The Epigenome and Transcriptional Dynamics of Fruit Ripening

Auxin responsive factor MdARF17 promotes ethylene synthesis in apple fruits by activating MdERF003 expression

KEY MESSAGE

Auxin (AUX) promotion of apple fruit ripening is ethylene-dependent, and AUX-MdARF17-MdERF003 plays a role in AUX-promoted ethylene synthesis in apple. Phytohormones play important roles in plant growth and fleshy fruit ripening, and the phytohormone auxin (AUX) can either promote or inhibit the ripening of fleshy fruits. Although AUX can influence ethylene (ETH) synthesis in apple (Malus domestica) fruits by affecting ETH system II, this mechanism remains to be explored. Here, we identified an ETH response factor (ERF) family transcription factor, MdERF003, whose expression could be activated by naphthalene acetic acid. The transient silencing of MdERF003 inhibited ETH synthesis in fruits, and MdERF003 could bind to the MdACS1 promoter. To explore the upstream target genes of MdERF003, we screened the MdARF family members by yeast one-hybrid assays of the MdERF003 promoter, and found that the transcription factor MdARF17, which showed AUX-promoted expression, could bind to the MdERF003 promoter and promote its expression. Finally, we silenced MdERF003 in apple fruits overexpressing MdARF17 and found that MdERF003 plays a role in MdARF17-promoted ETH synthesis in apple. Thus, AUX-MdARF17-MdERF003 promotes ETH synthesis in apple fruits.

Movement of ACC oxidase 3 mRNA from seeds to flesh promotes fruit ripening in apple

Xenia, the phenomenon in which the pollen genotype directly affects the phenotypic characteristics of maternal tissues (i.e., fruit ripening), has applications in crop production and breeding. However, the underlying molecular mechanism has yet to be elucidated. Here, we investigated whether mobile mRNAs from the pollen affect the ripening and quality-related characteristics of the fruit using cross-pollination between distinct Malus domestica (apple) cultivars. We demonstrated that hundreds of mobile mRNAs originating from the seeds are delivered to the fruit. We found that the movement of one of these mRNAs, ACC oxidase 3 (MdACO3), is coordinated with fruit ripening. Salicylic acid treatment, which can cause plasmodesmal closure, blocks MdACO3 movement, indicating that MdACO3 transcripts may move through the plasmodesmata. To assess the role of mobile MdACO3 transcripts in apple fruit, we created MdACO3-GFP-expressing apple seeds using MdACO3-GFP-overexpressing pollen for pollination and showed that MdACO3 transcripts in the transgenic seeds move to the flesh, where they promote fruit ripening. Furthermore, we demonstrated that MdACO3 can be transported from the seeds to fruit in the fleshy-fruited species tomato and strawberry. These results underscore the potential of mobile mRNAs from seeds to influence fruit characteristics, providing an explanation for the xenia phenomenon. Notably, our findings highlight the feasibility of leveraging diverse pollen genomic resources, without resorting to genome editing, to improve fruit quality.

A novel edible coating based on Albizia [Albizia lebbeck (L.) Benth.] gum delays softening and maintains quality of harvested guava fruits during storage

Guava, a commercially important fruit crop, is being grown in tropical and subtropical regions around the world. Due to the perishable nature of guava fruits, there are great losses during marketing, transport and storage. The application of edible coating is emerging as a low-cost, simple to implement and efficient method for extending the postharvest life of fresh horticultural produces, such as fruits and vegetables. This study aimed to assess the potential of Albizia gum (AZG) to improve storability and maintain the overall fruit quality of stored guava fruits. Freshly harvested guava fruits were coated with 0 % (control), 1.5 %, 3 % or 4.5 % AZG. After coating treatment, the fruits were stored at 20 ± 1 °C and 85-90 % relative humidity for 15 days. The results revealed that 4.5% AZG coating suppressed the weight loss and decay incidence up to 27 % and 36 %, respectively, as compared with control. The fruits coated with 4.5 % AZG had the maximum titratable acidity (0.40 %), ascorbic acid (104.47 mg·100 g-1), total antioxidants (118.84 mmol Trolox·100 g-1), total phenolics (285.57 mg·kg-1) and flavonoids (60.12 g·kg-1) on 15th day of storage. However, the minimum total soluble solids (11.97 %), sugar-acid ratio (29.31), relative ion leakage (68.40 %), malondialdehyde (0.11 nmol·kg-1 FW) and hydrogen peroxide (16.05 μmol·kg-1 FW) were recorded in the fruits of same treatment on 15th day of storage. Furthermore, the activities of antioxidant enzymes "i.e., superoxide dismutase (SOD), peroxidase (POD), catalase (CAT), and ascorbate peroxidase (APX)" were increased under the influence of AZG coating. Consequently, as compared to uncoated fruits, AZG-coated fruits exhibited reduced activities of fruit softening enzymes "i.e., cellulase, pectin methylesterase (PME), and polygalacturonase (PG)". To sum up, the application of AZG-based edible coating could markedly improve the storage life of guavas and maintain overall fruit quality.

Dynamic m6A mRNA methylation reveals the involvement of AcALKBH10 in ripening-related quality regulation in kiwifruit

Kiwifruit ripening is a complex and highly coordinated process that occurs in conjunction with the formation of fruit edible quality. The significance of epigenetic changes, particularly the impact of N6-methyladenosine (m6A) RNA modification on fruit ripening and quality formation, has been largely overlooked. We monitored m6A levels and gene expression changes in kiwifruit at four different stages using LC-MS/MS, MeRIP, RNA-seq, and validated the function of AcALKBH10 through heterologous transgenic expression in tomato. Notable m6A modifications occurred predominantly at the stop codons and the 3' UTRs and exhibited a gradual reduction in m6A levels during the fruit ripening process. Moreover, these m6A modifications in the aforementioned sites demonstrated a discernible inverse relationship with the levels of mRNA abundance throughout the ripening process, suggesting a repression effect of m6A modification in the modulation of kiwifruit ripening. We further demonstrated that AcALKBH10 rather than AcECT9 predominantly regulates m6A levels in ripening-related genes, thereby exerting the regulatory control over the ripening process and the accumulation of soluble sugars and organic acids, ultimately influencing fruit ripening and quality formation. In conclusion, our findings illuminate the epi-regulatory mechanism involving m6A in kiwifruit ripening, offering a fresh perspective for cultivating high-quality kiwifruit with enhanced nutritional attributes.

Graph-Based Pangenome of Actinidia chinensis Reveals Structural Variations Mediating Fruit Degreening

Fruit ripening is associated with the degreening process (loss of chlorophyll) that occurs in most fruit species. Kiwifruit is one of the special species whose fruits may maintain green flesh by accumulating a large amount of chlorophyll even after ripening. However, little is known about the genetic variations related to the fruit degreening process. Here, a graph-based kiwifruit pangenome by analyzing 14 chromosome-scale haplotype-resolved genome assemblies from seven representative cultivars or lines in Actinidia chinensis is built. A total of 49,770 non-redundant gene families are identified, with core genes constituting 46.6%, and dispensable genes constituting 53.4%. A total of 84,591 non-redundant structural variations (SVs) are identified. The pangenome graph integrating both reference genome sequences and variant information facilitates the identification of SVs related to fruit color. The SV in the promoter of the AcBCM gene determines its high expression in the late developmental stage of fruits, which causes chlorophyll accumulation in the green-flesh fruits by post-translationally regulating AcSGR2, a key enzyme of chlorophyll catabolism. Taken together, a high-quality pangenome is constructed, unraveled numerous genetic variations, and identified a novel SV mediating fruit coloration and fruit quality, providing valuable information for further investigating genome evolution and domestication, QTL genes function, and genomics-assisted breeding.

Key transcription factors regulate fruit ripening and metabolite accumulation in tomato

Fruit ripening is a complex process involving dynamic changes to metabolites and is controlled by multiple factors, including transcription factors (TFs). Several TFs are reportedly essential regulators of tomato (Solanum lycopersicum) fruit ripening. To evaluate the effects of specific TFs on metabolite accumulation during fruit ripening, we combined CRISPR/Cas9-mediated mutagenesis with metabolome and transcriptome analyses to explore regulatory mechanisms. Specifically, we generated various genetically engineered tomato lines that differed regarding metabolite contents and fruit colors. The metabolite and transcript profiles indicated that the selected TFs have distinct functions that control fruit metabolite contents, especially carotenoids and sugars. Moreover, a mutation to ELONGATED HYPOCOTYL5 (HY5) increased tomato fruit fructose and glucose contents by approximately 20% (relative to the wild-type levels). Our in vitro assay showed that HY5 can bind directly to the G-box cis-element in the Sugars Will Eventually be Exported Transporter (SWEET12c) promoter to activate expression, thereby modulating sugar transport. Our findings provide insights into the mechanisms regulating tomato fruit ripening and metabolic networks, providing the theoretical basis for breeding horticultural crops that produce fruit with diverse flavors and colors.

DNA methylation controlling abscisic acid catabolism responds to light to mediate strawberry fruit ripening

Phytohormones, epigenetic regulation and environmental factors regulate fruit ripening but their interplay during strawberry fruit ripening remains to be determined. In this study, bagged strawberry fruit exhibited delayed ripening compared with fruit grown in normal light, correlating with reduced abscisic acid (ABA) accumulation. Transcription of the key ABA catabolism gene, ABA 8'-hydroxylase FaCYP707A4, was induced in bagged fruit. With light exclusion whole genome DNA methylation levels were up-regulated, corresponding to a delayed ripening process, while DNA methylation levels in the promoter of FaCYP707A4 were suppressed, correlating with increases in transcript and decreased ABA content. Experiments indicated FaCRY1, a blue light receptor repressed in bagged fruit and FaAGO4, a key protein involved in RNA-directed DNA methylation, could bind to the promoter of FaCYP707A4. The interaction between FaCRY1 and FaAGO4, and an increased enrichment of FaAGO4 directed to the FaCYP707A4 promoter in fruit grown under light suggests FaCRY1 may influence FaAGO4 to modulate the DNA methylation status of the FaCYP707A4 promoter. Furthermore, transient overexpression of FaCRY1, or an increase in FaCRY1 transcription by blue light treatment, increases the methylation level of the FaCYP707A4 promoter, while transient RNA interference of FaCRY1 displayed opposite phenotypes. These findings reveal a mechanism by which DNA methylation influences ABA catabolism, and participates in light-mediated strawberry ripening.

From acidity to sweetness: a comprehensive review of carbon accumulation in grape berries

Most of the carbon found in fruits at harvest is imported by the phloem. Imported carbon provide the material needed for the accumulation of sugars, organic acids, secondary compounds, in addition to the material needed for the synthesis of cell walls. The accumulation of sugars during fruit development influences not only sweetness but also various parameters controlling fruit composition (fruit "quality"). The accumulation of organic acids and sugar in grape berry flesh cells is a key process for berry development and ripening. The present review presents an update of the research on grape berry development, anatomical structure, sugar and acid metabolism, sugar transporters, and regulatory factors.

A signaling cascade mediating fruit trait development via phosphorylation-modulated nuclear accumulation of JAZ repressor

It is generally accepted that jasmonate-ZIM domain (JAZ) repressors act to mediate jasmonate (JA) signaling via CORONATINE-INSENSITIVE1 (COI1)-mediated degradation. Here, we report a cryptic signaling cascade where a JAZ repressor, FvJAZ12, mediates multiple signaling inputs via phosphorylation-modulated subcellular translocation rather than the COI1-mediated degradation mechanism in strawberry (Fragaria vesca). FvJAZ12 acts to regulate flavor metabolism and defense response, and was found to be the target of FvMPK6, a mitogen-activated protein kinase that is capable of responding to multiple signal stimuli. FvMPK6 phosphorylates FvJAZ12 at the amino acid residues S179 and T183 adjacent to the PY residues, thereby attenuating its nuclear accumulation and relieving its repression for FvMYC2, which acts to control the expression of lipoxygenase 3 (FvLOX3), an important gene involved in JA biosynthesis and a diverse array of cellular metabolisms. Our data reveal a previously unreported mechanism for JA signaling and decipher a signaling cascade that links multiple signaling inputs with fruit trait development.

Effect of the ripening stage on the pulsed vacuum drying behavior of goji berry (Lycium barbarum L.): Ultrastructure, drying characteristics, and browning mechanism

In current work, the effect of ripening stages (I, II, and III) on pulsed vacuum drying (PVD) behavior of goji berry was explored. The shortest drying time of goji berry was observed at stage I (6.99 h) which was 13.95 %, and 28.85 % shorter than those at stages II, and III, respectively. This phenomenon was closely associated with the ripening stage, as contributed by the initial physiochemical differences, ultrastructure alterations, and moisture distribution. In addition, lower maturity suffered more severe browning, primarily due to the enzymatic and non-enzymatic reactions of phenolics, followed by pigment degradation and the Maillard reaction. Additionally, the PVD process promoted the rupture and transformation of the pectin fractions, also causing browning either directly or indirectly through participation in other chemical reactions. These findings suggest that the appropriate ripening stage of goji berry should be considered as having a significant impact on drying behaviors and quality attributes.

Revisiting the role of ascorbate oxidase in plant systems

Ascorbic acid (AsA) plays an indispensable role in plants, serving as both an antioxidant and a master regulator of the cellular redox balance. Ascorbate oxidase (AO) is a blue copper oxidase that is responsible for the oxidation of AsA with the concomitant production of water. For many decades, AO was erroneously postulated as an enzyme without any obvious advantage, as it decreases the AsA pool size and thus is expected to weaken plant stress resistance. It was only a decade ago that this perspective shifted towards the fundamental role of AO in orchestrating both AsA and oxygen levels by influencing the overall redox balance in the extracellular matrix. Consistent with its localization in the apoplast, AO is involved in cell expansion, division, resource allocation, and overall plant yield. An increasing number of transgenic studies has demonstrated that AO can also facilitate communication between the surrounding environment and the cell, as its gene expression is highly responsive to factors such as hormonal signaling, oxidative stress, and mechanical injury. This review aims to describe the multiple functions of AO in plant growth, development, and stress resilience, and explore any additional roles the enzyme might have in fruits during the course of ripening.

Ascorbate peroxidase in fruits and modulation of its activity by reactive species

Ascorbate peroxidase (APX) is one of the enzymes of the ascorbate-glutathione cycle and is the key enzyme that breaks down H2O2 with the aid of ascorbate as an electron source. APX is present in all photosynthetic eukaryotes from algae to higher plants and, at the cellular level, it is localized in all subcellular compartments where H2O2 is generated, including the apoplast, cytosol, plastids, mitochondria, and peroxisomes, either in soluble form or attached to the organelle membranes. APX activity can be modulated by various post-translational modifications including tyrosine nitration, S-nitrosation, persulfidation, and S-sulfenylation. This allows the connection of H2O2 metabolism with other relevant signaling molecules such as NO and H2S, thus building a complex coordination system. In both climacteric and non-climacteric fruits, APX plays a key role during the ripening process and during post-harvest, since it participates in the regulation of both H2O2 and ascorbate levels affecting fruit quality. Currently, the exogenous application of molecules such as NO, H2S, H2O2, and, more recently, melatonin is seen as a new alternative to maintain and extend the shelf life and quality of fruits because they can modulate APX activity as well as other antioxidant systems. Therefore, these molecules are being considered as new biotechnological tools to improve crop quality in the horticultural industry.

Identification and virus-induced gene silencing (VIGS) analysis of methyltransferase affecting tomato (Solanum lycopersicum) fruit ripening

MAIN CONCLUSION

Six methyltransferase genes affecting tomato fruit ripening were identified through genome-wide screening, VIGS assay, and expression pattern analysis. The data provide the basis for understanding new mechanisms of methyltransferases. Fruit ripening is a critical stage for the formation of edible quality and seed maturation, which is finely modulated by kinds of factors, including genetic regulators, hormones, external signals, etc. Methyltransferases (MTases), important genetic regulators, play vital roles in plant development through epigenetic regulation, post-translational modification, or other mechanisms. However, the regulatory functions of numerous MTases except DNA methylation in fruit ripening remain limited so far. Here, six MTases, which act on different types of substrates, were identified to affect tomato fruit ripening. First, 35 MTase genes with relatively high expression at breaker (Br) stage of tomato fruit were screened from the tomato MTase gene database encompassing 421 genes totally. Thereafter, six MTase genes were identified as potential regulators of fruit ripening via virus-induced gene silencing (VIGS), including four genes with a positive regulatory role and two genes with a negative regulatory role, respectively. The expression of these six MTase genes exhibited diverse patterns during the fruit ripening process, and responded to various external ripening-related factors, including ethylene, 1-methylcyclopropene (1-MCP), temperature, and light exposure. These results help to further elaborate the biological mechanisms of MTase genes in tomato fruit ripening and enrich the understanding of the regulatory mechanisms of fruit ripening involving MTases, despite of DNA MTases.

Transcription factor PpNAC1 and DNA demethylase PpDML1 synergistically regulate peach fruit ripening

Fruit ripening is accompanied by dramatic changes in color, texture, and flavor and is regulated by transcription factors (TFs) and epigenetic factors. However, the detailed regulatory mechanism remains unclear. Gene expression patterns suggest that PpNAC1 (NAM/ATAF1/2/CUC) TF plays a major role in peach (Prunus persica) fruit ripening. DNA affinity purification (DAP)-seq combined with transactivation tests demonstrated that PpNAC1 can directly activate the expression of multiple ripening-related genes, including ACC synthase1 (PpACS1) and ACC oxidase1 (PpACO1) involved in ethylene biosynthesis, pectinesterase1 (PpPME1), pectate lyase1 (PpPL1), and polygalacturonase1 (PpPG1) related to cell wall modification, and lipase1 (PpLIP1), fatty acid desaturase (PpFAD3-1), and alcohol acyltransferase1 (PpAAT1) involved in volatiles synthesis. Overexpression of PpNAC1 in the tomato (Solanum lycopersicum) nor (nonripening) mutant restored fruit ripening, and its transient overexpression in peach fruit induced target gene expression, supporting a positive role of PpNAC1 in fruit ripening. The enhanced transcript levels of PpNAC1 and its target genes were associated with decreases in their promoter mCG methylation during ripening. Declining DNA methylation was negatively associated with increased transcripts of DNA demethylase1 (PpDML1), whose promoter is recognized and activated by PpNAC1. We propose that decreased methylation of the promoter region of PpNAC1 leads to a subsequent decrease in DNA methylation levels and enhanced transcription of ripening-related genes. These results indicate that positive feedback between PpNAC1 and PpDML1 plays an important role in directly regulating expression of multiple genes required for peach ripening and quality formation.

Phytosulfokine promotes fruit ripening and quality via phosphorylation of transcription factor DREB2F in tomato

Phytosulfokine (PSK), a plant peptide hormone with a wide range of biological functions, is recognized by its receptor PHYTOSULFOKINE RECEPTOR 1 (PSKR1). Previous studies have reported that PSK plays important roles in plant growth, development, and stress responses. However, the involvement of PSK in fruit development and quality formation remains largely unknown. Here, using tomato (Solanum lycopersicum) as a research model, we show that exogenous application of PSK promotes the initiation of fruit ripening and quality formation, while these processes are delayed in pskr1 mutant fruits. Transcriptomic profiling revealed that molecular events and metabolic pathways associated with fruit ripening and quality formation are affected in pskr1 mutant lines and transcription factors are involved in PSKR1-mediated ripening. Yeast screening further identified that DEHYDRATION-RESPONSIVE ELEMENT BINDING PROTEIN 2F (DREB2F) interacts with PSKR1. Silencing of DREB2F delayed the initiation of fruit ripening and inhibited the promoting effect of PSK on fruit ripening. Moreover, the interaction between PSKR1 and DREB2F led to phosphorylation of DREB2F. PSK improved the efficiency of DREB2F phosphorylation by PSKR1 at the tyrosine-30 site, and the phosphorylation of this site increased the transcription level of potential target genes related to the ripening process and functioned in promoting fruit ripening and quality formation. These findings shed light on the involvement of PSK and its downstream signaling molecule DREB2F in controlling climacteric fruit ripening, offering insights into the regulatory mechanisms governing ripening processes in fleshy fruits.

Variations in Fruit Ploidy Level and Cell Size between Small- and Large-Fruited Olive Cultivars during Fruit Ontogeny

Olive (Olea europaea L.) is one of the major oil fruit tree crops worldwide. However, the mechanisms underlying olive fruit growth remain poorly understood. Here, we examine questions regarding the interaction of endoreduplication, cell division, and cell expansion with olive fruit growth in relation to the final fruit size by measuring fruit diameter, pericarp thickness, cell area, and ploidy level during fruit ontogeny in three olive cultivars with different fruit sizes. The results demonstrate that differences in the fruit size are related to the maximum growth rate between olive cultivars during early fruit growth, about 50 days post-anthesis (DPA). Differences in fruit weight between olive cultivars were found from 35 DPA, while the distinctive fruit shape became detectable from 21 DPA, even though the increase in pericarp thickness became detectable from 7 DPA in the three cultivars. During early fruit growth, intense mitotic activity appeared during the first 21 DPA in the fruit, whereas the highest cell expansion rates occurred from 28 to 42 DPA during this phase, suggesting that olive fruit cell number is determined from 28 DPA in the three cultivars. Moreover, olive fruit of the large-fruited cultivars was enlarged due to relatively higher cell division and expansion rates compared with the small-fruited cultivar. The ploidy level of olive fruit pericarp between early and late growth was different, but similar among olive cultivars, revealing that ploidy levels are not associated with cell size, in terms of different 8C levels during olive fruit growth. In the three olive cultivars, the maximum endoreduplication level (8C) occurred just before strong cell expansion during early fruit growth in fruit pericarp, whereas the cell expansion during late fruit growth occurred without preceding endoreduplication. We conclude that the basis for fruit size differences between olive cultivars is determined mainly by different cell division and expansion rates during the early fruit growth phase. These data provide new findings on the contribution of fruit ploidy and cell size to fruit size in olive and ultimately on the control of olive fruit development.

WUSCHEL-related homeobox transcription factor SlWOX13 regulates tomato fruit ripening

Fruit ripening is a complex, genetically programmed process involving the action of critical transcription factors (TFs). Despite the established importance of WUSCHEL-related homeobox (WOX) TFs in plant development, the involvement of WOX and its underlying mechanism in the regulation of fruit ripening remain unclear. Here, we demonstrate that SlWOX13 regulates fruit ripening in tomato (Solanum lycopersicum). Overexpression of SlWOX13 accelerates fruit ripening, whereas loss-of-function mutation in SlWOX13 delays this process. Moreover, ethylene synthesis and carotenoid accumulation are significantly inhibited in slwox13 mutant fruit but accelerated in SlWOX13 transgenic fruit. Integrated analyses of RNA-seq and chromatin immunoprecipitation (ChIP)-seq identified 422 direct targets of SlWOX13, of which 243 genes are negatively regulated and 179 are positively regulated by SlWOX13. Electrophoretic mobility shift assay, RT-qPCR, dual-luciferase reporter assay, and ChIP-qPCR analyses demonstrated that SlWOX13 directly activates the expression of several genes involved in ethylene synthesis and signaling and carotenoid biosynthesis. Furthermore, SlWOX13 modulates tomato fruit ripening through key ripening-related TFs, such as RIPENING INHIBITOR (RIN), NON-RIPENING (NOR), and NAM, ATAF1, 2, and CUC2 4 (NAC4). Consequently, these effects promote fruit ripening. Taken together, these results demonstrate that SlWOX13 positively regulates tomato fruit ripening via both ethylene synthesis and signaling and by transcriptional regulation of key ripening-related TFs.

Molecular mechanism of quality changes in solid endosperm of tender coconut during room temperature storage based on transcriptome and metabolome

Tender coconut (TC) is popular around the world. Postharvest storage of TC leads to a decline in its appearance quality and flavor in both liquid endosperm (LE) and solid endosperm (SE). While LE is the most consumed part and remains in a liquid state, SE is the only cellular tissue directly connected to LE and may be the main contributor to flavor deterioration during storage. This study focused on investigating SE changes during TC storage at 25 °C using computed tomographic technology, transcriptome and metabolome analyses. The results showed increased thickness and density, elevated protein and fat contents, and decreased reducing and soluble sugars in SE of TC during storage. Integrated transcriptome and metabolome analysis revealed that these changes were mainly associated with the gene transcription levels involved in amino acid, carbohydrate and lipid metabolisms, along with specific metabolites. These findings offer valuable insights for controlling TC quality during storage.

Rootstock vigor dictates the canopy light environment that regulates metabolite profile and internal fruit quality development in peach

Five rootstock cultivars of differing vigor: vigorous ('Atlas™' and 'Bright's Hybrid® 5'), standard ('Krymsk® 86' and 'Lovell') and dwarfing ('Krymsk® 1') grafted with 'Redhaven' as the scion were studied for their impact on productivity, mid-canopy photosynthetic active radiation transmission (i.e., light availability) and internal fruit quality. Αverage yield (kg per tree) and fruit count increased significantly with increasing vigor (trunk cross sectional area, TCSA). Α detailed peach fruit quality analysis on fruit of equal maturity (based on the index of absorbance difference, IAD) coming from trees with equal crop load (no. of fruit cm-2 of TCSA) characterized the direct impact of rootstock vigor on peach internal quality [dry matter content (DMC) and soluble solids concentration (SSC)]. DMC and SSC increased significantly with decreasing vigor and increasing light availability, potentially due to reduced intra-tree shading and better light distribution within the canopy. Physiologically characterized peach fruit mesocarp was further analyzed by non-targeted metabolite profiling using gas chromatography mass spectrometry (GC-MS). Metabolite distribution was associated with rootstock vigor class, mid-canopy light availability and fruit quality characteristics. Fructose, glucose, sorbose, neochlorogenic and quinic acids, catechin and sorbitol were associated with high light environments and enhanced quality traits, while sucrose, butanoic and malic acids related to low light conditions and inferior fruit quality. These outcomes show that while rootstock genotype and vigor are influencing peach tree productivity and yield, their effect on manipulating the light environment within the canopy also plays a significant role in fruit quality development.

Epigenomic mechanism regulating the quality and ripeness of apple fruit with differing harvest maturity

Harvest maturity significantly affects the quality of apple fruit in post-harvest storage process. Although the regulatory mechanisms underlying fruit ripening have been studied, the associated epigenetic modifications remain unclear. Thus, we compared the DNA methylation changes and the transcriptional responses of mature fruit (MF) and immature fruit (NF). There were significant correlations between DNA methylation and gene expression. Moreover, the sugar contents (sucrose, glucose, and fructose) were higher in MF than in NF, whereas the opposite pattern was detected for the starch content. The expression-level differences were due to DNA methylations and ultimately resulted in diverse fruit textures and ripeness. Furthermore, the higher ethylene, auxin, and abscisic acid levels in MF than in NF, which influenced the fruit texture and ripening, were associated with multiple differentially expressed genes in hormone synthesis, signaling, and response pathways (ACS, ACO, ZEP, NCED, and ABA2) that were regulated by DNA methylations. Multiple transcription factor genes involved in regulating fruit ripening and quality via changes in DNA methylation were identified, including MIKCC-type MADS-box genes and fruit ripening-related genes (NAP, SPL, WRKY, and NAC genes). These findings reflect the diversity in the epigenetic regulation of gene expression and may be relevant for elucidating the epigenetic regulatory mechanism underlying the ripening and quality of apple fruit with differing harvest maturity.

Dissection of mRNA ac4C acetylation modifications in AC and Nr fruits: insights into the regulation of fruit ripening by ethylene

N4-acetylcytidine (ac4C) modification of mRNA has been shown to be present in plant RNAs, but its regulatory function in plant remains largely unexplored. In this study, we investigated the differentially expressed mRNAs, lncRNAs and acetylation modifications of mRNAs in tomato fruits from both genotypes. By comparing wild-type (AC) tomato and the ethylene receptor-mutant (Nr) tomato from mature green (MG) to six days after the breaker (Br6) stage, we identified differences in numerous key genes related to fruit ripening and observed the corresponding lncRNAs positively regulated the target genes expression. At the post-transcriptional level, the acetylation level decreased and increased in AC and Nr tomatoes from MG to Br6 stage, respectively. The integrated analysis of RNA-seq and ac4C-seq data revealed the potential positive role of acetylation modification in regulating gene expression. Furthermore, we found differential acetylation modifications of certain transcripts (ACO, ETR, ERF, PG, CesA, β-Gal, GAD, AMY, and SUS) in AC and Nr fruits which may explain the differences in ethylene production, fruit texture, and flavor during their ripening processes. The present study provides new insights into the molecular mechanisms by which acetylation modification differentially regulates the ripening process of wild-type and mutant tomato fruits deficient in ethylene signaling.

Transcriptional regulation of tomato fruit ripening

An intrinsic and genetically determined ripening program of tomato fruits often depends upon the appropriate activation of tissue- and stage-specific transcription factors in space and time. The past two decades have yielded considerable progress in detailing these complex transcriptional as well as hormonal regulatory circuits paramount to fleshy fruit ripening. This non-linear ripening process is strongly controlled by the MADS-box and NOR family of proteins, triggering a transcriptional response associated with the progression of fruit ripening. Deepening insights into the connection between MADS-RIN and plant hormones related transcription factors, such as ERFs and ARFs, further conjugates the idea that several signaling units work in parallel to define an output fruit ripening transcriptome. Besides these TFs, the role of other families of transcription factors such as MYB, GLK, WRKY, GRAS and bHLH have also emerged as important ripening regulators. Other regulators such as EIN and EIL proteins also determine the transcriptional landscape of ripening fruits. Despite the abundant knowledge of the complex spectrum of ripening networks in the scientific domain, identifying more ripening effectors would pave the way for a better understanding of fleshy fruit ripening at the molecular level. This review provides an update on the transcriptional regulators of tomato fruit ripening.

Abscisic acid biosynthesis, metabolism and signaling in ripening fruit

Fruits are highly recommended nowadays in human diets because they are rich in vitamins, minerals, fibers and other necessary nutrients. The final stage of fruit production, known as ripening, plays a crucial role in determining the fruit's quality and commercial value. This is a complex physiological process, which involves many phytohormones and regulatory factors. Among the phytohormones involved in fruit ripening, abscisic acid (ABA) holds significant importance. ABA levels generally increase during the ripening process in most fruits, and applying ABA externally can enhance fruit flavor, hasten softening, and promote color development through complex signal regulation. Therefore, gaining a deeper understanding of ABA's mechanisms in fruit ripening is valuable for regulating various fruit characteristics, making them more suitable for consumption or storage. This, in turn, can generate greater economic benefits and reduce postharvest losses. This article provides an overview of the relationship between ABA and fruit ripening. It summarizes the effects of ABA on ripening related traits, covering the biochemical aspects and the underlying molecular mechanisms. Additionally, the article discusses the interactions of ABA with other phytohormones during fruit ripening, especially ethylene, and provides perspectives for future exploration in this field.

Quantitative proteomic analysis of tomato fruit ripening behavior in response to exogenous abscisic acid

BACKGROUND

To determine how abscisic acid (ABA) affects tomato fruit ripening at the protein level, mature green cherry tomato fruit were treated with ABA, nordihydroguaiaretic acid (NDGA) or sterile water (control, CK). The proteomes of treated fruit were analyzed and quantified using tandem mass tags (TMTs) at 7 days after treatment, and the gene transcription abundances of differently expressed proteins (DEPs) were validated with quantitative real-time polymerase chain reaction.

RESULTS

Postharvest tomato fruit underwent faster color transformation and ripening than the CK when treated with ABA. In total, 6310 proteins were identified among the CK and treatment groups, of which 5359 were quantified. Using a change threshold of 1.2 or 0.83 times, 1081 DEPs were identified. Among them, 127 were upregulated and 127 were downregulated in the ABA versus CK comparison group. According to KEGG and protein-protein interaction network analyses, the ABA-regulated DEPs were primarily concentrated in the photosynthesis system and sugar metabolism pathways, and 102 DEPs associated with phytohormones biosynthesis and signal transduction, pigment synthesis and metabolism, cell wall metabolism, photosynthesis, redox reactions, allergens and defense responses were identified in the ABA versus CK and NDGA versus CK comparison groups.

CONCLUSION

ABA affects tomato fruit ripening at the protein level to some extent. The results of this study provided comprehensive insights and data for further research on the regulatory mechanism of ABA in tomato fruit ripening. © 2023 Society of Chemical Industry.

Endoreduplication in plant organogenesis: a means to boost fruit growth

Endoreduplication is the major source of somatic endopolyploidy in higher plants, and leads to variation in cell ploidy levels due to iterative rounds of DNA synthesis in the absence of mitosis. Despite its ubiquitous occurrence in many plant organs, tissues, and cells, the physiological meaning of endoreduplication is not fully understood, although several roles during plant development have been proposed, mostly related to cell growth, differentiation, and specialization via transcriptional and metabolic reprogramming. Here, we review recent advances in our knowledge of the molecular mechanisms and cellular characteristics of endoreduplicated cells, and provide an overview of the multi-scale effects of endoreduplication on supporting growth in plant development. In addition, the effects of endoreduplication in fruit development are discussed, since it is highly prominent during fruit organogenesis where it acts as a morphogenetic factor supporting rapid fruit growth, as illustrated by case of the model fleshy fruit, tomato (Solanum lycopersicum).

Identification of watermelon H3K4 and H3K27 genes and their expression profiles during watermelon fruit development

BACKGROUND

The ClaH3K4s and ClaH3K27s gene families are subfamilies of the SET family, each with a highly conserved SET structure domain and a PHD structural domain. Both participate in histone protein methylation, which affects the chromosome structure and gene expression, and is essential for fruit growth and development.

METHODS AND RESULTS

In order to demonstrate the structure and expression characteristics of ClaH3K4s and ClaH3K27s in watermelon, members of the watermelon H3K4 and H3K27 gene families were identified, and their chromosomal localization, gene structure, and protein structural domains were analyzed. The phylogeny and covariance of the gene families with other species were subsequently determined, and the expression profiles were obtained by performing RNA-Seq and qRT-PCR. The watermelon genome had five H3K4 genes with 3207-8043 bp nucleotide sequence lengths and four H3K27 genes with a 1107-5499 bp nucleotide sequence. Synteny analysis revealed the close relationship between watermelon and cucumber, with the majority of members displaying a one-to-one covariance. Approximately half of the 'Hua-Jing 13 watermelon' ClaH3K4s and ClaH3K27s genes were expressed more in the late fruit development stages, while the changes were minimal for the remaining half. H3K4-2 expression was observed to be slightly greater on day 21 compared to other periods. Moreover, ClaH3K27-1 and ClaH3K27-2 were hardly expressed throughout the developing period, and ClaH3K27-4 exhibited the highest expression.

CONCLUSION

These results serve as a basis for further functional characterization of the H3K4 and H3K27 genes in the fruit development of watermelon.

Identification of Late Ripening Citrus Mutant, Ara-unshiu (Citrus unshiu), and Its Selectable Marker

'Miyagawa-wase' mandarin (Citrus unshiu Marc. cv. Miyagawa-wase early) is one of the most widely cultivated citrus varieties on Jeju Island in Korea. Mutation breeding is a useful tool for the induction of genetic diversity for the rapid creation of new plant variants. We previously reported the use of gamma irradiation for the development of new citrus varieties. Here, we report a new mutant, Ara-unshiu, with a unique late fruit ripening phenotype. We investigated the fruit morphological characteristics including weight, vertical/transverse diameter, peel thickness, hardness, and color difference, as well as sugar and acid contents of the Ara-unshiu compared to wild-type controls. We then used whole genome re-sequencing and functional annotation by gene ontology to identify and characterize single nucleotide polymorphism (SNP) and insertion/deletion (InDel) variants in the Ara-unshiu, finding a greater abundance of annotated genes containing InDels compared to SNPs. Finally, we used allele-specific PCR to identify molecular markers among the homozygous SNPs detected from the Ara-unshiu genome sequencing. We report a primer set that effectively distinguishes the Ara-unshiu from the wild-type control and other citrus varieties. Our findings provide insights into the mechanisms controlling the timing of fruit ripening and tools for the molecular breeding of citrus varieties.

Epigenetic regulation in tomato fruit ripening

Fruit ripening is a crucial stage in quality development, influenced by a diverse array of internal and external factors. Among these factors, epigenetic regulation holds significant importance and has garnered substantial research attention in recent years. Here, this review aims to discuss the breakthrough in epigenetic regulation of tomato (Solanum lycopersicum) fruit ripening, including DNA methylation, N6-Methyladenosine mRNA modification, histone demethylation/deacetylation, and non-coding RNA. Through this brief review, we seek to enhance our understanding of the regulatory mechanisms governing tomato fruit ripening, while providing fresh insights for the precise modulation of these mechanisms.

Exogenous melatonin delays strawberry fruit ripening by suppressing endogenous ABA signaling

Ripening as a physico-chemical change is part of a continuous developmental process and hormones play a major role in this processes. The present study was carried out to investigate the effect of external melatonin (0 and 10 μM) injection at the light green stage on the ripening of strawberry fruit. The fruit was sampled for morphological, biochemical, and gene expression analysis during (0, 5, 10, and 15 days after treatment). The results showed a lower accumulation of anthocyanin content was observed in fruits treated with 10 μM. The injection of 10 μM melatonin caused a lower total soluble solid content and fruit color, and higher titratable acidity and softening. The total phenol content was higher in fruit treated with 10 µM melatonin, accompanied by increased PAL enzyme activity and gene expression, increased DPPH scavenging capacity, and higher content of quercetin, gallic, caffeic, and chlorogenic acids. The delay in fruit ripening was associated with suppression of H2O2 level and endogenous ABA accumulation caused by lower expression of NCEDs genes. In general, it is concluded that activating the melatonin ROS scavenging cascade might be responsible for the delayed ripening and development of strawberry fruit. Therefore, our study demonstrates that the exogenous application of 10 μM melatonin can slow the ripening of strawberry fruit.

Banana MKK1 modulates fruit ripening via the MKK1-MPK6-3/11-4-bZIP21 module

The mitogen-activated protein kinase (MAPK) cascade consisting of MKKK, MKK, and MPK plays an indispensable role in various plant physiological processes. Previously, we showed that phosphorylation of MabZIP21 by MaMPK6-3 is involved in banana fruit ripening, but the regulatory mechanism by which MKK controls banana fruit ripening remains unclear. Here, ripening-induced MaMKK1 from banana fruit is characterized, and transiently overexpressing and silencing of MaMKK1 in banana fruit accelerates and inhibits fruit ripening, respectively, possibly by influencing phosphorylation and activity of MPK. MaMKK1 interacts with and phosphorylates MaMPK6-3 and MaMPK11-4 mainly at the pTEpY residues, resulting in MPK activation. MaMPK11-4 phosphorylates MabZIP21 to elevate its transcriptional activation ability. Transgenic tomato fruit expressing MabZIP21 ripen quickly with a concomitant increase in MabZIP21 phosphorylation. Additionally, MabZIP21 activates MaMPK11-4 and MaMKK1 transcription to form a regulatory feedback loop. Collectively, here we report a regulatory pathway of the MaMPK6-3/11-4-MabZIP21 module in controlling banana fruit ripening.

DNA methylation mediated by RdDM pathway and demethylation affects furanone accumulation through regulation of QUINONE OXIDOREDUCTASE in strawberry

Recently, increasing evidence suggests that DNA methylation plays a crucial role in fruit ripening. However, the role of DNA methylation in regulating specific traits, such as flavor, remains unclear. Here, we report a role of DNA methylation in affecting furanone biosynthesis in strawberry. Strawberry quinone oxidoreductase (FaQR) is a key enzyme in furanone biosynthesis. There are four FaQR homologs in strawberry cultivar 'Yuexin', and one of them, FaQR3, contributes ~50% of FaQR transcripts, indicating a major role of FaQR3 in furanone biosynthesis. Through characterization of levels of DNA methylation and FaQR3 transcript and furanone contents during fruit ripening and after the application of DNA methylation inhibitor, we found that the DNA methylation level of the FaQR3 promoter was negatively correlated with FaQR3 expression and furanone accumulation, suggesting that DNA methylation may be involved in furanone biosynthesis through adjusting FaQR3 expression, and responded to different temperatures consistently. In addition, transient expression of a gene in the RNA-directed DNA methylation (RdDM) pathway, FaAGO4, and enrichment analysis of the 24-nucleotide siRNAs suggested that DNA methylation in the FaQR3 promoter is mediated by the RdDM pathway. Transient RNA interference (RNAi) of FaDML indicated that the demethylation pathway may be involved in regulating furanone accumulation. These findings provide new insights into the role of DNA methylation and demethylation in affecting flavor quality in strawberry during fruit ripening.

An Integrative Transcriptomics and Proteomics Approach to Identify Putative Genes Underlying Fruit Ripening in Tomato near Isogenic Lines with Long Shelf Life

The elucidation of the ripening pathways of climacteric fruits helps to reduce postharvest losses and improve fruit quality. Here, we report an integrative study on tomato ripening for two near-isogenic lines (NIL115 and NIL080) with Solanum pimpinellifolium LA0722 introgressions. A comprehensive analysis using phenotyping, molecular, transcript, and protein data were performed. Both NILs show improved fruit firmness and NIL115 also has longer shelf life compared to the cultivated parent. NIL115 differentially expressed a transcript from the APETALA2 ethylene response transcription factor family (AP2/ERF) with a potential role in fruit ripening. E4, another ERF, showed an upregulated expression in NIL115 as well as in the wild parent, and it was located physically close to a wild introgression. Other proteins whose expression levels changed significantly during ripening were identified, including an ethylene biosynthetic enzyme (ACO3) and a pectate lyase (PL) in NIL115, and an alpha-1,4 glucan phosphorylase (Pho1a) in NIL080. In this study, we provide insights into the effects of several genes underlying tomato ripening with potential impact on fruit shelf life. Data integration contributed to unraveling ripening-related genes, providing opportunities for assisted breeding.

Experimental approaches in studying active biomolecules modulating fruit ripening: Melatonin as a case study

Phytohormones are naturally occurring small organic molecules found at low concentrations in plants. They perform essential functions in growth and developmental processes, from organ initiation to senescence, including fruit ripening. These regulatory molecules are studied using different experimental approaches, such as performing exogenous applications, evaluating endogenous levels, and/or obtaining genetically modified lines. Here, we discuss the advantages and limitations of current experimental approaches used to study active biomolecules modulating fruit ripening, focusing on melatonin. Although melatonin has been implicated in fruit ripening in several model fruit crops, current knowledge is affected by the different experimental approaches used, which have given different and sometimes even contradictory results. The methods of application and the doses used have produced different results in studies based on exogenous applications, while different measurement methods and ways of expressing results explain most of the variability in studies using correlative analyses. Furthermore, studies on genetically modified crops have focused on tomato (Solanum lycopersicum L.) plants only. However, TILLING and CRISPR methodologies are becoming essential tools to complement the results from the experimental approaches described above. This will not only help the scientific community better understand the role of melatonin in modulating fruit ripening, but it will also help develop technological advances to improve fruit yield and quality in major crops. The combination of various experimental approaches will undoubtedly lead to a complete understanding of the function of melatonin in fruit ripening in the near future, so that this knowledge can be effectively transferred to the field.

Current insights into posttranscriptional regulation of fleshy fruit ripening

Fruit ripening is a complicated process that is accompanied by the formation of fruit quality. It is not only regulated at the transcriptional level via transcription factors or DNA methylation but also fine-tuned after transcription occurs. Here, we review recent advances in our understanding of key regulatory mechanisms of fleshy fruit ripening after transcription. We mainly highlight the typical mechanisms by which fruit ripening is controlled, namely, alternative splicing, mRNA N6-methyladenosine RNA modification methylation, and noncoding RNAs at the posttranscriptional level; regulation of translation efficiency and upstream open reading frame-mediated translational repression at the translational level; and histone modifications, protein phosphorylation, and protein ubiquitination at the posttranslational level. Taken together, these posttranscriptional regulatory mechanisms, along with transcriptional regulation, constitute the molecular framework of fruit ripening. We also critically discuss the potential usage of some mechanisms to improve fruit traits.

Recent advances in epigenetic triggering of climacteric fruit ripening

During ripening, fleshy fruits undergo irreversible changes in color, texture, sugar content, aroma, and flavor to appeal to seed-dispersal vectors. The onset of climacteric fruit ripening is accompanied by an ethylene burst. Understanding the factors triggering this ethylene burst is important for manipulating climacteric fruit ripening. Here, we review the current understanding and recent insights into the possible factors triggering climacteric fruit ripening: DNA methylation and histone modification, including methylation and acetylation. Understanding the initiation factors of fruit ripening is important for exploring and accurately regulating the mechanisms of fruit ripening. Lastly, we discuss the potential mechanisms responsible for climacteric fruit ripening.

Composition, metabolism and postharvest function and regulation of fruit cuticle: A review

The cuticle of plants, a hydrophobic membrane that covers their aerial organs, is crucial to their ability to withstand biotic and abiotic stressors. Fruit is the reproductive organ of plants, and an important dietary source that can offer a variety of nutrients for the human body, and fruit cuticle performs a crucial protective role in fruit development and postharvest quality. This review discusses the universality and diversity of the fruit cuticle composition, and systematically summarizes the metabolic process of fruit cuticle, including the biosynthesis, transport and regulatory factors (including transcription factors, phytohormones and environmental elements) of fruit cuticle. Additionally, we emphasize the postharvest functions and postharvest regulatory technologies of fruit cuticle, and propose future research directions for fruit cuticle.

Elucidating the Mesocarp Drupe Transcriptome of Açai (Euterpe oleracea Mart.): An Amazonian Tree Palm Producer of Bioactive Compounds

Euterpe oleracea palm, endemic to the Amazon region, is well known for açai, a fruit violet beverage with nutritional and medicinal properties. During E. oleracea fruit ripening, anthocyanin accumulation is not related to sugar production, contrarily to grape and blueberry. Ripened fruits have a high content of anthocyanins, isoprenoids, fibers, and proteins, and are poor in sugars. E. oleracea is proposed as a new genetic model for metabolism partitioning in the fruit. Approximately 255 million single-end-oriented reads were generated on an Ion Proton NGS platform combining fruit cDNA libraries at four ripening stages. The de novo transcriptome assembly was tested using six assemblers and 46 different combinations of parameters, a pre-processing and a post-processing step. The multiple k-mer approach with TransABySS as an assembler and Evidential Gene as a post-processer have shown the best results, with an N50 of 959 bp, a read coverage mean of 70x, a BUSCO complete sequence recovery of 36% and an RBMT of 61%. The fruit transcriptome dataset included 22,486 transcripts representing 18 Mbp, of which a proportion of 87% had significant homology with other plant sequences. Approximately 904 new EST-SSRs were described, and were common and transferable to Phoenix dactylifera and Elaeis guineensis, two other palm trees. The global GO classification of transcripts showed similar categories to that in P. dactylifera and E. guineensis fruit transcriptomes. For an accurate annotation and functional description of metabolism genes, a bioinformatic pipeline was developed to precisely identify orthologs, such as one-to-one orthologs between species, and to infer multigenic family evolution. The phylogenetic inference confirmed an occurrence of duplication events in the Arecaceae lineage and the presence of orphan genes in E. oleracea. Anthocyanin and tocopherol pathways were annotated entirely. Interestingly, the anthocyanin pathway showed a high number of paralogs, similar to in grape, whereas the tocopherol pathway exhibited a low and conserved gene number and the prediction of several splicing forms. The release of this exhaustively annotated molecular dataset of E. oleracea constitutes a valuable tool for further studies in metabolism partitioning and opens new great perspectives to study fruit physiology with açai as a model.

Analyses of genes encoding the Glycogen Synthase Kinases in rice and Arabidopsis reveal mechanisms which regulate their expression during development and responses to abiotic stresses

Plant Glycogen Synthase Kinases (GSKs) enable a crosstalk among the brassinosteroid signaling and phytohormonal- and stress-response pathways to regulate various physiological processes. Initial information about regulation of the GSK proteins' activity was obtained, however, mechanisms that modulate expression of the GSK genes during plant development and stress responses remain largely unknown. Taking into account the importance of the GSK proteins, combined with the lack of in-depth knowledge about modulation of their expression, research in this area may provide a significant insight into mechanisms regulating these aspects of plant biology. In the current study, a detailed analysis of the GSK promoters in rice and Arabidopsis was performed, including identification of the CpG/CpNpG islands, tandem repeats, cis-acting regulatory elements, conserved motifs, and transcription factor-binding sites. Moreover, characterization of expression profiles of the GSK genes in different tissues, organs and under various abiotic stress conditions was perfomed. Additionally, protein-protein interactions between products of the GSK genes were predicted. Results of this study provided intriguing information about these aspects and insight into various regulatory mechanisms that influence non-redundant and diverse functions of the GSK genes during development and stress responses.Therefore, they may constitute a reference for future research in other plant species.

E3 ligase BRG3 persulfidation delays tomato ripening by reducing ubiquitination of the repressor WRKY71

Hydrogen sulfide (H2S) is a gaseous signaling molecule reported to play multiple roles in fruit ripening. However, the molecular mechanisms underlying H2S-mediated delay in fruit ripening remain to be established. Here, the gene encoding a WRKY transcription factor, WRKY71, was identified as substantially upregulated in H2S-treated tomato (Solanum lycopersicum) via transcriptome profiling. The expression of WRKY71 was negatively associated with that of CYANOALANINE SYNTHASE1 (CAS1). Transient and stable genetic modification experiments disclosed that WRKY71 acts as a repressor of the tomato ripening process. CAS1 appears to play an opposite role, based on the finding that the ripening process was delayed in the cas1 mutant and accelerated in CAS1-OE tomatoes. Dual-luciferase reporter assay, yeast one-hybrid, electrophoretic mobility shift assay, and transient transformation experiments showed that WRKY71 bound to the CAS1 promoter and suppressed its activation. Moreover, the persulfidation of WRKY71 enhanced its binding ability to the CAS1 promoter. Data from luciferase complementation and Y2H assays confirmed that WRKY71 interacts with a BOI-related E3 ubiquitin-protein ligase 3 (BRG3) and is ubiquitinated in vitro. Further experiments showed that modification of BRG3 via persulfidation at Cys206 and Cys212 led to reduced ubiquitination activity. Our findings support a model whereby BRG3 undergoes persulfidation at Cys206 and Cys212, leading to reduced ubiquitination activity and decreased interactions with the WRKY71 transcript, with a subsequent increase in binding activity of the persulfidated WRKY71 to the CAS1 promoter, resulting in its transcriptional inhibition and thereby delayed ripening of tomatoes. Our collective findings provide insights into a mechanism of H2S-mediated regulation of tomato fruit ripening.

Unlocking the Secret to Higher Crop Yield: The Potential for Histone Modifications

Histone modifications are epigenetic mechanisms, termed relative to genetics, and they refer to the induction of heritable changes without altering the DNA sequence. It is widely known that DNA sequences precisely modulate plant phenotypes to adapt them to the changing environment; however, epigenetic mechanisms also greatly contribute to plant growth and development by altering chromatin status. An increasing number of recent studies have elucidated epigenetic regulations on improving plant growth and adaptation, thus making contributions to the final yield. In this review, we summarize the recent advances of epigenetic regulatory mechanisms underlying crop flowering efficiency, fruit quality, and adaptation to environmental stimuli, especially to abiotic stress, to ensure crop improvement. In particular, we highlight the major discoveries in rice and tomato, which are two of the most globally consumed crops. We also describe and discuss the applications of epigenetic approaches in crop breeding programs.

Suppression of the target of rapamycin kinase accelerates tomato fruit ripening through reprogramming the transcription profile and promoting ethylene biosynthesis

Tomato fruit ripening is a unique process of nutritional and energy metabolism. Target of rapamycin (TOR), a conserved serine/threonine protein kinase in eukaryotes, controls cell growth and metabolism by integrating nutrient, energy, and hormone signals. However, it remains unclear whether TOR participates in the modulation of tomato fruit ripening. Here, we showed that the manipulation of SlTOR by chemical or genetic methods greatly alters the process of tomato fruit maturation. Expression pattern analysis revealed that the transcripts of SlTOR declined as fruit ripening progressed. Moreover, suppression of SlTOR by TOR inhibitor AZD8055 or knock down of its transcripts by inducible RNA interference, accelerated fruit ripening, and led to overall effects on fruit maturity, including changes in colour and metabolism, fruit softening, and expression of ripening-related genes. Genome-wide transcription analysis indicated that silencing SlTOR reprogrammed the transcript profile associated with ripening, including cell wall and phytohormone pathways, elevated the expression of ethylene biosynthetic genes, and further promoted ethylene production. In contrast, the ethylene action inhibitor 1-MCP efficiently blocked fruit maturation, even following SlTOR inhibition. These results suggest that accelerated fruit ripening caused by SlTOR inhibition depends on ethylene, and that SlTOR may function as a regulator in ethylene metabolism.

Reducing crop losses by gene-editing control of organ developmental physiology

Some physiological processes in reproductive organs, if not controlled, can lead to crop loss even in the absence of environmental stress. These processes may occur pre- or post- harvest, and in diverse species and include abscission processes in cereal grain, e.g., shattering and in immature fruit, e.g., preharvest drop, preharvest sprouting of cereals, and postharvest senescence in fruit. Some of the molecular mechanisms and genetic determinants underlying these processes are now better detailed, making it possible to refine them by gene editing. Here, we discuss using advanced genomics to identify genetic determinants underlying crop physiological traits. Examples of improved phenotypes developed for preharvest problems are provided, and suggestions for reducing postharvest fruit losses by gene and promoter editing were made.

Transcriptomic, metabolomic, and ATAC-seq analysis reveal the regulatory mechanism of senescence of post-harvest tomato fruit

Several physiological changes occur during fruit storage, which include the regulation of genes, metabolisms and transcription factors. In this study, we compared 'JF308' (a normal tomato cultivar) and 'YS006' (a storable tomato cultivar) to determine the difference in accumulated metabolites, gene expression, and accessible chromatin regions through metabolome, transcriptome, and ATAC-seq analysis. A total of 1006 metabolites were identified in two cultivars. During storage time, sugars, alcohols and flavonoids were found to be more abundant in 'YS006' compared to 'JF308' on day 7, 14, and 21, respectively. Differentially expressed genes, which involved in starch and sucrose biosynthesis were observed higher in 'YS006'. 'YS006' had lower expression levels of CesA (cellulose synthase), PL (pectate lyase), EXPA (expansin) and XTH (xyglucan endoglutransglucosylase/hydrolase) than 'JF308'. The results showed that phenylpropanoid pathway, carbohydrate metabolism and cell wall metabolism play important roles in prolonging the shelf life of tomato (Solanum lycopersicum) fruit. The ATAC-seq analysis revealed that the most significantly up-regulated transcription factors during storage were TCP 2,3,4,5, and 24 in 'YS006' compared to 'JF308' on day 21. This information on the molecular regulatory mechanisms and metabolic pathways of post-harvest quality changes in tomato fruit provides a theoretical foundation for slowing post-harvest decay and loss, and has theoretical importance and application value in breeding for longer shelf life cultivars.

Comprehensive profiling of endogenous phytohormones and expression analysis of 1-aminocyclopropane-1-carboxylic acid synthase gene family during fruit development and ripening in octoploid strawberry (Fragaria× ananassa)

The non-climacteric octoploid strawberry (Fragaria × ananassa Duchesne ex Rozier) was used as a model to study its regulation during fruit ripening. High performance liquid chromatography electrospray tandem-mass spectrometry (HPLC-ESI-MS/MS) was employed to profile 28 different endogenous phytohormones in strawberry. These include auxins, cytokinins (CKs), abscisic acid (ABA), ethylene precursor 1-aminocyclopropane-1-carboxylic acid (ACC), jasmonates, and phenolic compounds salicylic acid (SA), benzoic acid (BzA) and phenylacetic acid (PAA) together with their various metabolic forms that have remained largely unexplored thus far. ABA, ACC and CK N⁶-(Δ²-isopentenyl)adenine (iP) were found to be associated with ripening while ABA catabolites 9-hydroxy-ABA and phaseic acid mimicked the pattern of climacteric decline at the turning phase of strawberry ripening. The content of other CK forms except iP decreased as fruit ripened, as also that of auxins indole-3-acetic acid (IAA) and oxo-IAA, and of jasmonates. Data presented here also suggest that both the transition and progression of strawberry fruit ripening are associated with N⁶-(Δ²-isopentenyl)adenosine-5'-monophosphate (iPRMP) → N⁶-(Δ²-isopentenyl)adenosine (iPR) → iP as the preferred CK metabolic pathway. In contrast, the ethylene precursor ACC was present at higher levels, with its abundance increasing from the onset of ripening to the red ripe stage. Further investigation of ripening-specific ACC accumulation revealed the presence of a large ACC synthase (ACS) encoding gene family in octoploid strawberry that was previously unknown. Seventeen ACS genes were found differentially expressed in fruit tissues, while six of them showed induced expression during strawberry fruit ripening. These data suggest a possible role(s) of ACC, ABA, and iP in strawberry fruit ripening. These data add new dimension to the existing knowledge of the interplay of different endogenous phytohormones in octoploid strawberry, paving the way for further investigation of their individual role(s) in fruit ripening.

Carbon sufficiency boosts phenylpropanoid biosynthesis early in peach fruit development priming superior fruit quality

Manipulating the crop load in peach trees determines carbon supply and optimum balance between fruit yield and quality potentials. The impact of carbon supply on peach fruit quality was assessed in three development stages (S2, S3, S4) on fruit of equal maturity from trees that were carbon (C) starved (unthinned) and sufficient (thinned). Previous studies determined that primary metabolites of peach fruit mesocarp are mainly linked with developmental processes, thus, the secondary metabolite profile was assessed using non-targeted liquid chromatography mass-spectrometry (LC-MS). Carbon sufficient (C-sufficient) fruit demonstrated superior quality attributes as compared to C-starved fruit. Early metabolic shifts in the secondary metabolome appear to prime quality at harvest. Enhanced C-availability facilitated the increased and consistent synthesis of flavonoids, like catechin, epicatechin and eriodyctiol, via the phenylpropanoid pathway, providing a link between the metabolome and fruit quality, and serving as signatures of C-sufficiency during peach fruit development.

A xanthophyll-derived apocarotenoid regulates carotenogenesis in tomato chromoplasts

Carotenoids possess important biological functions that make them essential components of the human diet. β-Carotene and some other carotenoids have vitamin A activity while lutein and zeaxanthin, typically referred to as the macular pigments, are involved in good vision and in delaying the onset of age-related eye diseases. In order to create a zeaxanthin-producing tomato fruit, two transgenic lines, one with a high β-carotene cyclase activity and the other with a high β-carotene hydroxylase activity, have been genetically crossed. Ripe fruits from the resulting progeny contained significant levels of violaxanthin, antheraxanthin, and xanthophyll esters. However, their zeaxanthin content was not as high as expected, and the total level of carotenoids was only 25% of the carotenoids found in ripe fruits of the comparator line. Targeted transcript analysis and apocarotenoids determinations indicated that transcriptional regulation of the pathway or degradation of synthesized carotenoids were not responsible for the low carotenoid content of hybrid fruits which instead appeared to result from a substantial reduction of carotenoid biosynthesis. Notably, the content of an unidentified hydroxylated cyclic (C13) apocarotenoid was 13 times higher in the hybrid fruits than in the control fruits. Furthermore, a GC-MS-based metabolite profiling demonstrated a perturbation of carotenogenesis in ripening hybrid fruits compatible with a block of the pathway. Moreover, carotenoid profiling on leaf, fruit, and petal samples from a set of experimental lines carrying the hp3 mutation, in combination with the two transgenes, indicated that the carotenoid biosynthesis in petal and fruit chromoplasts could be regulated. Altogether the data were consistent with the hypothesis of the regulation of the carotenoid pathway in tomato chromoplasts through a mechanism of feedback inhibition mediated by a xanthophyll-derived apocarotenoid. This chromoplast-specific post-transcriptional mechanism was disclosed in transgenic fruits of HU hybrid owing to the abnormal production of zeaxanthin and antheraxanthin, the more probable precursors of the apocarotenoid signal. A model describing the regulation of carotenoid pathway in tomato chromoplasts is presented.

Physicochemical properties and transcriptional changes underlying the quality of 'Gala' apples (Malus × domestica Borkh.) under atmosphere manipulation in long-term storage

BACKGROUND

The year-round availability of apples (Malus × domestica Borkh.) depends on post-harvest technologies, which are essential for the retention of fruit sensory and chemical properties by delaying senescence. The effectiveness of strategies for preserving the quality of apples depends on complex interactions between the storage environment and endogenous biological factors. In the current work, we integrated instrumental, sensory, and transcriptional data to determine the role of conservation technologies cold storage, controlled atmosphere, and 1-methylcyclopropene-mediated ethylene blockage on the long-term conservation of apples.

RESULTS

The results demonstrated that inhibition of the consumer's perception of the apples' ethylene content is essential for long-term cold storage, and such quality conservation can be achieved by reducing oxygen pressure. Overall appreciation of apples after storage was determined mainly by their texture, with crispness and juiciness contributing favorably, and mealiness contributing negatively. Reduced oxygen pressure and inhibition of ethylene perception exerted distinct effects on the transcription of candidate genes associated with ripening in apple. Hexose and cell-wall carbohydrate metabolism genes exhibit distinct expression patterns under storage.

CONCLUSION

Inhibition of ethylene perception and reduction of relative oxygen pressure under cold storage both promote similar conservation of apple sensory traits under long-term cold storage. Texture was the main contributor to global appreciation of apples subjected to long-term storage. The conditions that were investigated were able to delay, but not fully prevent, senescence, as evidenced by physicochemical and gene expression analyses. The expression of gene-encoding enzymes involved in hexose metabolism was mainly developmentally regulated, whereas storage conditions exerted a stronger effect on the expression of genes associated with cell-wall metabolism. © 2022 Society of Chemical Industry.