To investigate the regulation of seed metabolism and to estimate the degree of metabolic natural variability, metabolite profiling and network analysis were applied to a collection of 76 different homozygous tomato introgression lines (ILs) grown in the field in two consecutive harvest seasons. Factorial ANOVA confirmed the presence of 30 metabolite quantitative trait loci (mQTL). Amino acid contents displayed a high degree of variability across the population, with similar patterns across the two seasons, while sugars exhibited significant seasonal fluctuations. Upon integration of data for tomato pericarp metabolite profiling, factorial ANOVA identified the main factor for metabolic polymorphism to be the genotypic background rather than the environment or the tissue. Analysis of the coefficient of variance indicated greater phenotypic plasticity in the ILs than in the M82 tomato cultivar. Broad-sense estimate of heritability suggested that the mode of inheritance of metabolite traits in the seed differed from that in the fruit. Correlation-based metabolic network analysis comparing metabolite data for the seed with that for the pericarp showed that the seed network displayed tighter interdependence of metabolic processes than the fruit. Amino acids in the seed metabolic network were shown to play a central hub-like role in the topology of the network, maintaining high interactions with other metabolite categories, i.e., sugars and organic acids. Network analysis identified six exceptionally highly co-regulated amino acids, Gly, Ser, Thr, Ile, Val, and Pro. The strong interdependence of this group was confirmed by the mQTL mapping. Taken together these results (i) reflect the extensive redundancy of the regulation underlying seed metabolism, (ii) demonstrate the tight co-ordination of seed metabolism with respect to fruit metabolism, and (iii) emphasize the centrality of the amino acid module in the seed metabolic network. Finally, the study highlights the added value of integrating metabolic network analysis with mQTL mapping.

Seed germination is regulated in a concerted manner that involves generating growth potential in the embryo to overcome the mechanical resistance of the endosperm. The wake-up call of a dry seed includes the reorganization of subcellular structures and the reactivation of metabolism in a dense, oxygen-poor environment. Pools of unbound metabolites and solutes produced by the degradation of storage reserves, including starch, proteins and oils, in the embryo can contribute to the generation of the embryo growth potential and radicle protrusion. Recent genomics studies have contributed a vast amount of data on protein, metabolite and gene transcript profiles during germination, which can be integrated to explore the seed metabolism from water imbibition to radicle protrusion. To what extent are free pools of metabolites relevant to the reorganization of seed metabolism? How is energy built to support embryo growth and radicle protrusion? Elucidating these fundamental questions in seed biology is the key to the understanding of the germination process. Here we have attempted to summarize the recent scientific knowledge to provide a comprehensive description of the ignition, reassembling and regulation of metabolism during seed germination.

Autophagy is an evolutionarily conserved mechanism that mediates the degradation of cytoplasmic components in eukaryotic cells. In plants, autophagy has been extensively associated with the recycling of proteins during carbon-starvation conditions. Even though lipids constitute a significant energy reserve, our understanding of the function of autophagy in the management of cell lipid reserves and components remains fragmented. To further investigate the significance of autophagy in lipid metabolism, we performed an extensive lipidomic characterization of Arabidopsis (Arabidopsis thaliana) autophagy mutants (atg) subjected to dark-induced senescence conditions. Our results revealed an altered lipid profile in atg mutants, suggesting that autophagy affects the homeostasis of multiple lipid components under dark-induced senescence. The acute degradation of chloroplast lipids coupled with the differential accumulation of triacylglycerols (TAGs) and plastoglobuli indicates an alternative metabolic reprogramming toward lipid storage in atg mutants. The imbalance of lipid metabolism compromises the production of cytosolic lipid droplets and the regulation of peroxisomal lipid oxidation pathways in atg mutants.

BackgroundThe metabolite content of a seed and its ability to germinate are determined by genetic makeup and environmental effects during development. The interaction between genetics, environment and seed metabolism and germination was studied in 72 tomato homozygous introgression lines (IL) derived from Solanum pennelli and S. esculentum M82 cultivar. Plants were grown in the field under saline and fresh water irrigation during two consecutive seasons, and collected seeds were subjected to morphological analysis, gas chromatograph-mass spectrometry (GC-MS) metabolic profiling and germination tests.ResultsSeed weight was under tight genetic regulation, but it was not related to germination vigor. Salinity significantly reduced seed number but had little influence on seed metabolites, affecting only 1% of the statistical comparisons. The metabolites negatively correlated to germination were simple sugars and most amino acids, while positive correlations were found for several organic acids and the N metabolites urea and dopamine. Germination tests identified putative loci for improved germination as compared to M82 and in response to salinity, which were also characterized by defined metabolic changes in the seed.ConclusionsAn integrative analysis of the metabolite and germination data revealed metabolite levels unambiguously associated with germination percentage and rate, mostly conserved in the different tested seed development environments. Such consistent relations suggest the potential for developing a method of germination vigor prediction by metabolic profiling, as well as add to our understanding of the importance of primary metabolic processes in germination.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-3376-9) contains supplementary material, which is available to authorized users.

Lipids are fascinating due to their chemical diversity, which is especially vast in the plant kingdom thanks to the high plasticity of the plant biosynthetic machinery. Lipidomic studies aim to simultaneously analyze a large number of lipid compounds of diverse classes in a given sample. The method presented here uses liquid chromatography–mass spectrometry (LC‐MS)‐based lipidomic profiling in a relatively fast, robust, and high‐throughput manner for high‐coverage quantification and annotation of lipophilic compounds. Protocols cover sample preparation, LC‐MS‐based measurement, and data extraction and annotation. An extensive lipid library for triacylglycerols, galactolipids, and phospholipids is provided. The extended profiling described here could be used in a range of applications and is suitable for integration with other omic datasets. © 2020 by John Wiley & Sons, Inc.Basic Protocol 1: Sample preparation and metabolite extractionBasic Protocol 2: Liquid chromatography–mass spectrometry (LC‐MS) analysisBasic Protocol 3: Data extraction, annotation, and quantification