Metabolomics provides a view of endogenous metabolic patterns not only during plant growth and development but also in response to genetic events, environment and disease. We evaluated the influence of genetic background (high polyamine lines; low methyl jasmonate line; low ethylene line; and isogenic genotypes carrying double transgenic events) and environments (hairy vetch, rye, plastic black mulch and bare soil mulching systems) on the metabolomic profile of isogenic reverse genetic mutations and selected mulch based cropping systems in tomato fruit. NMR spectroscopy was used for quantifying metabolites that are central to primary metabolism. High endogenous polyamine content exhibited strong effects on amino acids, Krebs cycle intermediates and energy molecules in ripening fruits of plants grown under different agroecosystem environments. The metabolic response to high polyamine genotypes was similar to the response to hairy vetch cover crop mulch. The changes in primary metabolites of genotypes mutated for the deficiency of ethylene or methyl jasmonate were unique under all growth conditions and opposite of high polyamine genotype results. Our results affirm that interactions between metabolite pathways and growth environments are affected by genotype, and influence the metabolite quality of a crop.
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