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Plants are very vulnerable to pathogen attacks and environmental stress as they are exposed to harsh environments in natural conditions. However, they have evolved a self-defense system whereby reactive oxygen and nitrogen species (RONS) act as double-edged swords by imposing (at higher concentration) and mitigating (at lower concentration) environmental stress. Cold plasma is emerging as a feasible option to produce a variety of RONS in a controlled manner when amalgamate with water. Cold plasma activated/treated water (PAW) contains a variety of RONS at concentrations, which may help to activate the plant’s defense system components. In the present study, we examine the effect of cold atmospheric-air jet plasma exposure (15 min, 30 min, and 60 min) on the water’s RONS level, as well as the impact of PAW irrigation, (assigned as 15PAW, 30PAW, and 60PAW) on tomato seedlings growth and defense response. We found that PAW irrigation (priming) upregulate seedlings growth, endogenous RONS, defense hormone (salicylic acid and jasmonic acid), and expression of key pathogenesis related (PR) gene. 30 min PAW contains RONS at concentrations which can induce non-toxic signaling. The present study suggests that PAW irrigation can be beneficial for agriculture as it modulates plant growth as well as immune response components.

In plants, genomic DNA methylation which contributes to development and stress responses can be actively removed by DEMETER-like DNA demethylases (DMLs). Indeed, in Arabidopsis DMLs are important for maternal imprinting and endosperm demethylation, but only a few studies demonstrate the developmental roles of active DNA demethylation conclusively in this plant. Here, we show a direct cause and effect relationship between active DNA demethylation mainly mediated by the tomato DML, SlDML2, and fruit ripening- an important developmental process unique to plants. RNAi SlDML2 knockdown results in ripening inhibition via hypermethylation and repression of the expression of genes encoding ripening transcription factors and rate-limiting enzymes of key biochemical processes such as carotenoid synthesis. Our data demonstrate that active DNA demethylation is central to the control of ripening in tomato.

The extensive use of chemical fertilizers poses serious collateral problems such as environmental pollution, pest resistance development and food safety decline. Researches focused on applying plant-beneficial microorganisms to partially replace chemical fertilizer use is increasing due to the requirement of sustainable agriculture development. Thus to investigate the possibility of a plant-beneficial Trichoderma strain and its bio-organic fertilizer product in saving chemical fertilizer application and in improving crop quality, a field trial and continuous pot experiments were carried out with tomato. Four treatments were set up: a reduced application of chemical fertilizer (75% of the conventional application) plus Trichoderma -enriched bio-organic fertilizer (BF), organic fertilizer (OF) or Trichoderma spore suspension (SS), with using the 100% rate of the conventional chemical fertilizer as the control (CF). The results showed that the total soluble sugar, Vitamin C and nitrate accumulations were, respectively, +up to 24%, +up to 57% and –up to 62% in the tomatoes of the BF treatment compared to those of the control (CF). And both of the pot and field trials revealed that reduced rates of chemical fertilizer plus bio-organic fertilizer produced tomato yields equivalent to those obtained using the 100% of the chemical fertilizer. However, application with the inoculant alone (SS) or combined with the organic fertilizer alone (OF) would lead to a yield decreases of 6–38% and 9–35% over the control. Since the increased abundance of soil microflora and the enhanced soil fertility frequently showed positive linear correlations especially in the BF-treated soils, we conclude that the efficacy of this bio-organic fertilizer for maintaining a stable tomato yield and improving tomato quality may be due to the improved soil microbial activity. Thus, the results suggest that the Trichoderma bio-organic fertilizer could be employed in combination with the appropriate rates of chemical fertilizers to get maximum benefits regarding yield, quality and fertilizer savings.

The plant hormone ethylene plays a key role in climacteric fruit ripening. Studies on components of ethylene signaling have revealed a linear transduction pathway leading to the activation of ethylene response factors. However, the means by which ethylene selects the ripening-related genes and interacts with other signaling pathways to regulate the ripening process are still to be elucidated. Using tomato (Solanum lycopersicum) as a reference species, the present review aims to revisit the mechanisms by which ethylene regulates fruit ripening by taking advantage of new tools available to perform in silico studies at the genomewide scale, leading to a global view on the expression pattern of ethylene biosynthesis and response genes throughout ripening. Overall, it provides new insights on the transcriptional network by which this hormone coordinates the ripening process and emphasizes the interplay between ethylene and ripening-associated developmental factors and the link between epigenetic regulation and ethylene during fruit ripening.

There is increasing interest in the plant microbiome as it relates to both plant health and agricultural sustainability. One key unanswered question is whether we can select for a plant microbiome that is robust after colonization of target hosts. We used a successive passaging experiment to address this question by selecting upon the tomato phyllosphere microbiome. Beginning with a diverse microbial community generated from field-grown tomato plants, we inoculated replicate plants across 5 plant genotypes for 4 45-d passages, sequencing the microbial community at each passage. We observed consistent shifts in both the bacterial (16S amplicon sequencing) and fungal (internal transcribed spacer region amplicon sequencing) communities across replicate lines over time, as well as a general loss of diversity over the course of the experiment, suggesting that much of the naturally observed microbial community in the phyllosphere is likely transient or poorly adapted within the experimental setting. We found that both host genotype and environment shape microbial composition, but the relative importance of genotype declines through time. Furthermore, using a community coalescence experiment, we found that the bacterial community from the end of the experiment was robust to invasion by the starting bacterial community. These results highlight that selecting for a stable microbiome that is well adapted to a particular host environment is indeed possible, emphasizing the great potential of this approach in agriculture and beyond. In light of the consistent response of the microbiome to selection in the absence of reciprocal host evolution (coevolution) described here, future studies should address how such adaptation influences host health.

Whole-genome bisulfite sequencing reveals that global reprogramming of the epigenome occurs during the maturation of tomato fruits, potentially identifying new targets for breeders. Ripening of tomato fruits is triggered by the plant hormone ethylene, but its effect is restricted by an unknown developmental cue to mature fruits containing viable seeds. To determine whether this cue involves epigenetic remodeling, we expose tomatoes to the methyltransferase inhibitor 5-azacytidine and find that they ripen prematurely. We performed whole-genome bisulfite sequencing on fruit in four stages of development, from immature to ripe. We identified 52,095 differentially methylated regions (representing 1% of the genome) in the 90% of the genome covered by our analysis. Furthermore, binding sites for RIN, one of the main ripening transcription factors, are frequently localized in the demethylated regions of the promoters of numerous ripening genes, and binding occurs in concert with demethylation. Our data show that the epigenome is not static during development and may have been selected to ensure the fidelity of developmental processes such as ripening. Crop-improvement strategies could benefit by taking into account not only DNA sequence variation among plant lines, but also the information encoded in the epigenome.

Recently, long non-coding RNAs (lncRNAs) have been shown to play critical regulatory roles in model plants, such as Arabidopsis, rice, and maize. However, the presence of lncRNAs and how they function in fleshy fruit ripening are still largely unknown because fleshy fruit ripening is not present in the above model plants. Tomato is the model system for fruit ripening studies due to its dramatic ripening process. To investigate further the role of lncRNAs in fruit ripening, it is necessary and urgent to discover and identify novel lncRNAs and understand the function of lncRNAs in tomato fruit ripening. Here it is reported that 3679 lncRNAs were discovered from wild-type tomato and ripening mutant fruit. The lncRNAs are transcribed from all tomato chromosomes, 85.1% of which came from intergenic regions. Tomato lncRNAs are shorter and have fewer exons than protein-coding genes, a situation reminiscent of lncRNAs from other model plants. It was also observed that 490 lncRNAs were significantly up-regulated in ripening mutant fruits, and 187 lncRNAs were down-regulated, indicating that lncRNAs could be involved in the regulation of fruit ripening. In line with this, silencing of two novel tomato intergenic lncRNAs, lncRNA1459 and lncRNA1840, resulted in an obvious delay of ripening of wild-type fruit. Overall, the results indicated that lncRNAs might be essential regulators of tomato fruit ripening, which sheds new light on the regulation of fruit ripening.

Despite decades of research, the effects of spectral quality on plant growth, and development are not well understood. Much of our current understanding comes from studies with daily integrated light levels that are less than 10% of summer sunlight thus making it difficult to characterize interactions between light quality and quantity. Several studies have reported that growth is increased under fluorescent lamps compared to mixtures of wavelengths from LEDs. Conclusions regarding the effect of green light fraction range from detrimental to beneficial. Here we report the effects of eight blue and green light fractions at two photosynthetic photon fluxes (PPF; 200 and 500 μmol m-2 s-1; with a daily light integral of 11.5 and 29 mol m-2 d-1) on growth (dry mass), leaf expansion, stem and petiole elongation, and whole-plant net assimilation of seven diverse plant species. The treatments included cool, neutral, and warm white LEDs, and combinations of blue, green and/or red LEDs. At the higher PPF (500), increasing blue light in increments from 11 to 28% reduced growth in tomato, cucumber, and pepper by 22, 26, and 14% respectively, but there was no statistically significant effect on radish, soybean, lettuce or wheat. At the lower PPF (200), increasing blue light reduced growth only in tomato (41%). The effects of blue light on growth were mediated by changes in leaf area and radiation capture, with minimal effects on whole-plant net-assimilation. In contrast to the significant effects of blue light, increasing green light in increments from 0 to 30% had a relatively small effect on growth, leaf area and net assimilation at either low or high PPF. Surprisingly, growth of three of the seven species was not reduced by a treatment with 93% green light compared to the broad spectrum treatments. Collectively, these results are consistent with a shade avoidance response associated with either low blue or high green light fractions.

Early blight is a disease that greatly affects Solanaceae, mainly damaging tomato plants, and causing significant economic losses. Although there are methods of biological control, these are very expensive and often their mode of action is slow. Due to this, there is a need to use new techniques that allow a more efficient control of pathogens. Nanotechnology is a new alternative to solve these problems, allowing the creation of new tools for the treatment of diseases in plants, as well as the control of pathogens. The aim of the present investigation was to evaluate the foliar application of selenium and copper in the form of nanoparticles in a tomato crop infested by Alternaria solani. The severity of Alternaria solani, agronomic variables of the tomato crop, and the changes in the enzymatic and non-enzymatic antioxidant compounds were evaluated. The joint application of Se and Cu nanoparticles decreases the severity of this pathogen in tomato plants. Moreover, high doses generated an induction of the activity of the enzymes superoxide dismutase, ascorbate peroxidase, glutathione peroxidase (GPX) and phenylalanine ammonia lyase in the leaves, and the enzyme GPX in the fruit. Regarding non-enzymatic compounds in the leaves, chlorophyll a, b, and totals were increased, whereas vitamin C, glutathione, phenols, and flavonoids were increased in fruits. The application of nanoparticles generated beneficial effects by increasing the enzymatic and non-enzymatic compounds and decreasing the severity of Alternaria solani in tomato plants.

Zachary Lippman and colleagues report mutations in the tomato ortholog of CLV1 and a gene encoding a hydroxyproline O-arabinosyltransferase enzyme that modifies CLV3, both of which cause fasciated flowers and fruits owing to increased meristem size. They also find that a natural mutation in CLV3 was a major target of selection during tomato domestication. Shoot meristems of plants are composed of stem cells that are continuously replenished through a classical feedback circuit involving the homeobox WUSCHEL ( WUS ) gene and the CLAVATA ( CLV ) gene signaling pathway. In CLV signaling, the CLV1 receptor complex is bound by CLV3, a secreted peptide modified with sugars. However, the pathway responsible for modifying CLV3 and its relevance for CLV signaling are unknown. Here we show that tomato inflorescence branching mutants with extra flower and fruit organs due to enlarged meristems are defective in arabinosyltransferase genes. The most extreme mutant is disrupted in a hydroxyproline O-arabinosyltransferase and can be rescued with arabinosylated CLV3. Weaker mutants are defective in arabinosyltransferases that extend arabinose chains, indicating that CLV3 must be fully arabinosylated to maintain meristem size. Finally, we show that a mutation in CLV3 increased fruit size during domestication. Our findings uncover a new layer of complexity in the control of plant stem cell proliferation.