Metabolomics-Driven Mining of Metabolite Resources: Applications and Prospects for Improving Vegetable Crops

Abstract

Vegetable crops possess a prominent nutri-metabolite pool that not only contributes to the crop performance in the fields, but also offers nutritional security for humans. In the pursuit of identifying, quantifying and functionally characterizing the cellular metabolome pool, biomolecule separation technologies, data acquisition platforms, chemical libraries, bioinformatics tools, databases and visualization techniques have come to play significant role. High-throughput metabolomics unravels structurally diverse nutrition-rich metabolites and their entangled interactions in vegetable plants. It has helped to link identified phytometabolites with unique phenotypic traits, nutri-functional characters, defense mechanisms and crop productivity. In this study, we explore mining diverse metabolites, localizing cellular metabolic pathways, classifying functional biomolecules and establishing linkages between metabolic fluxes and genomic regulations, using comprehensive metabolomics deciphers of the plant’s performance in the environment. We discuss exemplary reports covering the implications of metabolomics, addressing metabolic changes in vegetable plants during crop domestication, stage-dependent growth, fruit development, nutri-metabolic capabilities, climatic impacts, plant-microbe-pest interactions and anthropogenic activities. Efforts leading to identify biomarker metabolites, candidate proteins and the genes responsible for plant health, defense mechanisms and nutri-rich crop produce are documented. With the insights on metabolite-QTL (mQTL) driven genetic architecture, molecular breeding in vegetable crops can be revolutionized for developing better nutritional capabilities, improved tolerance against diseases/pests and enhanced climate resilience in plants.

Proteomics analysis of wild and cultivated tomato species challenged with Alternaria solani unveiled differential tolerance mechanisms

“…The differentiation between stress-susceptible and stress-tolerant plant genotypes can be analyzed from their transcriptomic, proteomic, and metabolomic responses to pathogen invasion (Singh et al, 2022). Understanding the global proteomic responses of susceptible and tolerant plants to pathogenic challenges is crucial, as the plant proteome plays a pivotal role in driving defense, growth, and developmental processes.…”

Widely Targeted Metabolomics Reveals Metabolite Diversity in Jalapeño and Serrano Chile Peppers (Capsicum annuum L.)

“…Chile pepper fruits possess many compounds of high nutritive values which can be integrated in the human diet to mitigate nutritional deficiencies. Crop nutrition is important not only for offering quality and economic value to growers, but also for providing nutritional security to consumers [ 27 ]. Since their initial application to examine plant functional genomics in the early 2000s [ 28 , 29 , 30 ], metabolomics approaches have been used to understand the different biochemical and physiological pathways for the selection of optimal alleles for the improvement of crops [ 31 ].…”

Untargeted Metabolomics of Alternaria solani-Challenged Wild Tomato Species Solanum cheesmaniae Revealed Key Metabolite Biomarkers and Insight into Altered Metabolic Pathways

“…However, mechanisms underlying plant responses in leaves of moderately disease-resistant wild tomato S. cheesmaniae after A. solani interaction in terms of metabolite profile and metabolic pathways have not yet been investigated. Untargeted metabolomics indicate differential metabolite profiles and biosynthetic pathways as plant responses against stress and aid to identify key functional biomarker metabolites [ 23 ]. Such a comprehensive approach enables metabolite profiling to analyze complex plant metabolic responses, products, and processes to identify crucial defense-related biosynthetic pathways and elucidate secondary metabolic networks [ 24 ].…”