Metabolomics facilitates the deduction ofbiologically relevant hypotheses as to putative metabolic pathways and genes responsible for metabolic reactions. The assignment of candidate genes for crop improvement will be accelerated as the body of tomato genomic data increases. High-throughput metabolic profiling holds vast potential for screening promising tomato genes, varieties, and species for metabolite-oriented molecular breeding (Fig. 13). Firstly, profiling of complex secondary metabolites will support the breeding of novel tomato varieties with enhanced health benefits in addition to quality and productivity. Towards this end, metabolic profiling of a wide range of genotypes is required, along with correlations among metabolic traits and agronomic traits, and the development of associated molecular markers. Secondly, tomato is known to contain potentially toxic alkaloids (see Sect. 1.14.1). To check whether a novel overexpressing variety is free of potentially hazardous levels of metabolites will be important to consumers.
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