Crop plants represent the primary source of amino acids (AAs) for humans and livestock. Metabolite profiling and correlation-based network analysis (CNA) of seeds of a tomato Introgression Line mapping population revealed a clique of proteinogenic amino acids (Gly, Leu, Pro, Ser, Thr, and Val) concertedly changing at the metabolite level and sharing a set of closely related metabolic genes. QTL analysis revealed co-localization of the six amino acids on chromosome 2, 4 and 10. In silico analysis was used to quantify the effect of the clique on seminal structural network properties, highlighting its centrality in the network. Sequence analysis identified a unique set of 10 genes on chromosome 2 only, which were associated with amino acid metabolism and specifically the metabolism of Ser-Gly and their conversion into branched chain amino acids. Metabolite profiling of a set of sublines, with introgressions in chromosome 2, identified a significant change in the abundance of the six amino acids in comparison to M82. Expression analysis of candidate genes affecting Ser metabolism matched the observation from the metabolite data, suggesting a tightly coordinated regulation of the level of these amino acids.
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