Transcriptional changes associated with chilling tolerance and susceptibility in ‘Micro-Tom’ tomato fruit using RNA-Seq

A comprehensive study from the micro- to the nanometric scale: Evaluation of chilling injury in tomato fruit (Solanum lycopersicum)

Tomato fruit is susceptible to chilling injury (CI) during its postharvest handling at low temperature. The symptoms caused by this physiological disorder have been commonly evaluated by visual inspection at a macro-observation scale on fruit surface; however, the structure at deeper scales is also affected by CI. This work aimed to propose a descriptive model of the CI development in tomato tissue under the micro-scale, micro-nano-scale and nano-scale approaches using fractal analysis. For that, quality and fractal parameters were determined. In this sense, light microscopy, Environmental Scanning Electron Microscopy (ESEM) and Atomic Force Microscopy (AFM) were applied to analyse micro-, micro-nano- and nano-scales, respectively. Results showed that the morphology of tomato tissue at the micro-scale level was properly described by the multifractal behaviour. Also, generalised fractal dimension (Dq=0) and texture fractal dimension (FD) of CI-damaged pericarp and cuticle were higher (1.659, 1.601 and 1.746, respectively) in comparison to non-chilled samples (1.606, 1.578 and 1.644, respectively); however, FD was unsuitable to detect morphological changes at the nano-scale. On the other hand, lacunarity represented an appropriate fractal parameter to detect CI symptoms at the nano-scale due to differences observed between damaged and regular ripe tissue (0.044 and 0.025, respectively). The proposed multi-scale approach could improve the understanding of CI as a complex disorder to the development of novel techniques to avoid this postharvest issue at different observation scales.

Gamma irradiation delays tomato (Solanum lycopersicum) ripening by inducing transcriptional changes

BACKGROUND

Tomato (Solanum lycopersicum) has a relatively short shelf life as a result of rapid ripening, limiting its transportability and marketability. Recently, gamma irradiation has emerged as a viable method for delaying tomato fruit ripening. Although few studies have shown that gamma irradiation delays the ripening of tomatoes, the underlying mechanism remains unknown. Therefore, the present study aimed to examine the effects of gamma irradiation on tomato fruit ripening and the underlying mechanisms using transcriptomics.

RESULTS

Following gamma irradiation, the total microbial count, weight loss, and decay rate of tomatoes significantly reduced during storage. Furthermore, the redness (a*), color change (∆E), and lycopene content of gamma-irradiated tomatoes decreased in a dose-dependent manner during storage. Moreover, gamma irradiation significantly upregulated the expression levels of genes associated with DNA, chloroplast, and oxidative damage repairs, whereas those of ethylene and auxin signaling-, ripening-, and cell wall metabolism-related, as well as carotenoid genes, were downregulated.

CONCLUSION

Gamma irradiation effectively delayed ripening by downregulating the expression of ripening-related genes and inhibiting microbial growth, which prevented decay and prolonged the shelf life of tomatoes. © 2023 The Authors. Journal of The Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

Transcriptomic analysis in tomato fruit reveals divergences in genes involved in cold stress response and fruit ripening

Cold storage is widely used to extend the postharvest life of most horticultural crops, including tomatoes, but this practice triggers cold stress and leads to the development of undesirable chilling injury (CI) symptoms. The underlying mechanisms of cold stress response and CI development in fruits remain unclear as they are often intermingled with fruit ripening changes. To gain insight into cold responses in fruits, we examined the effect of the potent ethylene signaling inhibitor 1-methylcyclopropene (1-MCP) on fruit ripening, CI occurrence and gene expression in mature green tomatoes during storage at 20°C and 5°C. 1-MCP treatments effectively inhibited ethylene production and peel color changes during storage at 20°C. Storage at 5°C also inhibited both ethylene production and peel color change; during rewarming at 20°C, 1-MCP treatments inhibited peel color change but failed to inhibit ethylene production. Furthermore, fruits stored at 5°C for 14 d developed CI symptoms (surface pitting and decay) during the rewarming period at 20°C regardless of 1-MCP treatment. Subsequent RNA-Seq analysis revealed that cold stress triggers a large-scale transcriptomic adjustment, as noticeably more genes were differentially expressed at 5°C (8,406) than at 20°C (4,814). More importantly, we have found some important divergences among genes involved in fruit ripening (up- or down-regulated at 20°C; inhibited by 1-MCP treatment) and those involved in cold stress (up- or down-regulated at 5°C; unaffected by 1-MCP treatment). Transcriptomic adjustments unique to cold stress response were associated with ribosome biogenesis, NcRNA metabolism, DNA methylation, chromatin formation/remodeling, and alternative splicing events. These data should foster further research into cold stress response mechanisms in fruits with the ultimate aim of improving tolerance to low temperature and reduction of CI symptoms during cold storage.

Drought tolerance improvement in Solanum lycopersicum: an insight into "OMICS" approaches and genome editing

Solanum lycopersicum (tomato) is an internationally acclaimed vegetable crop that is grown worldwide. However, drought stress is one of the most critical challenges for tomato production, and it is a crucial task for agricultural biotechnology to produce drought-resistant cultivars. Although breeders have done a lot of work on the tomato to boost quality and quantity of production and enhance resistance to biotic and abiotic stresses, conventional tomato breeding approaches have been limited to improving drought tolerance because of the intricacy of drought traits. Many efforts have been made to better understand the mechanisms involved in adaptation and tolerance to drought stress in tomatoes throughout the years. "Omics" techniques, such as genomics, transcriptomics, proteomics, and metabolomics in combination with modern sequencing technologies, have tremendously aided the discovery of drought-responsive genes. In addition, the availability of biotechnological tools, such as plant transformation and the recently developed genome editing system for tomatoes, has opened up wider opportunities for validating the function of drought-responsive genes and the generation of drought-tolerant varieties. This review highlighted the recent progresses for tomatoes improvement against drought stress through "omics" and "multi-omics" technologies including genetic engineering. We have also discussed the roles of non-coding RNAs and genome editing techniques for drought stress tolerance improvement in tomatoes.

Additional Blue LED during Cultivation Induces Cold Tolerance in Tomato Fruit but Only to an Optimum

Simple Summary

LED lighting is increasingly applied to increase yield and quality of greenhouse produced crops, especially tomatoes. Tomatoes cannot be stored at cold temperatures due to chilling injury that manifests as quick quality deterioration during shelf life. The aim of this study is to investigate whether additional blue LED lighting can mitigate the negative effects of cold storage for ‘Foundation’ tomatoes. We applied three treatments, 0, 12 or 24% additional blue light during cultivation, and investigated quality attributes at harvest, after cold storage and subsequent shelf-life. We observed that red harvested tomatoes cultivated with 12% additional blue light acquired cold tolerance. Interestingly, these tomatoes were slightly less red colored at harvest and showed a faster loss of red color during cold storage. The measured red color is closely related to the lycopene concentration. We hypothesize that lycopene, a known antioxidant, present in 12% additional blue cultivated tomatoes mitigates chilling injury. Other antioxidants present in tomatoes were only affected by the ripeness at harvest and were therefore not involved in the acquired cold tolerance. The cultivation of tomatoes using additional blue LED is an attractive way to produce tomatoes that can withstand long transport at cold temperatures at the expense of a slightly less red tomato at the consumer.

Abstract

Tomato is a chilling-sensitive fruit. The aim of this study is to examine the role of preharvest blue LED lighting (BL) to induce cold tolerance in ‘Foundation’ tomatoes. Blue and red supplemental LED light was applied to achieve either 0, 12 or 24% additional BL (0B, 12B and 24B). Mature green (MG) or red (R) tomatoes were harvested and cold stored at 4 °C for 0, 5, 10, 15 and 20 d, and then stored for 20 d at 20 °C (shelf life). Chilling injury (CI) indices, color and firmness, hydrogen peroxide, malondialdehyde, ascorbic acid and catalase activity were characterized. At harvest, R tomatoes cultivated at 12B were firmer and showed less coloration compared to fruit of other treatments. These fruits also showed higher loss of red color during cold storage and lower CI symptoms during shelf-life. MG tomatoes cultivated at 12B showed delayed coloring (non-chilled) and decreased weight loss (long cold stored) during shelf life compared to fruit in the other treatments. No effects of light treatments, both for MG and R tomatoes, were observed for the selected antioxidant capacity indicators. Improved cold tolerance for R tomatoes cultivated at 12B points to lycopene having higher scavenging activity at lower concentrations to mitigate chilling injury.

Brassinosteroid Biosynthetic Gene SlCYP90B3 Alleviates Chilling Injury of Tomato (Solanum lycopersicum) Fruits during Cold Storage

Tomato is susceptible to chilling injury during cold storage. In this study, we found that low temperature promoted the expression of brassinosteroid (BR) biosynthetic genes in tomato fruits. The overexpression of SlCYP90B3 (SlCYP90B3-OE), a key BR biosynthetic gene, alleviated the chilling injury with decreased electrical conductivity and malondialdehyde. In SlCYP90B3-OE tomato fruits, the activities of antioxidant enzymes, including ascorbate peroxidase (APX), catalase (CAT), peroxidase (POD), and superoxide dismutase (SOD), were markedly increased, while the activity of membranous lipolytic enzymes, lipoxygenase (LOX), and phospholipase D (PLD), were significantly decreased when compared with the wild-type in response to cold storage. Furthermore, the expression level of the cold-response-system component, SlCBF1, was higher in SlCYP90B3-OE fruits than in the wild-type fruits. These results indicated that SlCYP90B3 might be involved in the chilling tolerance of tomato fruits during cold storage, possibly by regulating the antioxidant enzyme system and SlCBF1 expression.

Metabolic changes associated with chilling injury tolerance in tomato fruit with hot water pretreatment

Hot water treatment (HWT) of tomato (Solanum lycopersicum L.) fruit reduces the symptoms of chilling injury (CI). The aim of this study was to identify metabolites associated with HWT-induced CI tolerance in tomato fruit cv. Imperial. Mature green tomatoes with HWT (42°C/5 min) and control were stored under chilling conditions (5°C/20 days) and then ripened (21°C/7 days). Methanol extracts from pericarp were analyzed for total phenolics (TP), antioxidant activity (AoxA), and metabolic profiling by UPLC-DAD-MS and GC-MS. After cold storage and ripening, HWT fruit showed less CI, higher TP, and AoxA than control. It also showed an increased accumulation of phenolics, sugars, and some alkaloids that may be mediated by azelaic acid, glutamine, and tryptophan. The levels of N-feruloyl putrescine, esculeoside AII, and hydroxy-α-tomatine II were reduced. The better metabolic performance of HWT fruit under cold storage was associated with a higher accumulation of several metabolites (e.g., antioxidants and osmolytes) in ripening fruit. PRACTICAL APPLICATION: The identification of metabolites associated with the reduction of chilling injury (CI) symptoms in HWT tomato fruit extends the understanding of the mechanisms involved in CI tolerance. This information provides targets that could be used to develop strategies for preventing CI (e.g., genetic improvement of tomato, direct application of key metabolites). The application of such strategies will increase the economic value and decrease postharvest losses.

Transcriptome Responses of Ripe Cherry Tomato Fruit Exposed to Chilling and Rewarming Identify Reversible and Irreversible Gene Expression Changes

Tomato fruit stored below 12°C lose quality and can develop chilling injury upon subsequent transfer to a shelf temperature of 20°C. The more severe symptoms of altered fruit softening, uneven ripening and susceptibility to rots can cause postharvest losses. We compared the effects of exposure to mild (10°C) and severe chilling (4°C) on the fruit quality and transcriptome of 'Angelle', a cherry-type tomato, harvested at the red ripe stage. Storage at 4°C (but not at 10°C) for 27 days plus an additional 6 days at 20°C caused accelerated softening and the development of mealiness, both of which are commonly related to cell wall metabolism. Transcriptome analysis using RNA-Seq identified a range of transcripts encoding enzymes putatively involved in cell wall disassembly whose expression was strongly down-regulated at both 10 and 4°C, suggesting that accelerated softening at 4°C was due to factors unrelated to cell wall disassembly, such as reductions in turgor. In fruit exposed to severe chilling, the reduced transcript abundances of genes related to cell wall modification were predominantly irreversible and only partially restored upon rewarming of the fruit. Within 1 day of exposure to 4°C, large increases occurred in the expression of alternative oxidase, superoxide dismutase and several glutathione S-transferases, enzymes that protect cell contents from oxidative damage. Numerous heat shock proteins and chaperonins also showed large increases in expression, with genes showing peak transcript accumulation after different times of chilling exposure. These changes in transcript abundance were not induced at 10°C, and were reversible upon transfer of the fruit from 4 to 20°C. The data show that genes involved in cell wall modification and cellular protection have differential sensitivity to chilling temperatures, and exhibit different capacities for recovery upon rewarming of the fruit.

Carbon Dioxide Pretreatment and Cold Storage Synergistically Delay Tomato Ripening through Transcriptional Change in Ethylene-Related Genes and Respiration-Related Metabolism

The effects of CO₂ pretreatment before cold storage on tomato quality were investigated using physicochemical and transcriptome changes. Harvested tomatoes were treated with 30% or 60% CO₂ for 3 h before storage at 4 °C for 14 d (cold storage), followed by transfer to 20 °C for 8 d (ambient conditions). The CO₂-treated fruits were firmer with a better appearance than untreated fruits, even after being transferred from 4 °C storage to 20 °C for 8 d. CO₂ pretreatment coupled with cold storage synergistically delayed tomato ripening by reducing respiration and lowering lycopene production. The tomatoes treated with 30% and 60% CO₂ had fewer pits than untreated fruits after cold storage, even after being transferred to ambient conditions. Moreover, the 60% CO₂ treatment significantly suppressed the decay rate. Transcriptome and metabolome functional enrichment analyses commonly showed the involvement of CO₂-responsive genes or metabolites in sucrose and starch metabolism, as well as biosynthesis of secondary metabolites—in particular, glycolysis reduction. The most frequently detected domain was the ethylene-responsive factor. These results indicate that altered ethylene biosynthesis and ethylene signaling, via ethylene-responsive transcription factors and respiration-related pathways, appear to control CO₂-induced fruit quality.

Functional characterization of class I SlHSP17.7 gene responsible for tomato cold-stress tolerance

Small heat shock proteins (sHSPs) increase stress tolerance in a wide variety of organisms and enable them to endure changes in their environment. However, the molecular mechanism by which sHSPs protect plants against cold stress is unknown. Here, the sHSP of tomato named SlHSP17.7 (Solyc06g076540.1.1) has the characteristic of low temperature induced expression in BL21(DE3) E. coli and a molecular chaperone function in vitro. Overexpression of SlHSP17.7 showed a tolerant response to cold stress treatment due to an induce intracellular sucrose and less accumulation of ROS. Yeast two-hybrid assays showed that SlHSP17.7 is a binding partner of the cation/Ca²⁺ exchanger (SlCCX1-like; Solyc07g006370.1.1). This interaction was confirmed by pull down and bimolecular fluorescence complementation (BiFC) assays. High SlHSP17.7 and low SlCCX1-like levels alleviated programed cell death (PCD) under cold stress. Thus, SlHSP17.7 might be a cofactor of SlCCX1-like targeting endoplasmic reticulum (ER) membrane proteins, retaining intracellular Ca²⁺ homeostasis, and decreasing cold stress sensitivity. These findings provide a sound basis for genetic engineering of cold stress tolerance in tomato.

SlGRAS4 mediates a novel regulatory pathway promoting chilling tolerance in tomato

Tomato (Solanum lycopersicum L.) plants are cold-sensitive, and the fruit are susceptible to postharvest chilling injury when stored at low temperature. However, the mechanisms underlying cold stress responses in tomato are poorly understood. We demonstrate that SlGRAS4, encoding a transcription factor induced by low temperature, promotes chilling tolerance in tomato leaves and fruit. Combined genome-wide ChIP-seq and RNA-seq approaches identified among cold stress-associated genes those being direct targets of SlGRAS4 and protein studies revealed that SlGRAS4 forms a homodimer to self-activate its own promoter. SlGRAS4 can also directly bind tomato SlCBF promoters to activate their transcription without inducing any growth retardation. The study identifies the SlGRAS4-regulon as a new cold response pathway conferring cold stress tolerance in tomato independently of the ICE1-CBF pathway. This provides new track for breeding strategies aiming to improve chilling tolerance of cultivated tomatoes and to preserve sensory qualities of tomato fruit often deteriorated by storage at low temperatures.

Phenolic profile associated with chilling tolerance induced by the application of a hot water treatment in bell pepper fruit

Hot water treatment (HT) has proved to alleviate chilling injury (CI) in bell pepper and other Solanaceae species, this has been associated with the presence of metabolites such as sugars and polyamines, which protect the plasmatic membrane. However, it is unknown if the phenolic compounds in bell pepper play a role in the CI tolerance induced by the application of a HT. The aim of this study was to identify the specific phenolics associated with induced CI tolerance in bell pepper by HT (53 °C, 1 to 3 min). Fruit treated for 1 min (HT-1 min) exhibited CI tolerance (the lowest symptom development, electrolyte leakage, and vitamin C loss) and was the chosen treatment for further experiments. The phenolic composition was affected by HT-1 min and CI. Phenolics presented a strong correlation with the antioxidant activity. In fruit with CI tolerance, the concentration of seven compounds was increased, being quercetin-O-rhamnoside-O-hexoside and chlorogenic acid the most remarkable. Quercetin-3-O-rhamnoside was accumulated only in fruit with induced tolerance, meanwhile orientin was particularly sensitive to heat and cold exposure. Thus, HT-1 min (53 °C, 1 min) is a useful technology to induce CI tolerance in bell pepper and such tolerance is associated with the phenolic composition that may reduce the prevalence of oxidative stress during the storage under CI conditions. PRACTICAL APPLICATION: Phenolics induced by CI and HT may be useful to detect early stages of heat and chilling injuries in bell pepper and prevent the negative effect of such stresses even before its harvest and during commercial storage. Additionally, the phenolics associated with CI tolerance may be used as markers in breeding programs to create new chilling resistant cultivars.

Metabolite Changes during Postharvest Storage: Effects on Fruit Quality Traits

Metabolic changes occurring in ripe or senescent fruits during postharvest storage lead to a general deterioration in quality attributes, including decreased flavor and ‘off-aroma’ compound generation. As a consequence, measures to reduce economic losses have to be taken by the fruit industry and have mostly consisted of storage at cold temperatures and the use of controlled atmospheres or ripening inhibitors. However, the biochemical pathways and molecular mechanisms underlying fruit senescence in commercial storage conditions are still poorly understood. In this sense, metabolomic platforms, enabling the profiling of key metabolites responsible for organoleptic and health-promoting traits, such as volatiles, sugars, acids, polyphenols and carotenoids, can be a powerful tool for further understanding the biochemical basis of postharvest physiology and have the potential to play a critical role in the identification of the pathways affected by fruit senescence. Here, we provide an overview of the metabolic changes during postharvest storage, with special attention to key metabolites related to fruit quality. The potential use of metabolomic approaches to yield metabolic markers useful for chemical phenotyping or even storage and marketing decisions is highlighted.

Generation of fruit postharvest gene datasets and a novel motif analysis tool for functional studies: uncovering links between peach fruit heat treatment and cold storage responses

A survey of developed fruit gene-specific datasets and the implementation of a novel cis-element analysis tool indicate specific transcription factors as novel regulatory actors under HT response and CI protection. Heat treatment (HT) prior to cold storage (CS) has been successfully applied to ameliorate fruit chilling injury (CI) disorders. Molecular studies have identified several HT-driven benefits and putative CI-protective molecules and mechanisms. However, bioinformatic tools and analyses able to integrate fruit-specific information are necessary to begin functional studies and breeding projects. In this work, a HT-responsive gene dataset (HTds) and four fruit expression datasets (FEds), containing gene-specific information from several species and postharvest conditions, were developed and characterized. FEds provided information about HT-responsive genes, not only validating their sensitivity to HT in different systems but also revealing most of them as CS-responsive. A special focus was given to peach heat treatment-sensitive transcriptional regulation by the development of a novel Perl motif analysis software (cisAnalyzer) and a curated plant cis-elements dataset (PASPds). cisAnalyzer is able to assess sequence motifs presence, localization, enrichment and discovery on biological sequences. Its implementation for the enrichment analysis of PASPds motifs on the promoters of HTds genes rendered particular cis-elements that indicate certain transcription factor (TF) families as responsible of fruit HT-sensitive transcription regulation. Phylogenetic and postharvest expression data of these TFs showed a functional diversity of TF families, with members able to fulfil roles under HT, CS and/or both treatments. All integrated datasets and cisAnalyzer tool were deposited in FruitGeneDB (https://www.cefobi-conicet.gov.ar/FruitGeneDB/search1.php), a new available database with a great potential for fruit gene functional studies, including the markers of HT and CS responses whose study will contribute to unravel HT-driven CI-protection and select tolerant cultivars.

Tomato Fruit Development and Metabolism

Tomato (Solanum lycopersicum L.) belongs to the Solanaceae family and is the second most important fruit or vegetable crop next to potato (Solanum tuberosum L.). It is cultivated for fresh fruit and processed products. Tomatoes contain many health-promoting compounds including vitamins, carotenoids, and phenolic compounds. In addition to its economic and nutritional importance, tomatoes have become the model for the study of fleshy fruit development. Tomato is a climacteric fruit and dramatic metabolic changes occur during its fruit development. In this review, we provide an overview of our current understanding of tomato fruit metabolism. We begin by detailing the genetic and hormonal control of fruit development and ripening, after which we document the primary metabolism of tomato fruits, with a special focus on sugar, organic acid, and amino acid metabolism. Links between primary and secondary metabolic pathways are further highlighted by the importance of pigments, flavonoids, and volatiles for tomato fruit quality. Finally, as tomato plants are sensitive to several abiotic stresses, we briefly summarize the effects of adverse environmental conditions on tomato fruit metabolism and quality.

A Prunus persica genome-wide RNA-seq approach uncovers major differences in the transcriptome among chilling injury sensitive and non-sensitive varieties

Chilling injury represents a major constrain for crops productivity. Prunus persica, one of the most relevant rosacea crops, have early season varieties that are resistant to chilling injury, in contrast to late season varieties, which display chilling symptoms such as mealiness (dry, sandy fruit mesocarp) after prolonged storage at chilling temperatures. To uncover the molecular processes related to the ability of early varieties to withstand mealiness, postharvest and genome-wide RNA-seq assessments were performed in two early and two late varieties. Differences in juice content and ethylene biosynthesis were detected among early and late season fruits that became mealy after exposed to prolonged chilling. Principal component and data distribution analysis revealed that cold-stored late variety fruit displayed an exacerbated and unique transcriptome profile when compared to any other postharvest condition. A differential expression analysis performed using an empirical Bayes mixture modeling approach followed by co-expression and functional enrichment analysis uncover processes related to ethylene, lipids, cell wall, carotenoids and DNA metabolism, light response, and plastid homeostasis associated to the susceptibility or resistance of P. persica varieties to chilling stress. Several of the genes related to these processes are in quantitative trait loci (QTL) associated to mealiness in P. persica. Together, these analyses exemplify how P. persica can be used as a model for studying chilling stress in plants.

Overexpression of Solanum habrochaites microRNA319d (sha-miR319d) confers chilling and heat stress tolerance in tomato (S. lycopersicum)

BACKGROUND

MicroRNA319 (miR319) acts as an essential regulator of gene expression during plant development and under stress conditions. Although the role of miR319a in regulating leaf development has been well studied in tomato (Solanum lycopersicum), the function of the recently discovered wild tomato Solanum habrochaites miRNA319d (sha-miR319d) remains poorly understood. In this study, we overexpressed sha-miR319d in cultivated tomato 'Micro-Tom' to further investigate its role in tomato temperature stress responses.

RESULTS

Under chilling or heat stress, sha-miR319d-overexpressing plants showed enhanced stress tolerance, including lower relative electrolyte leakage (REL), malondialdehyde (MDA) concentration, O₂^- generation and H₂O₂ concentration and higher chlorophyll contents and Fv/Fm values than wild-type (WT) plants. Overexpression of sha-miR319d enhanced the activities of superoxide dismutase (SOD) and catalase (CAT), with possible correlation with elevated expression levels of the genes FeSOD, CuZnSOD and CAT. Moreover, different expression levels of key genes involved in chilling (MYB83 and CBF1), heat (HsfA1a, HsfA1b and Hsp90), and reactive oxygen species (ROS) (ZAT12 and ZAT10) signaling in transgenic plants and WT were determined, suggesting a role for sha-miR319d in regulating tomato temperature stress via chilling, heat and ROS signaling. Silencing GAMYB-like1 increased tomato chilling tolerance as well as the expression levels of CBF1, CuZnSOD, CAT, APX1, APX2, ZAT12 and ZAT10. Additionally, overexpression of sha-miR319d in tomato caused plant leaf crinkling and reduced height.

CONCLUSIONS

Overexpression of sha-miR319d confers chilling and heat stress tolerance in tomato. Sha-miR319d regulates tomato chilling tolerance, possibly by inhibiting expression of GAMYB-like1 and further alters chilling, heat and ROS signal transduction. Our research provides insight for further study of the role of sha-miR319d in tomato growth and stress regulation and lays a foundation for the genetic improvement of tomato.

Integrative comparative analyses of metabolite and transcript profiles uncovers complex regulatory network in tomato (Solanum lycopersicum L.) fruit undergoing chilling injury

Tomato fruit are especially susceptible to chilling injury (CI) when continuously exposed to temperatures below 12 °C. In this study, integrative comparative analyses of transcriptomics and metabolomics data were performed to uncover the regulatory network in CI tomato fruit. Metabolite profiling analysis found that 7 amino acids, 27 organic acids, 16 of sugars and 22 other compounds had a significantly different content while transcriptomics data showed 1735 differentially expressed genes (DEGs) were down-regulated and 1369 were up-regulated in cold-stored fruit. We found that the contents of citrate, cis-aconitate and succinate were increased, which were consistent with the expression of ATP-citrate synthase (ACS) and isocitrate dehydrogenase (IDH) genes in cold-treated tomato fruit. Cold stress promotes the expression of ACS and IDH which may increase the synthesis of citrate, cis-aconitate and succinate. Alanine and leucine had increased contents, which may result from alanine aminotransferase (ALT) and branched-chain amino acid aminotransferase (BcAT)'s high expression levels, respectively. Overall the transcriptomics and metabolomics data in our study explain the molecular mechanisms of the chilling injury and expands our understanding of the complex regulatory mechanisms of a metabolic network in response to chilling injury in tomato fruit.

Associating transcriptional regulation for rapid germination of rapeseed (Brassica napus L.) under low temperature stress through weighted gene co-expression network analysis

Slow germination speed caused by low temperature stress intensifies the risk posed by adverse environmental factors, contributing to low germination rate and reduced production of rapeseed. The purpose of this study was to understand the transcriptional regulation mechanism for rapid germination of rapeseed. The results showed that seed components and size do not determine the seed germination speed. Different temporal transcriptomic profiles were generated under normal and low temperature conditions in genotypes with fast and slow germination speeds. Using weight gene co-expression network analysis, 37 823 genes were clustered into 15 modules with different expression patterns. There were 10 233 and 9111 differentially expressed genes found to follow persistent tendency of up- and down-regulation, respectively, which provided the conditions necessary for germination. Hub genes in the continuous up-regulation module were associated with phytohormone regulation, signal transduction, the pentose phosphate pathway, and lipolytic metabolism. Hub genes in the continuous down-regulation module were involved in ubiquitin-mediated proteolysis. Through pairwise comparisons, 1551 specific upregulated DEGs were identified for the fast germination speed genotype under low temperature stress. These DEGs were mainly enriched in RNA synthesis and degradation metabolisms, signal transduction, and defense systems. Transcription factors, including WRKY, bZIP, EFR, MYB, B3, DREB, NAC, and ERF, are associated with low temperature stress in the fast germination genotype. The aquaporin NIP5 and late embryogenesis abundant (LEA) protein genes contributed to the water uptake and transport under low temperature stress during seed germination. The ethylene/H₂O₂-mediated signal pathway plays an important role in cell wall loosening and embryo extension during germination. The ROS-scavenging system, including catalase, aldehyde dehydrogenase, and glutathione S-transferase, was also upregulated to alleviate ROS toxicity in the fast germinating genotype under low temperature stress. These findings should be useful for molecular assisted screening and breeding of fast germination speed genotypes for rapeseed.

Trait discovery and editing in tomato

Tomato (Solanum lycopersicum), which is used for both processing and fresh markets, is a major crop species that is the top ranked vegetable produced over the world. Tomato is also a model species for research in genetics, fruit development and disease resistance. Genetic resources available in public repositories comprise the 12 wild related species and thousands of landraces, modern cultivars and mutants. In addition, high quality genome sequences are available for cultivated tomato and for several wild relatives, hundreds of accessions have been sequenced, and databases gathering sequence data together with genetic and phenotypic data are accessible to the tomato community. Major breeding goals are productivity, resistance to biotic and abiotic stresses, and fruit sensorial and nutritional quality. New traits, including resistance to various biotic and abiotic stresses and root architecture, are increasingly being studied. Several major mutations and quantitative trait loci (QTLs) underlying traits of interest in tomato have been uncovered to date and, thanks to new populations and advances in sequencing technologies, the pace of trait discovery has considerably accelerated. In recent years, clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 gene editing (GE) already proved its remarkable efficiency in tomato for engineering favorable alleles and for creating new genetic diversity by gene disruption, gene replacement, and precise base editing. Here, we provide insight into the major tomato traits and underlying causal genetic variations discovered so far and review the existing genetic resources and most recent strategies for trait discovery in tomato. Furthermore, we explore the opportunities offered by CRISPR/Cas9 and their exploitation for trait editing in tomato.

Expanding Alternative Splicing Identification by Integrating Multiple Sources of Transcription Data in Tomato

Tomato (Solanum lycopersicum) is an important vegetable and fruit crop. Its genome was completely sequenced and there are also a large amount of available expressed sequence tags (ESTs) and short reads generated by RNA sequencing (RNA-seq) technologies. Mapping transcripts including mRNA sequences, ESTs, and RNA-seq reads to the genome allows identifying pre-mRNA alternative splicing (AS), a post-transcriptional process generating two or more RNA isoforms from one pre-mRNA transcript. We comprehensively analyzed the AS landscape in tomato by integrating genome mapping information of all available mRNA and ESTs with mapping information of RNA-seq reads which were collected from 27 published projects. A total of 369,911 AS events were identified from 34,419 genomic loci involving 161,913 transcripts. Within the basic AS events, intron retention is the prevalent type (18.9%), followed by alternative acceptor site (12.9%) and alternative donor site (7.3%), with exon skipping as the least type (6.0%). Complex AS types having two or more basic event accounted for 54.9% of total AS events. Within 35,768 annotated protein-coding gene models, 23,233 gene models were found having pre-mRNAs generating AS isoform transcripts. Thus the estimated AS rate was 65.0% in tomato. The list of identified AS genes with their corresponding transcript isoforms serves as a catalog for further detailed examination of gene functions in tomato biology. The post-transcriptional information is also expected to be useful in improving the predicted gene models in tomato. The sequence and annotation information can be accessed at plant alternative splicing database (http://proteomics.ysu.edu/altsplice).

Transcriptomic changes in Cucurbita pepo fruit after cold storage: differential response between two cultivars contrasting in chilling sensitivity

Background

Zucchini fruit is susceptible to chilling injury (CI), but the response to low storage temperature is cultivar dependent. Previous reports about the response of zucchini fruit to chilling storage have been focused on the physiology and biochemistry of this process, with little information about the molecular mechanisms underlying it. In this work, we present a comprehensive analysis of transcriptomic changes that take place after cold storage in zucchini fruit of two commercial cultivars with contrasting response to chilling stress.

Results

RNA-Seq analysis was conducted in exocarp of fruit at harvest and after 14 days of storage at 4 and 20 °C. Differential expressed genes (DEGs) were obtained comparing fruit stored at 4 °C with their control at 20 °C, and then specific and common up and down-regulated DEGs of each cultivar were identified. Functional analysis of these DEGs identified similarities between the response of zucchini fruit to low temperature and other stresses, with an important number of GO terms related to biotic and abiotic stresses overrepresented in both cultivars. This study also revealed several molecular mechanisms that could be related to chilling tolerance, since they were up-regulated in cv. Natura (CI tolerant) or down-regulated in cv. Sinatra (CI sensitive). These mechanisms were mainly those related to carbohydrate and energy metabolism, transcription, signal transduction, and protein transport and degradation. Among DEGs belonging to these pathways, we selected candidate genes that could regulate or promote chilling tolerance in zucchini fruit including the transcription factors MYB76-like, ZAT10-like, DELLA protein GAIP, and AP2/ERF domain-containing protein.

Conclusions

This study provides a broader understanding of the important mechanisms and processes related to coping with low temperature stress in zucchini fruit and allowed the identification of some candidate genes that may be involved in the acquisition of chilling tolerance in this crop. These genes will be the basis of future studies aimed to identify markers involved in cold tolerance and aid in zucchini breeding programs.

Electronic supplementary material

The online version of this article (10.1186/s12864-018-4500-9) contains supplementary material, which is available to authorized users.

Transcriptome profiling of sweetpotato tuberous roots during low temperature storage

Sweetpotato [Ipomoea batatas (L.) Lam] is a globally important root crop with high industrial value. However, because sweetpotato tuberous roots undergo chilling injuries that negatively affect their quality at temperatures below 10 °C, postharvest damage during the winter season is a major constraint for industrialization. To understand chilling injury response during postharvest low temperature storage, we used next-generation sequencing technology to comprehensive analyze the transcriptome of tuberous roots stored at optimal (13 °C) or low temperature (4 °C) for 6 weeks. From nine cDNA libraries, we produced 298,765,564 clean reads, which were de novo assembled into 58,392 unigenes with an average length of 1100 bp. A total of 3216 differentially expressed genes (DEGs) were detected and categorized into six clusters, of which clusters 2, 4, and 5 (1464 DEGs) were up-regulated under low temperature. The genes in these three clusters are involved in biosynthesis of unsaturated fatty acids, pathogen defense, and phenylalanine metabolism. By contrast, genes in clusters 1, 3, and 6 (1752 DEGs), which were generally down-regulated at low temperature, encode antioxidant enzymes or are involved in glycerophospholipid, carbohydrate, or energy metabolism. We confirmed the results of the transcriptome analysis by quantitative RT-PCR. Our transcriptome analysis will advance our understanding of the comprehensive mechanisms of chilling injury during low temperature storage and facilitate improvements in postharvest storage of sweetpotato tuberous roots.

Small heat shock proteins and the postharvest chilling tolerance of tomato fruit

Plants have the largest number of small heat shock proteins (sHsps) (15-42 kDa) among eukaryotes, but little is known about their function in vivo. They accumulate in response to different stresses, and specific sHsps are also expressed during developmental processes such as seed development, germination, and ripening. The presence of organelle-specific sHsps appears to be unique to plants. The sHsps expression is regulated by heat stress transcription factors (Hsfs). In this work, it was explored the role of sHsps in the chilling injury of tomato fruit. The level of transcripts and proteins of cytoplasmic and organellar sHsps was monitored in fruit during ripening and after cold storage (4 weeks at 4°C). Expression of HsfA1, HsfA2, HsfA3, and HsfB1 was also examined. Two cultivars of tomato (Solanum lycopersicum) contrasting in chilling tolerance were assayed: Micro-Tom (chilling-tolerant) and Minitomato (chilling-sensitive). Results showed that sHsps were induced during ripening in fruit from both cultivars. However, sHsps were induced in Micro-Tom fruit but not in Minitomato fruit after storage at a low temperature. In particular, sHsp 17.4-CII and sHsp23.8-M transcripts strongly accumulated in Micro-Tom fruit and HsfA3 transcript diminished after cold storage. These data suggest that sHsps may be involved in the protection mechanisms against chilling stress and substantiate the hypothesis that sHsps may participate in the mechanism of tomato genotype chilling tolerance.

Salicylic-Acid-Induced Chilling- and Oxidative-Stress Tolerance in Relation to Gibberellin Homeostasis, C-Repeat/Dehydration-Responsive Element Binding Factor Pathway, and Antioxidant Enzyme Systems in Cold-Stored Tomato Fruit

Effects of salicylic acid (SA) on gibberellin (GA) homeostasis, C-repeat/dehydration-responsive element binding factor (CBF) pathway, and antioxidant enzyme systems linked to chilling- and oxidative-stress tolerance in tomato fruit were investigated. Mature green tomatoes (Solanum lycopersicum L. cv. Moneymaker) were treated with 0, 0.5, and 1 mM SA solution for 15 min before storage at 4 °C for 28 days. In comparison to 0 or 0.5 mM SA, 1 mM SA significantly decreased the chilling injury (CI) index in tomato fruit. In the SA-treated fruit, the upregulation of GA biosynthetic gene (GA3ox1) expression was followed by gibberellic acid (GA₃) surge and DELLA protein degradation. CBF1 participated in the SA-modulated tolerance and stimulated the expression of GA catabolic gene (GA2ox1). Furthermore, 1 mM SA enhanced activities of antioxidant enzymes and, thus, reduced reactive oxygen species accumulation. Our findings suggest that SA might protect tomato fruit from CI and oxidative damage through regulating GA metabolism, CBF1 gene expression, and antioxidant enzyme activities.

Chilling-induced tomato flavor loss is associated with altered volatile synthesis and transient changes in DNA methylation

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.

Transcriptional regulatory networks controlling woolliness in peach in response to preharvest gibberellin application and cold storage

BACKGROUND

Postharvest fruit conservation relies on low temperatures and manipulations of hormone metabolism to maintain sensory properties. Peaches are susceptible to chilling injuries, such as 'woolliness' that is caused by juice loss leading to a 'wooly' fruit texture. Application of gibberellic acid at the initial stages of pit hardening impairs woolliness incidence, however the mechanisms controlling the response remain unknown. We have employed genome wide transcriptional profiling to investigate the effects of gibberellic acid application and cold storage on harvested peaches.

RESULTS

Approximately half of the investigated genes exhibited significant differential expression in response to the treatments. Cellular and developmental process gene ontologies were overrepresented among the differentially regulated genes, whereas sequences in cell death and immune response categories were underrepresented. Gene set enrichment demonstrated a predominant role of cold storage in repressing the transcription of genes associated to cell wall metabolism. In contrast, genes involved in hormone responses exhibited a more complex transcriptional response, indicating an extensive network of crosstalk between hormone signaling and low temperatures. Time course transcriptional analyses demonstrate the large contribution of gene expression regulation on the biochemical changes leading to woolliness in peach.

CONCLUSION

Overall, our results provide insights on the mechanisms controlling the complex phenotypes associated to postharvest textural changes in peach and suggest that hormone mediated reprogramming previous to pit hardening affects the onset of chilling injuries.