to zero phenotypic correlations among environments. The two models (MDs and MDE with the random intercept of t...Continue Reading

References

Apr 6, 2001·Genetics·T H MeuwissenM E Goddard
Oct 24, 2008·Journal of Dairy Science·P M VanRaden
Jun 30, 2012·Genetics·Gustavo de Los CamposMario P L Calus
Jan 1, 2013·G3 : Genes - Genomes - Genetics·Paulino Pérez-RodríguezSusanne Dreisigacker
Sep 12, 2013·G3 : Genes - Genomes - Genetics·José CrossaRaman Babu
Dec 18, 2013·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Diego JarquínGustavo de los Campos
Feb 11, 2015·G3 : Genes - Genomes - Genetics·Marco Lopez-CruzGustavo de los Campos
Dec 18, 2015·Nucleic Acids Research·Robert D FinnAlex Bateman
Mar 16, 2016·G3 : Genes - Genomes - Genetics·Helena OakeyRobbie Waugh
Oct 30, 2016·G3 : Genes - Genomes - Genetics·Jaime CuevasGustavo de Los Campos
Dec 3, 2016·The Plant Genome·Jaime CuevasJuan Burgueño
Apr 30, 2017·G3 : Genes - Genomes - Genetics·Massaine Bandeira E SousaJose Crossa

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Citations

Aug 23, 2019·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Sang HeHans D Daetwyler
Jul 28, 2018·G3 : Genes - Genomes - Genetics·Italo GranatoRoberto Fritsche-Neto
Jul 11, 2019·G3 : Genes - Genomes - Genetics·Jaime CuevasJosé Crossa
May 4, 2021·Frontiers in Plant Science·Jose CrossaAlison R Bentley
Jun 11, 2021·Frontiers in Plant Science·Damiano PuglisiAgostino Fricano
Dec 10, 2021·Frontiers in Plant Science·Cathy C WesthuesTimothy M Beissinger
Dec 2, 2021·G3 : Genes - Genomes - Genetics·Osval Antonio Montesinos-LópezJosé Crossa

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Methods Mentioned

BETA
Genotyping
MDe

Software Mentioned

Ubuntu Linux
Bayesian Genomic G×E ( BGGE )
GB
GK
R
R library
MDs
BGGE
BGLR
GBLUP

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