GenoDrawing: An Autoencoder Framework for Image Prediction from SNP Markers

Abstract

Advancements in genome sequencing have facilitated whole-genome characterization of numerous plant species, providing an abundance of genotypic data for genomic analysis. Genomic selection and neural networks (NNs), particularly deep learning, have been developed to predict complex traits from dense genotypic data. Autoencoders, an NN model to extract features from images in an unsupervised manner, has proven to be useful for plant phenotyping. This study introduces an autoencoder framework, GenoDrawing, for predicting and retrieving apple images from a low-depth single-nucleotide polymorphism (SNP) array, potentially useful in predicting traits that are difficult to define. GenoDrawing demonstrates proficiency in its task using a small dataset of shape-related SNPs. Results indicate that the use of SNPs associated with visual traits has substantial impact on the generated images, consistent with biological interpretation. While using substantial SNPs is crucial, incorporating additional, unrelated SNPs results in performance degradation for simple NN architectures that cannot easily identify the most important inputs. The proposed GenoDrawing method is a practical framework for exploring genomic prediction in fruit tree phenotyping, particularly beneficial for small to medium breeding companies to predict economically substantial heritable traits. Although GenoDrawing has limitations, it sets the groundwork for future research in image prediction from genomic markers. Future studies should focus on using stronger models for image reproduction, SNP information extraction, and dataset balance in terms of phenotypes for more precise outcomes.

Plant phenotyping relevance

SNPからリンゴ画像を予測・再構成するGenoDrawingフレームワークを提案しており、果樹の視覚形質を推定する計算手法が研究の中心である。

Code and data availability

The authors publicly release their analysis code, notebooks, and trained model weights (autoencoder and embedding predictor) for the GenoDrawing framework in a GitHub repository. The apple images used for phenotyping are only available upon request from a prior study, so they do not qualify as public assets.