The Modern Plant Breeding Triangle: Optimizing the Use of Genomics, Phenomics, and Enviromics Data

The Importance of Dominance and Genotype-by-Environment Interactions on Grain Yield Variation in a Large-Scale Public Cooperative Maize Experiment

(2021) Anna R Rogers et al.   G3-Genes Genomes Genetics

Regularized selection indices for breeding value prediction using hyper-spectral image data

(2020) Marco Lopez-Cruz et al.   Scientific Reports

Genome‐based prediction of multiple wheat quality traits in multiple years

(2020) Maria Itria Ibba et al.   Plant Genome

Combining Crop Growth Modeling With Trait-Assisted Prediction Improved the Prediction of Genotype by Environment Interactions

(2020) Pauline Robert et al.   Frontiers in Plant Science

Nonlinear kernels, dominance, and envirotyping data increase the accuracy of genome-based prediction in multi-environment trials

(2020) Germano Costa-Neto et al.   HEREDITY

Enviromics in breeding: applications and perspectives on envirotypic-assisted selection

(2020) Rafael T. Resende et al.   THEORETICAL AND APPLIED GENETICS

A data-driven simulation platform to predict cultivars’ performances under uncertain weather conditions

(2020) Gustavo de los Campos et al.   Nature Communications

An R Package for Bayesian Analysis of Multi-environment and Multi-trait Multi-environment Data for Genome-Gased Prediction

(2019) Osval A. Montesinos-López et al.   G3-Genes Genomes Genetics

New Deep Learning Genomic-Based Prediction Model for Multiple Traits with Binary, Ordinal, and Continuous Phenotypes

(2019) Osval A. Montesinos-López et al.   G3-Genes Genomes Genetics

Integrating Molecular Markers and Environmental Covariates To Interpret Genotype by Environment Interaction in Rice (Oryza sativa L.) Grown in Subtropical Areas

(2019) Eliana Monteverde et al.   G3-Genes Genomes Genetics

Genomic prediction of maize yield across European environmental conditions

(2019) Emilie J. Millet et al.   NATURE GENETICS

Use of genomic selection in breeding rice (Oryza sativa L.) for resistance to rice blast (Magnaporthe oryzae)

(2019) Mao Huang et al.   MOLECULAR BREEDING

Deep Kernel for Genomic and Near Infrared Predictions in Multi-Environment Breeding Trials

(2019) Jaime Cuevas et al.   G3-Genes Genomes Genetics

Using crop growth model stress covariates and AMMI decomposition to better predict genotype-by-environment interactions

(2019) R. Rincent et al.   THEORETICAL AND APPLIED GENETICS

From QTLs to Adaptation Landscapes: Using Genotype-To-Phenotype Models to Characterize G×E Over Time

(2019) Daniela Bustos-Korts et al.   Frontiers in Plant Science

Single-Step Reaction Norm Models for Genomic Prediction in Multienvironment Recurrent Selection Trials

(2018) Odilon P. Morais Júnior et al.   CROP SCIENCE

Leveraging biological insight and environmental variation to improve phenotypic prediction: Integrating crop growth models (CGM) with whole genome prediction (WGP)

(2018) C.D. Messina et al.   EUROPEAN JOURNAL OF AGRONOMY

Whole-genome prediction of reaction norms to environmental stress in bread wheat ( Triticum aestivum L.) by genomic random regression

(2018) Delphine Ly et al.   FIELD CROPS RESEARCH

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

(2018) Jaime Cuevas et al.   G3-Genes Genomes Genetics

Multi-environment Genomic Prediction of Plant Traits Using Deep Learners with Dense Architecture

(2018) Abelardo Montesinos-López et al.   G3-Genes Genomes Genetics

Multi-trait, Multi-environment Deep Learning Modeling for Genomic-Enabled Prediction of Plant Traits

(2018) Osval A. Montesinos-Lopez et al.   G3-Genes Genomes Genetics

A Benchmarking Between Deep Learning, Support Vector Machine and Bayesian Threshold Best Linear Unbiased Prediction for Predicting Ordinal Traits in Plant Breeding

(2018) Osval A. Montesinos-López et al.   G3-Genes Genomes Genetics

Quantitative Genetics and Genomics Converge to Accelerate Forest Tree Breeding

(2018) Dario Grattapaglia et al.   Frontiers in Plant Science

Genomic Bayesian functional regression models with interactions for predicting wheat grain yield using hyper-spectral image data

(2017) Abelardo Montesinos-López et al.   Plant Methods

Optimization of multi-environment trials for genomic selection based on crop models

(2017) R. Rincent et al.   THEORETICAL AND APPLIED GENETICS

Genomic Selection in Plant Breeding: Methods, Models, and Perspectives

(2017) José Crossa et al.   TRENDS IN PLANT SCIENCE

Rapid Cycling Genomic Selection in a Multiparental Tropical Maize Population

(2017) Xuecai Zhang et al.   G3-Genes Genomes Genetics

Prospects for Genomic Selection in Cassava Breeding

(2017) Marnin D. Wolfe et al.   Plant Genome

Use of Genomic Estimated Breeding Values Results in Rapid Genetic Gains for Drought Tolerance in Maize

(2017) B.S. Vivek et al.   Plant Genome

Use of Crop Growth Models with Whole-Genome Prediction: Application to a Maize Multienvironment Trial

(2016) Mark Cooper et al.   CROP SCIENCE

Changes in genetic selection differentials and generation intervals in US Holstein dairy cattle as a result of genomic selection

(2016) Adriana García-Ruiz et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Genomic Bayesian Multi-trait and Multi-environment Model

(2016) Osval A. Montesinos-López et al.   G3-Genes Genomes Genetics

Genomic Prediction of Genotype × Environment Interaction Kernel Regression Models

(2016) Jaime Cuevas et al.   Plant Genome

Genome-Enabled Prediction Models for Yield Related Traits in Chickpea

(2016) Manish Roorkiwal et al.   Frontiers in Plant Science

Genetic Gains in Grain Yield Through Genomic Selection in Eight Bi-parental Maize Populations under Drought Stress

(2015) Yoseph Beyene et al.   CROP SCIENCE

A reaction norm model for genomic selection using high-dimensional genomic and environmental data

(2013) Diego Jarquín et al.   THEORETICAL AND APPLIED GENETICS

Integrating environmental covariates and crop modeling into the genomic selection framework to predict genotype by environment interactions

(2013) Nicolas Heslot et al.   THEORETICAL AND APPLIED GENETICS

Factors Affecting the Accuracy of Genotype Imputation in Populations from Several Maize Breeding Programs

(2012) John M. Hickey et al.   CROP SCIENCE

Genomic Prediction of Breeding Values when Modeling Genotype × Environment Interaction using Pedigree and Dense Molecular Markers

(2012) Juan Burgueño et al.   CROP SCIENCE

Genomewide Selection versus Marker-assisted Recurrent Selection to Improve Grain Yield and Stover-quality Traits for Cellulosic Ethanol in Maize

(2012) Jon M. Massman et al.   CROP SCIENCE

Linear, bilinear, and linear-bilinear fixed and mixed models for analyzing genotype × environment interaction in plant breeding and agronomy

(2010) J. Crossa et al.   CANADIAN JOURNAL OF PLANT SCIENCE