[HTML][HTML] A guide for kernel generalized regression methods for genomic-enabled prediction

A Montesinos-López, OA Montesinos-López… - Heredity, 2021 - nature.com
The primary objective of this paper is to provide a guide on implementing Bayesian
generalized kernel regression methods for genomic prediction in the statistical software R …

[HTML][HTML] Genome-Based Genotype × Environment Prediction Enhances Potato (Solanum tuberosum L.) Improvement Using Pseudo-Diploid and Polysomic Tetraploid …

R Ortiz, J Crossa, F Reslow… - Frontiers in Plant …, 2022 - frontiersin.org
Potato breeding must improve its efficiency by increasing the reliability of selection as well
as identifying a promising germplasm for crossing. This study shows the prediction accuracy …

Genomic prediction methods accounting for nonadditive genetic effects

L Varona, A Legarra, MA Toro, ZG Vitezica - Genomic Prediction of …, 2022 - Springer
The use of genomic information for prediction of future phenotypes or breeding values for
the candidates to selection has become a standard over the last decade. However, most …

[HTML][HTML] Opportunities and limits of combining microbiome and genome data for complex trait prediction

M Pérez-Enciso, LM Zingaretti… - Genetics Selection …, 2021 - Springer
Background Analysis and prediction of complex traits using microbiome data combined with
host genomic information is a topic of utmost interest. However, numerous questions remain …

Modeling genotype × environment interaction for single and multitrait genomic prediction in potato (Solanum tuberosum L.)

J Cuevas, F Reslow, J Crossa, R Ortiz - G3, 2023 - academic.oup.com
In this study, we extend research on genomic prediction (GP) to polysomic polyploid plant
species with the main objective to investigate single-trait (ST) and multitrait (MT) …

Efficient algorithms for calculating epistatic genomic relationship matrices

Y Jiang, JC Reif - Genetics, 2020 - academic.oup.com
The genomic relationship matrix plays a key role in the analysis of genetic diversity, genomic
prediction, and genome-wide association studies. The epistatic genomic relationship matrix …

Use of continuous genotypes for genomic prediction in sugarcane

S Yadav, EM Ross, X Wei, S Liu, LT Nguyen… - The Plant …, 2024 - Wiley Online Library
Genomic selection in sugarcane faces challenges due to limited genomic tools and high
genomic complexity, particularly because of its high and variable ploidy. The classification of …

[HTML][HTML] Accounting for epistasis improves genomic prediction of phenotypes with univariate and bivariate models across environments

E Vojgani, T Pook, JWR Martini, AC Hölker… - Theoretical and Applied …, 2021 - Springer
Abstract Key Message The accuracy of genomic prediction of phenotypes can be increased
by including the top-ranked pairwise SNP interactions into the prediction model. Abstract We …

[HTML][HTML] Approximate genome-based kernel models for large data sets including main effects and interactions

J Cuevas, OA Montesinos-López, JWR Martini… - Frontiers in …, 2020 - frontiersin.org
The rapid development of molecular markers and sequencing technologies has made it
possible to use genomic prediction (GP) and selection (GS) in animal and plant breeding …

On Hadamard and Kronecker products in covariance structures for genotype× environment interaction

JWR Martini, J Crossa, FH Toledo… - The Plant …, 2020 - Wiley Online Library
When including genotype× environment interactions (G× E) in genomic prediction models,
Hadamard or Kronecker products have been used to model the covariance structure of …