GenoDrawing: An Autoencoder Framework for Image Prediction from SNP Markers
Publication date
2023-11-03ISSN
2643-6515
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, particularly deep learning, have been developed to predict complex traits from dense genotypic data. Autoencoders, a neural network 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 demonstrated proficiency in its task while using a small dataset of shape-related SNPs, and multiple experiments were conducted to evaluate the impact of SNP selection and shape relation. Results indicated that the correct relationship of SNPs with visual traits had a significant impact on the generated images, consistent with biological interpretation. While using significant 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 significant 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 improved dataset balance in terms of shape for more precise outcomes.
Document Type
Article
Document version
Published version
Language
English
Subject (CDU)
633 - Field crops and their production
Pages
9
Publisher
American Association for the Advancement of Science; Nanjing Agricultural University
Is part of
Plant Phenomics
Citation
Jurado-Ruiz, Federico, David Rousseau, Juan A. Botía, and María José Aranzana. 2023. “GenoDrawing: An Autoencoder Framework for Image Prediction from SNP Markers.” Plant Phenomics 5 (January). doi:10.34133/plantphenomics.0113.
Grant agreement number
MC/Programa Estatal para impulsar la investigación científico-técnica y su transferencia/PID2021-128885OB-I00/ES/ /
EC/H2020/817970/EU/INnovations in plant VarIety Testing in Europe to foster the introduction of new varieties better adapted to varying biotic and abiotic conditions and to more sustainable crop management practices/INVITE
MINECO/Programa Estatal de fomento de la investigación científica y técnica de excelencia/SEV-2015-0533/ES/ /
MICIU/Programa Estatal de generación del conocimiento y fortalecimiento científico y tecnológico del sistema I+D+I/CEX2019-000902-S/ES/ /
FEDER/ / /EU/ /
Program
Genòmica i Biotecnologia
This item appears in the following Collection(s)
- ARTICLES CIENTÍFICS [2555]
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Except where otherwise noted, this item's license is described as http://creativecommons.org/licenses/by/4.0/