Metabolic correlation networks have been used in several instances to obtain a deeper insight into the complexity of plant metabolism as a whole. In tomato (Solanum lycopersicum), metabolites have a major influence on taste and overall fruit quality traits. Previously a broad spectrum of metabolic and phenotypic traits has been described using a Solanum pennellii introgression-lines (ILs) population. To obtain insights into tomato fruit metabolism, we performed metabolic network analysis from existing data, covering a wide range of metabolic traits, including lipophilic and volatile compounds, for the first time. We provide a comprehensive fruit correlation network and show how primary, secondary, lipophilic, and volatile compounds connect to each other and how the individual metabolic classes are linked to yield-related phenotypic traits. Results revealed a high connectivity within and between different classes of lipophilic compounds, as well as between lipophilic and secondary metabolites. We focused on lipid metabolism and generated a gene-expression network with lipophilic metabolites to identify new putative lipid-related genes. Metabolite–transcript correlation analysis revealed key putative genes involved in lipid biosynthesis pathways. The overall results will help to deepen our understanding of tomato metabolism and provide candidate genes for transgenic approaches toward improving nutritional qualities in tomato.

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Most studies investigating quantitative traits focus on mean levels per genotype rather than the variation between different individuals of one genotype or the variation elicited by different environments. Consequently, the genes that govern this effect are not well understood. The concept, named canalization, which describes a lack of variation, is well-known in the context of developmental processes but is poorly studied for quantitative traits such as metabolism. In this study, we selected eight putative candidate genes from previously identified canalized metabolic quantitative trait loci (cmQTL) and created genome-edited tomato (Solanum lycopersicum) mutants of these genes for experimental validation. Most lines showed wild-type morphology, except for an ADP-ribosylation factor (ARLB) mutant showing aberrant phenotypes in the form of scarred fruit cuticles. In greenhouse trials with different irrigation conditions, whole-plant traits showed a general increase of their level towards the more optimal irrigation conditions, whereas most metabolic traits showed an increase towards the other end of the gradient. Mutants of a PANTOTHENATE KINASE 4 (PANK4), the AIRP ubiquitin gene LOSS OF GDU2 (LOG2), and TRANSPOSON PROTEIN 1 (TRANSP1) grown under these conditions showed an overall improved plant performance. Additional effects, on both target and other metabolites in tomato fruits, regarding the mean level at specific conditions and, ergo, the cross-environment coefficient of variation (CV), were observed. However, variation between individuals remained unaffected. In conclusion, this study supports the idea of distinct sets of genes regulating different types of variation.

Varying light conditions elicit metabolic responses as part of acclimation with changes in ascorbate levels being an important component. Here, we adopted a genome-wide association-based approach to characterize the response in ascorbate levels on high light acclimation in a panel of 315 Arabidopsis (Arabidopsis thaliana) accessions. These studies revealed statistically significant SNPs for total and reduced ascorbate under high light conditions at a locus in chromosome 2. Ascorbate levels under high light and the region upstream and within PAS/LOV PROTEIN (PLP) were strongly associated. Intriguingly, subcellular localization analyses revealed that the PLPA and PLPB splice variants co-localized with VITAMIN C DEFECTIVE2 (VTC2) and VTC5 in both the cytosol and nucleus. Yeast 2-hybrid and Bimolecular fluorescence complementation analyses revealed that PLPA and PLPB interact with VTC2 and that blue light diminishes this interaction. Furthermore, PLPB knockout mutants were characterized by 1.5- to 1.7- fold elevations in their ascorbate levels, whereas knockout mutants of the cry2 cryptochromes displayed 1.2- to 1.3- fold elevations compared to WT. Our results collectively indicate that PLP plays a critical role in the elevation of ascorbate levels, which is a signature response of high light acclimation. The results strongly suggest that this is achieved via release of the inhibitory effect of PLP on VTC2 upon blue light illumination, as the VTC2-PLPB interaction is stronger under darkness. The conditional importance of the cryptochrome receptors under different environmental conditions suggests a complex hierarchy underpinning the environmental control of ascorbate levels. However, the data we present here clearly demonstrate that PLP dominates during high light acclimation.

Modern genetics and biochemistry have revolutionized our understanding of plant biology. However, biochemical genetics can be traced to the foundation of Mendelian genetics indeed one of the milestone discoveries of Mendels seven characteristics of pea plants could later be ascribed to be due to mutation in starch branching enzyme. Here we review both current and historical strategies for the elucidation of plant metabolic pathways and the genes which encode their component enzymes and regulators. We utilize this historical review to discuss a range of classical genetic phenomena including, epistasis, canalization and heterosis as viewed through the lens of contemporary high-throughput data obtained via the array of approaches currently adopted in multi-omics studies.