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Sustainable agriculture requires replacing agrochemicals with environmentally friendly products. One alternative is bacterial inoculants with plant-growth-promoting (PGP) activity. Bacterial consortia offer advantages over single-strain inoculants, as they possess more PGP traits and allow the exploitation of bacterial synergies. Synthetic bacterial communities (SynComs) can be used as inoculants that are thoroughly characterized and assessed for efficiency and safety. Here, we describe the construction of a SynCom composed of seven bacterial strains isolated from the rhizosphere of tomato plants and other orchard vegetables. The strains were identified by 16S rDNA sequencing as Pseudomonas spp. (two isolates), Rhizobium sp., Ensifer sp., Microbacterium sp., Agromyces sp., and Chryseobacterium sp. The metagenome of the combined strains was sequenced, allowing the identification of PGP traits and the assembly of their individual genomes. These traits included nutrient mobilization, phytostimulation, and biocontrol. When inoculated into tomato plants in an agricultural soil, the SynCom caused minor effects in soil and rhizosphere bacterial communities. However, it had a high impact on the gene expression pattern of tomato plants. These effects were more significant at the systemic than at the local level, indicating a priming effect in the plant, as signaling through jasmonic acid and ethylene appeared to be altered.

Transglutaminase (TGase), the ubiquitous protein in plants, catalyzes the post-translational transformation of proteins and plays a vital role in photosynthesis. However, its role and mechanism in tomato subjected to heat stress still remain unknown. Here, we carried out a transcriptomic assay to compare the differentially expressed genes (DEGs) between wild type (WT) and TGase overexpression (TGaseOE) plants employed to high-temperature at 42 °C and samples were collected after 0, 6, and 12 h, respectively. A total of 11,516 DEGs were identified from heat-stressed seedlings, while 1,148 and 1,353 DEGs were up-and down-regulated, respectively. The DEGs upon high-temperature stress were closely associated with the pathways encompassing protein processing in the endoplasmic reticulum, carbon fixation, and photosynthetic metabolism. In addition, 425 putative transcription factors (TFs) were identified, and the majority of them associated with the bHLH, HSF, AP2/ERF, MYB, and WRKY families. RNA-seq data validation further confirmed that 8 genes were linked to protein processing and photosynthesis, and the mRNA level of these genes in TGaseOE was higher than that in WT plants, which is consistent in transcriptome results. In conclusion, these results reveal the transcriptional regulation between WT and TGaseOE in tomato under heat stress and shed light on a new dimension of knowledge of TGase-mediated thermotolerance mechanism at the molecular level.

Plant metabolism is altered in response to various environmental changes. In vegetable crops such as tomato (Solanum lycopersicum), the metabolic composition of fruits varies depending on the variety or cultivar as well as the cultivation method used. Few studies have examined the metabolic fluctuations in fruits under stress conditions, such as drought. We previously examined the metabolomes of mature green tomato fruits, which undergo drastic changes in chemical composition during ripening, and mature red fruits in response to drought stress. We detected or predicted fluctuations in the levels of fatty acids and phospholipid constituents, such as inositol and ethanolamine. In this study, we determined the localizations of these metabolites in fruits using mass spectrometry imaging. The accumulation patterns of stearic acid and palmitic acid were similar, but unlike these fatty acids, oleic acid accumulated to high levels in the placenta. Inositol is involved in various physiological processes; under drought conditions, this metabolite is synthesized by a different pathway compared to under normal conditions. The biosynthesis of pectin, a component of the gel surrounding the seeds, was suppressed under drought stress but increased in seeds. We propose that under drought conditions, a shift to phospholipid biosynthesis occurs that protects seeds from dehydration.

• Wounding triggers de novo organogenesis, vascular reconnection and defense response but how wound stress evoke such a diverse array of physiological responses remains unknown. • We previously identified AP2/ERF transcription factors, WOUND INDUCED DEDIFFERENTIATION1 (WIND1) and its homologs, WIND2, WIND3 and WIND4, as key regulators of wound-induced cellular reprogramming in Arabidopsis. To understand how WIND transcription factors promote downstream events, we performed time-course transcriptome analyses after WIND1 induction. • We observed a significant overlap between WIND1-induced genes and genes implicated in cellular reprogramming, vascular formation and pathogen response. We demonstrated that WIND transcription factors induce several reprogramming genes to promote callus formation at wound sites. We, in addition, showed that WIND transcription factors promote tracheary element formation, vascular reconnection and resistance to Pseudomonas syringae pv. tomato DC3000. • These results indicate that WIND transcription factors function as key regulators of woundinduced responses by promoting dynamic transcriptional alterations. This study provides deeper mechanistic insights into how plants control multiple physiological responses after wounding.

Fruit ripening and disease resistance are two essential biological processes for quality formation and maintenance. DNA methylation, in the form of 5‐methylcytosine (5mC), has been elucidated to modulate fruit ripening, but its role in regulating fruit disease resistance remains poorly understood. In this study, we show that mutation of SlDML2 , the DNA demethylase gene essential for fruit ripening, affects multiple developmental processes of tomato besides fruit ripening, including seed germination, leaf length and width and flower branching. Intriguingly, loss of SlDML2 function decreased the resistance of tomato fruits against the necrotrophic fungal pathogen Botrytis cinerea. Comparative transcriptomic analysis revealed an obvious transcriptome reprogramming caused by SlDML2 mutation during B. cinerea invasion. Among the thousands of differentially expressed genes, SlβCA3 encoding a β‐carbonic anhydrase and SlFAD3 encoding a ω‐3 fatty acid desaturase were demonstrated to be transcriptionally activated by SlDML2‐mediated DNA demethylation and positively regulate tomato resistance to B. cinerea probably in the same genetic pathway with SlDML2 . We further show that the pericarp tissue surrounding B. cinerea infection exhibited a delay in ripening with singnificant decrease in expression of ripening genes that are targeted by SlDML2 and increase in expression of SlβCA3 and SlFAD3 . Taken together, our results uncover an essential layer of gene regulation mediated by DNA methylation upon B. cinerea infection and raise the possible that the DNA demethylase gene SlDML2 , as a multifunctional gene, participates in modulating the trade‐off between fruit ripening and disease resistance.

Many important cell-to-cell communication events in multicellular organisms are mediated by peptides, but only a few peptides have been identified in plants. In an attempt to address the difficulties in identifying plant signaling peptides, we developed a novel peptidomics approach and used this approach to discover defense signaling peptides in plants. In addition to the canonical peptide systemin, several novel peptides were confidently identified in tomato (Solanum lycopersicum) and quantified to be induced by both wounding and methyl jasmonate (MeJA). A wounding or wounding plus MeJA-induced peptide derived from the pathogenesis-related protein 1 (PR-1) family was found to induce significant antipathogen and minor antiherbivore responses in tomato. This study highlights a role for PR-1 in immune signaling and suggests the potential application of plant endogenous peptides in efforts to defeat biological threats in crop production. As PR-1 is highly conserved across many organisms and the putative peptide from At-PR1 was also found to be bioactive in Arabidopsis thaliana, our results suggest that this peptide may be useful for enhancing resistance to stress in other plant species.

Tomato, one of the most important vegetable crops around the world, is sensitive to heat stress. Identifying heat-tolerant genes and breeding resilient varieties are vital for addressing the challenges of global warming and ensuring food security. In this study, we compared seedlings of a cultivated tomato accession ( Solanum lycopersicum , M82) with those of a wild accession ( S. pimpinellifolium , LA1589) at both physio-biochemical and transcriptomic levels under a 42℃ heat treatment. Various physio-biochemical indicators demonstrated that LA1589 exhibited superior heat tolerance compared to M82 at the seedling stage. We conducted dynamic transcriptome analyses of these two genotypes under heat treatment, identifying 10,681 differentially expressed genes (DEGs) in LA1589 and 10,462 DEGs in M82. Among these, 1,857 genes were specifically up-regulated and 1,228 genes were specifically down-regulated in LA1589, while 1,916 genes were specifically up-regulated and 1,021 genes were specifically down-regulated in M82. The enrichment analyses indicated that DEGs were significantly clustered in biological processes and pathways associated with heat resistance. Notably, the specifically down-regulated genes in LA1589 were significantly enriched only in the plasma membrane pathway, whereas in M82, these genes were enriched in chloroplast-associated processes and other pathways. Weighted gene co-expression network analysis identified heat-response modules, including TM11, PM3 and PM23. Further analysis revealed the involvement of SlHsfA7 , heat shock proteins and chloroplast-related genes in the center of the heat-responsive regulatory network in tomato. Our findings provide a solid foundation for further functional elucidation of candidate heat-tolerant genes and their underlying molecular mechanisms in tomato.

Traditional substrate cultivation is now a routine practice in vegetable facility breeding. However, finding renewable substrates that can replace traditional substrates is urgent in today’s production. In this study, we used the ‘Pindstrup’ substrate as control and two types of composite substrates made from fermented corn straw (i.e. 0–3 and 3–5 mm) to identify appropriate substrate conditions for tomato seedling growth under winter greenhouse conditions. Seedling growth potential related data and substrate water content related data were tested to carry out data-oriented support. Since the single physiological data cannot well explain the mechanism of tomato seedlings under winter greenhouse condition, transcriptomic analysis of tomato root and leaf tissues were conducted to provide theoretical basis. The physiological data of tomato seedlings and substrate showed that compared with 0–3 mm and Pindstrup substrate, tomato seedlings planted in 3–5 mm had stronger growth potential and stronger water retention, and were more suitable for planting tomato seedlings. Transcriptome analysis revealed a greater number of DEGs between the Pindstrup and the 3–5 mm. The genes in this group contribute to tomato growth as well as tomato stress response mechanisms, such as ABA-related genes, hormone-related genes and some TFs. The simulation network mechanism diagram adds evidence to the above conclusions. Overall, these results demonstrate the potential benefits of using the fermented corn straw of 3–5 mm for growing tomato seedlings and present a novel method of utilizing corn straw.

Commercial tomatoes are widely perceived by consumers as lacking flavor. A major part of that problem is a postharvest handling system that chills fruit. Low-temperature storage is widely used to slow ripening and reduce decay. However, chilling results in loss of flavor. Flavor-associated volatiles are sensitive to temperatures below 12 °C, and their loss greatly reduces flavor quality. Here, we provide a comprehensive view of the effects of chilling on flavor and volatiles associated with consumer liking. Reduced levels of specific volatiles are associated with significant reductions in transcripts encoding key volatile synthesis enzymes. Although expression of some genes critical to volatile synthesis recovers after a return to 20 °C, some genes do not. RNAs encoding transcription factors essential for ripening, including RIPENING INHIBITOR (RIN), NONRIPENING, and COLORLESS NONRIPENING are reduced in response to chilling and may be responsible for reduced transcript levels in many downstream genes during chilling. Those reductions are accompanied by major changes in the methylation status of promoters, including RIN. Methylation changes are transient and may contribute to the fidelity of gene expression required to provide maximal beneficial environmental response with minimal tangential influence on broader fruit developmental biology.

Tomato brown rugose fruit virus (ToBRFV) is a newly-emerging tobamovirus which was first reported on tomatoes in Israel and Jordan, and which has now spread rapidly in Asia, Europe, North America, and Africa. ToBRFV can overcome the resistance to other tobamoviruses conferred by tomato Tm-1, Tm-2, and Tm-22 genes, and it has seriously affected global crop production. The rapid and comprehensive transcription reprogramming of host plant cells is the key to resisting virus attack, but there have been no studies of the transcriptome changes induced by ToBRFV in tomatoes. Here, we made a comparative transcriptome analysis between tomato leaves infected with ToBRFV for 21 days and those mock-inoculated as controls. A total of 522 differentially expressed genes were identified after ToBRFV infection, of which 270 were up-regulated and 252 were down-regulated. Functional analysis showed that DEGs were involved in biological processes such as response to wounding, response to stress, protein folding, and defense response. Ten DEGs were selected and verified by qRT-PCR, confirming the reliability of the high-throughput sequencing data. These results provide candidate genes or signal pathways for the response of tomato leaves to ToBRFV infection.