Classification and Visualization of Genotype x Phenotype Interactions in Biomass Sorghum

• URL: http://arxiv.org/abs/2108.04090v1
• Date: Mon, 9 Aug 2021 14:39:23 GMT
• Title: Classification and Visualization of Genotype x Phenotype Interactions in Biomass Sorghum
• Authors: Abby Stylianou, Robert Pless, Nadia Shakoor and Todd Mockler
• Abstract summary: We introduce a simple approach to understanding the relationship between single nucleotide polymorphisms (SNPs) and groups of related SNPs. The pipeline involves training deep convolutional neural networks (CNNs) to differentiate between images of plants with reference and alternate versions of various SNPs.
• Score: 7.9880851102831185
• License: http://arxiv.org/licenses/nonexclusive-distrib/1.0/
• Abstract: We introduce a simple approach to understanding the relationship between single nucleotide polymorphisms (SNPs), or groups of related SNPs, and the phenotypes they control. The pipeline involves training deep convolutional neural networks (CNNs) to differentiate between images of plants with reference and alternate versions of various SNPs, and then using visualization approaches to highlight what the classification networks key on. We demonstrate the capacity of deep CNNs at performing this classification task, and show the utility of these visualizations on RGB imagery of biomass sorghum captured by the TERRA-REF gantry. We focus on several different genetic markers with known phenotypic expression, and discuss the possibilities of using this approach to uncover genotype x phenotype relationships.

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