Recent applications of metabolomics in plant breeding

Abstract

Metabolites play a central role in maintaining organismal life and in defining crop phenotypes, such as nutritional value, fragrance, color, and stress resistance. Among the ‘omes’ in biology, the metabolome is the closest to the phenotype. Consequently, metabolomics has been applied to crop improvement as method for monitoring changes in chemical compositions, clarifying the mechanisms underlying cellular functions, discovering markers and diagnostics, and phenotyping for mQTL, mGWAS, and metabolite-genome predictions. In this review, 359 reports of the most recent applications of metabolomics to plant breeding-related studies were examined. In addition to the major crops, more than 160 other crops including rare medicinal plants were considered. One bottleneck associated with using metabolomics is the wide array of instruments that are used to obtain data and the ambiguity associated with metabolite identification and quantification. To further the application of metabolomics to plant breeding, the features and perspectives of the technology are discussed.

A comprehensive metabolomics and lipidomics atlas for the legumes common bean, chickpea, lentil and lupin

“…To this end, powerful functional genomics tools have been established in the past years to validate the biological function of identified candidate genes in the crops of interest using CRISPR/Cas‐mediated genome editing and hairy root transformation (Alamillo et al., 2023). Several ecophysiological aspects have been assessed using natural variation, e.g., as shown for metabolism in other important crop species (Alseekh, Kostova, et al., 2021; Bulut et al., 2022; Luo, 2015; Oikawa et al., 2008; Perez‐Fons et al., 2019; Sakurai, 2022; Sumner et al., 2015; Zhang et al., 2021). Finally, the integration of the metabolic fingerprints and mGWAS data with the creation of pan‐genomes will provide clear evidence of divergence in the Leguminosae family as well as the evolution of gene clusters and families (Bellucci et al., 2021).…”

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

“…Metabolomics can render insights into the different metabolites which can be targeted further for breeding and selection using different genomics tools such as metabolite-quantitative trait loci (mQTL) analyses, metabolite-based genome-wide association studies (mGWAS), and metabolite-genome predictions [ 50 ]. Variation in the phenolic acid content in chile peppers is affected by the varietal type, location, and growing season, and, hence, can impose challenges on performing breeding and selection [ 32 ].…”

Multi-Omics Approaches in Plant–Microbe Interactions Hold Enormous Promise for Sustainable Agriculture

“…Metabolites can be found using spectrophotometers at the appropriate wavelength. Another fingerprinting method is Fourier transform infrared (FTIR) spectroscopy, which can analyze thousands of samples each day of various metabolites without harming or wasting the samples [109,110].…”