Exploring synergies between plant metabolic modelling and machine learning

Abstract

As plants produce an enormous diversity of metabolites to help them adapt to the environment, the study of plant metabolism is of utmost importance to understand different plant phenotypes. Omics data have been generated at an unprecedented rate for several organisms, including plants, and are widely used to study the central dogma of molecular biology, connecting the genome to phenotypes. Constraint-based modelling (CBM) methods, working over genome-scale metabolic models (GSMMs), have been crucial for organising and analysing omics data by integrating them with biochemical knowledge. In 2009, the first plant GSMM was reconstructed and, since then, several advances have been made, including the creation of context- and multi-tissue models that have supported the study of plant metabolism. Nevertheless, plant metabolic modelling remains very challenging. In parallel, as omics datasets are complex and heterogeneous, machine learning (ML) models have been applied in their interpretation to foster knowledge discovery. Recently, the first studies combining both CBM and ML approaches have emerged and have shown promising results. Here, we present the major advances in plant metabolic modelling and review the main CBM-ML hybrid studies. Finally, we discuss the application of machine learning to address the unique challenges of plant metabolic modelling.