A comparison of classical and machine learning-based phenotype prediction methods on simulated data and three plant species

M John, F Haselbeck, R Dass, C Malisi… - Frontiers in Plant …, 2022 - frontiersin.org
Genomic selection is an integral tool for breeders to accurately select plants directly from
genotype data leading to faster and more resource-efficient breeding programs. Several …

[HTML][HTML] Plant genotype to phenotype prediction using machine learning

MF Danilevicz, M Gill, R Anderson, J Batley… - Frontiers in …, 2022 - frontiersin.org
Genomic prediction tools support crop breeding based on statistical methods, such as the
genomic best linear unbiased prediction (GBLUP). However, these tools are not designed to …

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 …

Design of training populations for selective phenotyping in genomic prediction

D Akdemir, J Isidro-Sánchez - Scientific reports, 2019 - nature.com
Phenotyping is the current bottleneck in plant breeding, especially because next-generation
sequencing has decreased genotyping cost more than 100.000 fold in the last 20 years …

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 …

[HTML][HTML] Machine learning approaches for crop improvement: Leveraging phenotypic and genotypic big data

H Tong, Z Nikoloski - Journal of plant physiology, 2021 - Elsevier
Highly efficient and accurate selection of elite genotypes can lead to dramatic shortening of
the breeding cycle in major crops relevant for sustaining present demands for food, feed …

The pursuit of genetic gain in agricultural crops through the application of machine-learning to genomic prediction

D Jones, R Fornarelli, M Derbyshire, M Gibberd… - Frontiers in …, 2023 - frontiersin.org
Current practice in agriculture applies genomic prediction to assist crop breeding in the
analysis of genetic marker data. Genomic selection methods typically use linear mixed …

A new deep learning calibration method enhances genome-based prediction of continuous crop traits

OA Montesinos-López, A Montesinos-López… - Frontiers in …, 2021 - frontiersin.org
Genomic selection (GS) has the potential to revolutionize predictive plant breeding. A
reference population is phenotyped and genotyped to train a statistical model that is used to …

Genomic prediction using machine learning: a comparison of the performance of regularized regression, ensemble, instance-based and deep learning methods on …

VM Lourenço, JO Ogutu, RAP Rodrigues, A Posekany… - BMC genomics, 2024 - Springer
Background The accurate prediction of genomic breeding values is central to genomic
selection in both plant and animal breeding studies. Genomic prediction involves the use of …

[HTML][HTML] Comparing genomic prediction models by means of cross validation

MF Schrauf, G de Los Campos, S Munilla - Frontiers in Plant Science, 2021 - frontiersin.org
In the two decades of continuous development of genomic selection, a great variety of
models have been proposed to make predictions from the information available in dense …