Classification and Visualization of Genotype x Phenotype Interactions in Biomass Sorghum

Cornell University
August 09, 2021

The researchers 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.

Sorghum is a cereal crop, used worldwide for a variety of purposes including for use as grain and as a source of biomass for bio-energy production, which is the context we primarily focus on in this paper. For biofuel production, the goal of both plant growers and breeders is to produce sorghum crops that grow as big as possible, as quickly as possible, with as few resources as possible. Plant breeders produce new lines of sorghum by crossing together candidate lines that have desirable traits, or known genes that correspond to desirable traits.

In this paper, we propose a simple pipeline for understanding and identifying interesting genetic markers that control visually observable traits. This pipeline could be leveraged by plant geneticists and breeders to understand the relationship between single nucleotide polymorpishms (SNPs, locations in the organism’s DNA that vary between different members of the population), or groups of related SNPs, and the phenotypes that they impact.

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