Network Analysis Provides Insight into Tomato Lipid Metabolism

Sea Fennel (Crithmum maritimum L.) as an Emerging Crop for the Manufacturing of Innovative Foods and Nutraceuticals

Sea fennel (Crithmum maritimum L.) is a perennial, strongly aromatic herb that has been used since ancient times in cuisine and folk medicine due to its renowned properties. Recently described as a "cash" crop, sea fennel is an ideal candidate for the promotion of halophyte agriculture in the Mediterranean basin due to its acknowledged adaptation to the Mediterranean climate, its resilience to risks/shocks related to climate changes, and its exploitability in food and non-food applications, which generates an alternative source of employment in rural areas. The present review provides insight into the nutritional and functional traits of this new crop as well as its exploitation in innovative food and nutraceutical applications. Various previous studies have fully demonstrated the high biological and nutritional potential of sea fennel, highlighting its high content of bioactive compounds, including polyphenols, carotenoids, ω-3 and ω-6 essential fatty acids, minerals, vitamins, and essential oils. Moreover, in previous studies, this aromatic halophyte showed good potential for application in the manufacturing of high-value foods, including both fermented and unfermented preserves, sauces, powders, and spices, herbal infusions and decoctions, and even edible films, as well as nutraceuticals. Further research efforts are needed to fully disclose the potential of this halophyte in view of its full exploitation by the food and nutraceutical industries.

Genome-wide association study of eigenvectors provides genetic insights into selective breeding for tomato metabolites

Background

Long-term domestication and intensive breeding of crop plants aim to establish traits desirable for human needs, and characteristics related to yield, disease resistance, and postharvest storage have traditionally received considerable attention. These processes have led also to negative consequences, as is the case of loss of variants controlling fruit quality, for instance in tomato. Tomato fruit quality is directly associated to metabolite content profiles; however, a full understanding of the genetics affecting metabolite content during tomato domestication and improvement has not been reached due to limitations of the single detection methods previously employed. Here, we aim to reach a broad understanding of changes in metabolite content using a genome-wide association study (GWAS) with eigenvector decomposition (EigenGWAS) on tomato accessions.

Results

An EigenGWAS was performed on 331 tomato accessions using the first eigenvector generated from the genomic data as a “phenotype” to understand the changes in fruit metabolite content during breeding. Two independent gene sets were identified that affected fruit metabolites during domestication and improvement in consumer-preferred tomatoes. Furthermore, 57 candidate genes related to polyphenol and polyamine biosynthesis were discovered, and a major candidate gene chlorogenate: glucarate caffeoyltransferase (SlCGT) was identified, which affected the quality and diseases resistance of tomato fruit, revealing the domestication mechanism of polyphenols.

Conclusions

We identified gene sets that contributed to consumer liking during domestication and improvement of tomato. Our study reports novel evidence of selective sweeps and key metabolites controlled by multiple genes, increasing our understanding of the mechanisms of metabolites variation during those processes. It also supports a polygenic selection model for the application of tomato breeding.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12915-022-01327-x.

Identification, Classification, and Expression Analysis of the Triacylglycerol Lipase (TGL) Gene Family Related to Abiotic Stresses in Tomato

Triacylglycerol Lipases (TGLs) are the major enzymes involved in triacylglycerol catabolism. TGLs hydrolyze long-chain fatty acid triglycerides, which are involved in plant development and abiotic stress responses. Whereas most studies of TGLs have focused on seed oil metabolism and biofuel in plants, limited information is available regarding the genome-wide identification and characterization of the TGL gene family in tomato (Solanum lycopersicum L.). Based on the latest published tomato genome annotation ITAG4.0, 129 SlTGL genes were identified and classified into 5 categories according to their structural characteristics. Most SlTGL genes were distributed on 3 of 12 chromosomes. Segment duplication appeared to be the driving force underlying expansion of the TGL gene family in tomato. The promoter analysis revealed that the promoters of SlTGLs contained many stress responsiveness cis-elements, such as ARE, LTR, MBS, WRE3, and WUN-motifs. Expression of the majority of SlTGL genes was suppressed following exposure to chilling and heat, while it was induced under drought stress, such as SlTGLa9, SlTGLa6, SlTGLa25, SlTGLa26, and SlTGLa13. These results provide valuable insights into the roles of the SlTGL genes family and lay a foundation for further functional studies on the linkage between triacylglycerol catabolism and abiotic stress responses in tomato.

Identification of a lipase gene with a role in tomato fruit short-chain fatty acid-derived flavor volatiles by genome-wide association

Fatty acid-derived volatile organic compounds (FA-VOCs) make significant contributions to tomato (Solanum lycopersicum) fruit flavor and human preferences. Short-chain FA-VOCs (C5 and C6) are among the most abundant and important volatile compounds in tomato fruits. The precursors of these volatiles, linoleic acid (18:2) and linolenic acid (18:3), are derived from cleavage of glycerolipids. However, the initial step in synthesis of these FA-VOCs has not been established. A metabolite-based genome-wide association study combined with genetic mapping and functional analysis identified a gene encoding a novel class III lipase family member, Sl-LIP8, that is associated with accumulation of short-chain FA-VOCs in tomato fruit. In vitro assays indicated that Sl-LIP8 can cleave 18:2 and 18:3 acyl groups from glycerolipids. A CRISPR/Cas9 gene edited Sl-LIP8 mutant had much lower content of multiple fruit short-chain FA-VOCs, validating an important role for this enzyme in the pathway. Sl-LIP8 RNA abundance was correlated with FA-VOC content, consistent with transcriptional regulation of the first step in the pathway. Taken together, our work indicates that glycerolipid turnover by Sl-LIP8 is an important early step in the synthesis of multiple short-chain FA-VOCs.

Special Issue on "Fruit Metabolism and Metabolomics"

Over the past 10 years, knowledge about several aspects of fruit metabolism has been greatly improved. Notably, high-throughput metabolomic technologies have allowed quantifying metabolite levels across various biological processes, and identifying the genes that underly fruit development and ripening. This Special Issue is designed to exemplify the current use of metabolomics studies of temperate and tropical fruit for basic research as well as practical applications. It includes articles about different aspects of fruit biochemical phenotyping, fruit metabolism before and after harvest, including primary and specialized metabolisms, and bioactive compounds involved in growth and environmental responses. The effect of genotype, stages of development or fruit tissue on metabolomic profiles and corresponding metabolism regulations are addressed, as well as the combination of other omics with metabolomics for fruit metabolism studies.