A wide foodomics approach coupled with metagenomics elucidates the environmental signature of potatoes.

The term "terroir" has been widely employed to link differential geographic phenotypes with sensorial signatures of agricultural food products, influenced by agricultural practices, soil type, and climate. Nowadays, the geographical indications labeling has been developed to safeguard the quality of plant-derived food that is linked to a certain terroir and is generally considered as an indication of superior organoleptic properties. As the dynamics of agroecosystems are highly intricate, consisting of tangled networks of interactions between plants, microorganisms, and the surrounding environment, the recognition of the key molecular components of terroir fingerprinting remains a great challenge to protect both the origin and the safety of food commodities. Furthermore, the contribution of microbiome as a potential driver of the terroir signature has been underestimated. Herein, we present a first comprehensive view of the multi-omic landscape related to transcriptome, proteome, epigenome, and metagenome of the popular Protected Geographical Indication potatoes of Naxos.

Disclosing the molecular basis of salinity priming in olive trees using proteogenomic model discovery.

Plant responses to salinity are becoming increasingly understood, however, salt priming mechanisms remain unclear, especially in perennial fruit trees. Herein, we showed that low-salt pre-exposure primes olive (Olea europaea) plants against high salinity stress. We then performed a proteogenomic study to characterize priming responses in olive roots and leaves. Integration of transcriptomic and proteomic data along with metabolic data revealed robust salinity changes that exhibit distinct or overlapping patterns in olive tissues, among which we focused on sugar regulation. Using the multi-crossed -omics data set, we showed that major differences between primed and nonprimed tissues are mainly associated with hormone signaling and defense-related interactions. We identified multiple genes and proteins, including known and putative regulators, that reported significant proteomic and transcriptomic changes between primed and nonprimed plants. Evidence also supported the notion that protein post-translational modifications, notably phosphorylations, carbonylations and S-nitrosylations, promote salt priming. The proteome and transcriptome abundance atlas uncovered alterations between mRNA and protein quantities within tissues and salinity conditions. Proteogenomic-driven causal model discovery also unveiled key interaction networks involved in salt priming. Data generated in this study are important resources for understanding salt priming in olive tree and facilitating proteogenomic research in plant physiology.

Unraveling salt-responsive tissue-specific metabolic pathways in olive tree.

Salinity is a serious constraint that reduces olive crop productivity. Here, we defined metabolite and gene expression changes in various tissues of olive trees (cv. "Chondrolia Chalkidikis") exposed to 75 mM NaCl for 45 days. Results showed that salinity induced foliar symptoms and impaired growth and photosynthetic parameters. The content of Na+ and Cl- in roots, xylem, phloem and leaves increased, although the Na+ levels in old leaves and Cl- in young leaves remained unaffected. Mannitol was accumulated in roots and old leaves challenged by salinity. NaCl-treated trees have a decreased TCA-associated metabolites, such as citric and malic acid, as well as changes in phenylpropanoid-associated metabolites (i.e., pinoresinol and vanillic acid) and genes (OePLRTp2 and OeCA4H). Salt treatment resulted in hydroxyl-decarboxylmethyl eleuropein aglycone accumulation and OeGTF up-regulation in new leaves, possibly suggesting that oleuropein metabolism was modified by NaCl. Tyrosine metabolism, particularly verbascoside levels and OePPO and OehisC expressions, was modulated by salinity. Both genes (e.g., OeAtF3H and OeFNSII) and metabolites (e.g., apigenin and luteolin) involved in flavonoid biosynthesis were induced in old leaves exposed to NaCl. Based on these data, we constructed an interaction scheme of changes in metabolites and transcripts across olive tissues upon salinity. Particularly, several metabolites involved in carbohydrate metabolism were reduced in roots, while many sugars, carbohydrates and flavonoids were increased in leaves. This study provided a framework for better understanding the possible mechanisms that govern the tissue-specific response of olive tree to salinity stress, with insights into molecules that can be used for olive crop improvement projects.

Olive Fruit Development and Ripening: Break on through to the "-Omics" Side.

The olive tree (Olea europaea L. subsp. europaea) is the most important perennial crop in the Mediterranean region, producing table olives and oil, both appreciated for their nutraceutical value. Although olive oil quality traits have been extensively studied, much less attention has been paid to olive drupe. Olive drupe ripening is an extremely complex process involving numerous physiological and molecular changes that are unique in this fruit crop species. This review underlines the contribution of "-omics" techniques and of the recent advances in bioinformatics and analytical tools, notably next-generation sequencing and mass spectrometry, for the characterization of the olive ripening syndrome. The usage of high-dimensional datasets, such as transcriptomics, proteomics, and metabolomics, will provide a systematical description of the molecular-specific processes regulating olive fruit development and ripening. However, the incomplete sequence of the O. europaea L. reference genome has largely hampered the utilization of omics tools towards olive drupe research. Due to this disadvantage, the most reported -omics studies on fruit trees concern metabolomics and only a few transcriptomics and proteomics. In this review, up-to-date applications of -omics technologies towards olive drupe biology are addressed, and future perspectives in olive fruit research are highlighted.

Silicon influenced ripening metabolism and improved fruit quality traits in apples.

The benefits of silicon against abiotic stress in different annual plant species have been described in many studies, however the regulation of ripening of fruit tree crops by silicon remains largely uncharacterized. Therefore, the present study aimed to explore the impact of foliar silicon application in the apple (cv. 'Fuji') fruit ripening traits along with the effect of silicon in the nutrient and metabolic changes in the fully expanded leaves, annual shoots, fruit outer pericarp (peel) and fruit mesocarp (skin) tissues. Data indicated that fruit firmness and apple peel color attributes, such as redness (a*) and percentage of red-blushed surface were induced by silicon application. Moreover, several fruit ripening traits, such as titratable acidity, soluble solid content and respiration rate were unaffected by silicon. Endogenous silicon level in leaves shoots and peel tissues were increased by exogenously applied silicon while several elements (i.e., P, Mg, Mn, Fe and Cu) were altered in the tested tissues that exposed to silicon. In addition, silicon increased the accumulation of total phenolic and total anthocyanin compounds in the various apple tissues. The level of various primary metabolites including sorbitol, fructose, maltose cellobiose, malic acid, phosphoric acid and gluconic acid was also notably affected by silicon in a tissue-specific manner. Overall, this study provides a valuable resource for future research, aiming in the elucidation of the role of silicon in fruit tree physiology.

Proteo-metabolomic journey across olive drupe development and maturation.

Maturity is one of the most important factors associated with the quality of olive products, however the molecular events underlying olive drupe development remain poorly characterized. Using proteomic and metabolomic approaches, this study investigated the changes in the olive drupes (cv. Chondrolia Chalkidikis) across six developmental stages (S1-S6) that characterize the dynamics of fruit growth and color. Primary metabolites, including carbohydrates and organic acids (i.e., xylose, malic acid), showed significant accumulation in the black maturation stage. Temporal changes in various secondary metabolites (e.g., oleuropein, oleacin and tyrosol) were also observed. Proteins involved in oxidation-reduction (i.e., LOX1/5), carbohydrate metabolism (i.e., GLUA, PG) and photosynthesis (i.e., chlorophyll a-b binding proteins) significantly altered in the turning black compared to the green mature stage. By providing the first proteometabolomic study of olive drupe development, this investigation offers a novel framework for further studies on this economically relevant crop.