DNNGP, a deep neural network-based method for genomic prediction using multi-omics data in plants

K Wang, MA Abid, A Rasheed, J Crossa, S Hearne… - Molecular Plant, 2023 - cell.com
Genomic prediction is an effective way to accelerate the rate of agronomic trait improvement
in plants. Traditional methods typically use linear regression models with clear assumptions; …

Multi-environment genomic prediction of plant traits using deep learners with dense architecture

A Montesinos-López… - G3: Genes …, 2018 - academic.oup.com
Genomic selection is revolutionizing plant breeding and therefore methods that improve
prediction accuracy are useful. For this reason, active research is being conducted to build …

A deep convolutional neural network approach for predicting phenotypes from genotypes

W Ma, Z Qiu, J Song, J Li, Q Cheng, J Zhai, C Ma - Planta, 2018 - Springer
Main conclusion Deep learning is a promising technology to accurately select individuals
with high phenotypic values based on genotypic data. Abstract Genomic selection (GS) is a …

A review of deep learning applications for genomic selection

OA Montesinos-López, A Montesinos-López… - BMC genomics, 2021 - Springer
Abstract Background Several conventional genomic Bayesian (or no Bayesian) prediction
methods have been proposed including the standard additive genetic effect model for which …

A guide on deep learning for complex trait genomic prediction

M Pérez-Enciso, LM Zingaretti - Genes, 2019 - mdpi.com
Deep learning (DL) has emerged as a powerful tool to make accurate predictions from
complex data such as image, text, or video. However, its ability to predict phenotypic values …

Multi-trait, multi-environment deep learning modeling for genomic-enabled prediction of plant traits

OA Montesinos-López… - G3: Genes, genomes …, 2018 - academic.oup.com
Multi-trait and multi-environment data are common in animal and plant breeding programs.
However, what is lacking are more powerful statistical models that can exploit the correlation …

Deep learning for predicting complex traits in spring wheat breeding program

KS Sandhu, DN Lozada, Z Zhang… - Frontiers in Plant …, 2021 - frontiersin.org
Genomic selection (GS) is transforming the field of plant breeding and implementing models
that improve prediction accuracy for complex traits is needed. Analytical methods for …

Deep kernel and deep learning for genome-based prediction of single traits in multienvironment breeding trials

J Crossa, JWR Martini, D Gianola… - Frontiers in …, 2019 - frontiersin.org
Deep learning (DL) is a promising method for genomic-enabled prediction. However, the
implementation of DL is difficult because many hyperparameters (number of hidden layers …

A benchmarking between deep learning, support vector machine and Bayesian threshold best linear unbiased prediction for predicting ordinal traits in plant breeding

OA Montesinos-López, J Martín-Vallejo… - G3: Genes …, 2019 - academic.oup.com
Genomic selection is revolutionizing plant breeding. However, still lacking are better
statistical models for ordinal phenotypes to improve the accuracy of the selection of …

Exploring deep learning for complex trait genomic prediction in polyploid outcrossing species

LM Zingaretti, SA Gezan, LFV Ferrão… - Frontiers in plant …, 2020 - frontiersin.org
Genomic prediction (GP) is the procedure whereby the genetic merits of untested candidates
are predicted using genome wide marker information. Although numerous examples of GP …