Advances in Metabolomics-Driven Diagnostic Breeding and Crop Improvement

Abstract

Climate change continues to threaten global crop output by reducing annual productivity. As a result, global food security is now considered as one of the most important challenges facing humanity. To address this challenge, modern crop breeding approaches are required to create plants that can cope with increased abiotic/biotic stress. Metabolomics is rapidly gaining traction in plant breeding by predicting the metabolic marker for plant performance under a stressful environment and has emerged as a powerful tool for guiding crop improvement. The advent of more sensitive, automated, and high-throughput analytical tools combined with advanced bioinformatics and other omics techniques has laid the foundation to broadly characterize the genetic traits for crop improvement. Progress in metabolomics allows scientists to rapidly map specific metabolites to the genes that encode their metabolic pathways and offer plant scientists an excellent opportunity to fully explore and rationally harness the wealth of metabolites that plants biosynthesize. Here, we outline the current application of advanced metabolomics tools integrated with other OMICS techniques that can be used to: dissect the details of plant genotype-metabolite-phenotype interactions facilitating metabolomics-assisted plant breeding for probing the stress-responsive metabolic markers, explore the hidden metabolic networks associated with abiotic/biotic stress resistance, facilitate screening and selection of climate-smart crops at the metabolite level, and enable accurate risk-assessment and characterization of gene edited/transgenic plants to assist the regulatory process. The basic concept behind metabolic editing is to identify specific genes that govern the crucial metabolic pathways followed by the editing of one or more genes associated with those pathways. Thus, metabolomics provides a superb platform for not only rapid assessment and commercialization of future genome-edited crops, but also for accelerated metabolomics-assisted plant breeding. Furthermore, metabolomics can be a useful tool to expedite the crop research if integrated with speed breeding in future.

Keywords: climate change; crop improvement; gene-edited crops; metabolic editing; metabolomics; metabolomics-assisted breeding.

Figure 1

An illustration of the applications of metabolomics for crop improvement. Metabolomics can be integrated with other omics tools to elucidate the molecular phenotype corresponding to the desired trait of interest and to assist in the mapping of unique genes regulating different metabolic pathways under different conditions (we use climate stress as an example). Molecular information collected from genomics and phenomics can be used to correlate traits or genes through quantitative trait loci (QTL) and genome-wide association studies (GWAS). Metabolomics-based QTL (mQTL) and metabolomics-based GWAS (mGWAS) measure variations in molecular phenotype without requiring any genetic information, and thereby remove the genotype–phenotype gap efficiently.

Figure 2

Overview of metabolomics-assisted breeding using metabolomics tools to study abiotic and biotic stress regulation in plants. Primary metabolism produces essential metabolites which are necessary for the plant growth and development, while the secondary metabolism produces specialized metabolites that are triggered by exposure to various stressors. These stress-induced metabolites are crucial for plants to adapt to harsh environmental conditions.

Figure 3

Schematic representation of how metabolic engineering/editing is done in plants through multiplexed genome editing and multiplexed base editing systems. (a) The CRISPR/Cas9-mediated multiplexed genome editing system consists of multiple single-guide RNAs (gRNAs), and the Cas9 protein is activated via trans-activating CRISPR RNA (tracrRNA) and guided by CRISPR RNA (crRNA) to generate site-specific double-standard breaks (DSBs) at different points on the DNA. The gRNAs detect a unique sequence of 20 nucleotides (red) and the Cas9/gRNAs complex cuts the DNA at a protospacer adjacent motif (PAM) site that is three bases upstream of the target sequence via the RuvC and HNH domains. The DSBs can be repaired either through a homology-directed repair pathway (HDR) or nonhomologous end-joining (NHEJ). (b) shows the modern base-editing system which can be used to edit multiple bases in different pathways for precise metabolic editing. It comprises dead Cas9 (dCas9), which is connected with cytidine deaminase (light blue). The dCas9 is guided by gRNA to target desire single base (yellow) in the DNA sequence and substitute it with another base (brown) distal to the PAM.

Figure 4

A schematic diagram portraying the benefits of metabolomics for risk-assessment of genome-edited crops.

Figure 5

Depiction of the potential applications of metabolomics-assisted speed breeding to accelerate the crop breeding program.