Genomic selection (GS) is a promising breeding strategy by which the phenotypes of plant individuals are usually predicted based on genome-wide markers of genotypes. Conventional GS models typically make strong assumptions, resulting in difficulty capturing complex relationships within genotypes and between genotypes and phenotypes. To address this problem, we presented a deep learning (DL)-based model, named DeepGS, to automatically learn complex relationships without pre-defined rules. The experimental results indicate that DeepGS can be used as a complement to the commonly used RR-BLUP for more accurately selecting individuals with high phenotypic values.

DeepGS software: DeepGS is an R package for predicting phenotypes from genotypes using a deep convolutional neural network approach.

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Figure. Pipeline of the Predicting Phenotypes from Genotypes by DeepGS.

Ma W, Qiu Z, Song J, et al. A deep convolutional neural network approach for predicting phenotypes from genotypes[J]. Planta, 2018(8).