SlERF.F12 modulates the transition to ripening in tomato fruit by recruiting the co-repressor TOPLESS and histone deacetylases to repress key ripening genes

SlPLT6 controls ripening initiation and quality traits through modulation of histone acetylation and methylation in tomato

Improving fruit growth and quality without compromising yield is a highly sought-after goal in crop breeding. Here, we report that an EAR motif-containing transcription factor SlPLT6 controls the onset of fruit ripening and quality traits in tomato. SlPLT6 knockout caused precocious ripening initiation and enhanced fruit qualities without penalizing yield in two tomato cultivars. SlPLT6 represses genes involved in ripening initiation and major quality traits by directly binding to their promoters. Moreover, SlPLT6 connects two repressive mechanisms by recruiting Histone Deacetylase 1 via its C-terminal EAR motif and LIKE HETEROCHROMATIN PROTEIN 1b through the first AP2 domain. Furthermore, Sly-miR159 acts upstream of SlPLT6 to release its repression. Taken together, our data provide insights into the operating mode of SlPLT6 in modulating fruit ripening and quality traits and define a unique gene for targeted crop improvement aimed at upgrading fruit quality without yield penalty.

Bi-functional transcription factor SlbHLH95 regulates fruits flavonoid metabolism and grey mould resistance in tomato

Flavonoids are polyphenolic secondary metabolites in tomato fruit with important roles in nutritional quality. Dissecting the transcriptional regulatory network modulating flavonoid metabolism is the first step to improve the nutritional quality of tomato fruits through molecular breeding technology. In this study, we identified a transcription factor SlbHLH95 as a key regulator in flavonoid metabolism through analysis of the MicroTom Metabolic Network (MMN) data set. Functional analyses revealed that knockout of SlbHLH95 increased the accumulation of naringenin, while the levels of rutin and nictoflorin decreased. Conversely, overexpression of SlbHLH95 resulted in an opposite pattern of accumulation of flavonoids. Transactivation assays showed that SlbHLH95 positively activated the expression of SlF3H and SlFLS, two key enzyme-encoding genes in the flavonoid pathway, while repressing the expression of SlCHS1. Electrophoretic mobility shift assays (EMSA) demonstrated that SlbHLH95 could directly bind to the promoters of SlF3H and SlFLS, although it could not bind to the promoter of SlCHS1. Furthermore, SlbHLH95 interacted with the transcription factor SlMYB12 and coordinately regulated the expression of SlF3H and SlFLS. Beyond its role in flavonoid metabolism, SlbHLH95 positively regulated the grey mould resistance in tomato fruits by repressing SlBG10. Overall, our findings revealed the important role of bi-functional SlbHLH95 in flavonoid metabolism and grey mould resistance in tomato fruits by acting as both a transcriptional activator and a repressor. This study provides new insights into strategies for improving fruit quality and enhancing fruit disease resistance through targeted genetic modulation.

Ethylene-Activated E3 Ubiquitin Ligase MdEAEL1 Promotes Apple Fruit Softening by Facilitating the Dissociation of Transcriptional Repressor Complexes

Fruit of most apple varieties soften after harvest, and although the hormone ethylene is known to induce softening, the associated pathway is not well resolved. In this study, it is determined that MdEAEL1 (Ethylene-activated E3 ubiquitin Like 1) is specifically expressed during apple fruit postharvest storage, activated by ethylene, and interacts with the transcription factor MdZFP3 (zinc finger protein3). MdZFP3 is found to rely on an EAR (ethylene-responsive element binding factor-associated amphiphilic repression) motif to form a transcriptional repression complex with MdTPL4 (TOPLESS4)-MdHDA19 (histone deacetylase19), thereby downregulating the histone acetylation levels of the promoters of a range of cell wall degradation-related genes and inhibiting their transcription. MdEAEL1 ubiquitinates and degrades MdZFP3, leading to the disassembly of the MdZFP3-MdTPL4-MdHDA19 transcriptional repression complex. This process promotes the transcription of cell wall degradation-related genes, resulting in fruit softening during storage. Furthermore, the disassembly of the MdZFP3-MdTPL4-MdHDA19 transcriptional repression complex, mediated by MdEAEL1, upregulates the transcription of MdEAEL1 itself, creating a feedback loop that further promotes softening. This study elucidates the interplay between post-translational modifications of a transcription factor and its epigenetic modification to regulate fruit softening, and highlights the complexity of ethylene-induced softening.

Genetic variation in a tandemly duplicated TPS gene cluster contributes to the diversity of aroma in lychee fruit

Fruits undergo a similar ripening process, yet they exhibit a range of differences in color, taste, and shape, both across different species and within the same species. How does this diversity arise? We uncovered a conserved fruit ripening process in lychee fruit in which a NAC transcription factor, LcNAC1, acts as a master regulator. LcNAC1 regulates the expression of two terpene synthase genes, LcTPSa1 and LcTPSa2, which belong to a gene cluster consisting of four TPS genes. LcTPSa1-LcTPSa3 are responsible for catalyzing the production of farnesol, which in turn dictates the aromatic diversity in fruit of different lychee varieties. Through comparative, transcriptomic, and genomic analyses across various lychee varieties, we found these four TPS genes exhibit distinct expression levels due to natural genetic variation. These include copy number variations, presence/absence variations, insertions and deletions, and single nucleotide polymorphisms, many of which affect the binding affinity of LcNAC1. A single nucleotide mutation in LcTPSa1 caused a premature translational termination, resulting in a truncated version of the TPS protein, which surprisingly remains functional. All these genomic changes in the LcNAC1-regulated TPS genes are likely to contribute to the great aromatic diversity observed in lychee fruit. This diversification of fruit aroma in lychee varieties offers a compelling example of how species- or variety-specific traits evolve - the phenotypic diversity is primarily derived from natural genetic variation accumulated in downstream structural genes within an evolutionarily conserved regulatory circuit.

The Dynamics, Degradation, and Afterlives of Pectins: Influences on Cell Wall Assembly and Structure, Plant Development and Physiology, Agronomy, and Biotechnology

Pectins underpin the assembly, molecular architecture, and physical properties of plant cell walls and through their effects on cell growth and adhesion influence many aspects of plant development. They are some of the most dynamic components of plant cell walls, and pectin remodeling and degradation by pectin-modifying enzymes can drive developmental programming via physical effects on the cell wall and the generation of oligosaccharides that can act as signaling ligands. Here, we introduce pectin structure and synthesis and discuss pectin functions in plants. We highlight recent advances in understanding the structure-function relationships of pectin-modifying enzymes and their products and how these advances point toward new approaches to bridging key knowledge gaps and manipulating pectin dynamics to control plant development. Finally, we discuss how a deeper understanding of pectin dynamics might enable innovations in agronomy and biotechnology, unlocking new benefits from these ubiquitous but complex polysaccharides.

ERF100 regulated by ERF28 and NOR controls pectate lyase 7, modulating fig (Ficus carica L.) fruit softening

The mechanism regulating fruit textural changes has not been fully elucidated. Transcription factor FcERF100 showed rapid transcription repression during drastic texture loss in fig (Ficus carica L.) fruit ripening. Transient overexpression of FcERF100 delayed fig fruit softening and significantly decreased the transcript abundance of a key cell wall-modifying pectate lyase gene, FcPL7. Yeast one-hybrid (Y1H) assay, chromatin immunoprecipitation-qPCR, electrophoretic mobility shift assay (EMSA), and dual-luciferase reporter assay revealed that FcERF100 represses FcPL7 transcription by direct promoter binding via GCC-box and DRE/CRT elements. Stable transgenic fig lines further verified FcERF100's inhibitory effect on FcPL7 expression. We detected FcERF28 as an upstream element of FcERF100 by Y1H and EMSA, revealing its binding to, and activation of FcERF100 by dual-luciferase assay. Taken together, the FcERF28-FcERF100 transcriptional cascade serves as a synergistic flow-limiting valve for FcPL7 abundance. We then identified a NAC transcription factor, FcNOR, using FcERF100 as the bait by yeast two-hybrid screening. FcNOR silencing retarded fig fruit softening, with decreased FcPL7 transcript and pectate lyase activity. FcNOR interacted with FcERF100 to form a protein complex, attenuating FcERF100's transcriptional repression of FcPL7. Moreover, FcNOR bound directly to the promoter of FcERF100 and inhibited its transcription. In addition, ethylene treatment upregulated FcNOR and FcPL7 expression and downregulated FcERF28 and FcERF100 expression. Our findings reveal a novel FcERF100-centered regulatory complex and resolve how the complex achieves the necessary cell wall modification during an early stage of fruit growth and implements drastic softening at fruit ripening by modulating component proportions.

EIL (ethylene-insensitive 3-like) transcription factors in apple affect both ethylene- and cold response-dependent fruit ripening

EIN3/EIL (ethylene-insensitive 3/EIN3-like) transcription factors are positive downstream transcriptional regulators of ethylene signalling. In apple (Malus × domestica), a small family of MdEIL genes was identified, with four expressed in fruit. Transgenic lines were generated to manipulate MdEIL1 expression, and fruits were sampled at harvest maturity and after cold treatment. Their fruit ripening behaviour was compared with control lines and contrasted to a ACC OXIDASE 1 antisense line (ACO1as) which produced no ripening associated ethylene. Two transgenic lines showed strong co-suppression of MdEIL1-4 expression as well as reduced ethylene production, softening and aroma production, while one overexpressing line showed enhanced ripening. Key genes involved in ethylene biosynthesis and ethylene-dependent genes involved in cell wall modification (MdXTH1, MdβGAL) and aroma biosynthesis (MdAFS1, MdoOMT1) were downregulated in the co-suppressed lines. Co-suppressed lines showed reduced softening/volatile production after cold treatment and in contrast to the ACO1as line, expression of cold response-dependent genes (MdCBF2, dehydrins MdDHN2, -14, -16 and MdNAC29a) remained cold-repressed. The action of MdEILs was shown using dual-luciferase reporter assays to occur through direct activation of MdAFS1, MdXTH1 and MdβGAL promoters. Exogenous ethylene was unable to further stimulate ripening promoter activation, but cold treatment could. Promoter deletion analysis identified potential EIL binding sites in the MdAFS1 and MdβGAL promoters and electrophoretic mobility shift assays showed that MdEIL1-3 could all bind to a 32 bp fragment in the MdAFS1 promoter. Together these results indicate that MdEILs contribute to a suite of apple fruit ripening attributes via activation of genes in an ethylene-dependent manner, but also in response to cold.

Molecular breeding of tomato: Advances and challenges

The modern cultivated tomato (Solanum lycopersicum) was domesticated from Solanum pimpinellifolium native to the Andes Mountains of South America through a "two-step domestication" process. It was introduced to Europe in the 16th century and later widely cultivated worldwide. Since the late 19th century, breeders, guided by modern genetics, breeding science, and statistical theory, have improved tomatoes into an important fruit and vegetable crop that serves both fresh consumption and processing needs, satisfying diverse consumer demands. Over the past three decades, advancements in modern crop molecular breeding technologies, represented by molecular marker technology, genome sequencing, and genome editing, have significantly transformed tomato breeding paradigms. This article reviews the research progress in the field of tomato molecular breeding, encompassing genome sequencing of germplasm resources, the identification of functional genes for agronomic traits, and the development of key molecular breeding technologies. Based on these advancements, we also discuss the major challenges and perspectives in this field.

Characterization of a tomato chlh mis-sense mutant reveals a new function of ChlH in fruit ripening

Tomato fruit ripening is a complex developmental process that is important for fruit quality and shelf life. Many factors, including ethylene and several key transcription factors, have been shown to play important roles in the regulation of tomato fruit ripening. However, our understanding of the regulation of tomato fruit ripening is still limited. Here, we describe mut26, an EMS-induced tomato (Solanum lycopersicum) mutant that exhibits chlorophyll-deficient phenotypes in various organs, including fruits. Genetic mapping and functional analyses revealed that a single-nucleotide substitution and a corresponding Pro398->Ser mis-sense mutation in SlChlH (GENOMES UNCOUPLED 5, GUN5), which encodes the H subunit of magnesium chelatase, are responsible for the defects in the mut26 strain. Transcript analyses towards the expression of many SlPhANGs revealed that mut26 is defective in plastid retrograde signalling during tomato fruit ripening initiation, namely the transition from mature green to breaker stage. mut26 exhibits delayed progression of fruit ripening characterized by reduced fruit ethylene emission, increased fruit firmness, reduced carotenoid content and delayed plastid conversion from chloroplast to chromoplast. Given that fruit ripening requires signalling from plastids to nucleus, these data support the hypothesis that GUN5-mediated plastid retrograde signalling promotes tomato fruit ripening. We further showed that the delayed fruit ripening of mut26 is not likely caused by reduced chlorophyll content. Taken together, we identified a new function of SlChlH in the promotion of tomato fruit ripening and ethylene biosynthesis, suggesting that GUN5-mediated plastid retrograde signalling plays a promotive role in tomato fruit ripening.

lncRNA1471 mediates tomato-ripening initiation by binding to the ASR transcription factor

The regulatory mechanisms underlying fruit ripening, including hormone regulation, transcription factor activity, and epigenetic modifications, have been discussed extensively. Nonetheless, the role of long non-coding RNAs (lncRNAs) in fruit ripening remains unclear. Here, we identified lncRNA1471 as a negative regulator of tomato fruit-ripening initiation. Knocking out lncRNA1471 via large fragment deletion resulted in accelerated initiation of fruit ripening, a shorter color-breaking stage (BR), deeper coloration, increased levels of ethylene, lycopene, and β-carotene, accelerated chlorophyll degradation, and reduced fruit firmness. These phenotypic changes were accompanied by alterations in the carotenoid pathway flux, ethylene biosynthesis, and cell wall metabolism, primarily mediated by the direct regulation of key genes involved in these processes. For example, in the CR-lncRNA1471 mutant, lycopene-related SlPSY1 and SlZISO were upregulated. Additionally, the expression levels of ethylene biosynthetic genes (SlACS2 and SlACS4), ripening-related genes (RIN, NOR, CNR, and SlDML2), and cell wall metabolism genes (SlPL, SlPG2a, SlEXP1, SlPMEI-like, and SlBG4) were significantly upregulated, which further strengthening the findings mentioned above. Furthermore, lncRNA1471 was identified to interact with the abscisic stress-ripening protein (ASR) transcription factor by chromatin isolation by RNA purification coupled with mass spectrometry (ChIRP-MS) and protein pull-down assay in vitro, which might regulate key genes involved in tomato ripening. The discovery of the significant non-coding regulator lncRNA1471 enhances our understanding of the complex regulatory landscape governing fruit ripening. These findings provide valuable insights into the mechanisms underlying ripening, particularly regarding the involvement of lncRNAs in ripening.

Repressor MrERF4 and Activator MrERF34 Synergistically Regulate High Flavonol Accumulation Under UV-B Irradiation in Morella rubra Leaves

Flavonols are important plant photoprotectants to defence UV-B irradiation, however, the underlying transcriptional regulatory mechanism of rapid flavonol accumulation in response to UV-B remains unknown. In this study, content of flavonols was significantly induced from 0.11 to 3.80 mg/g fresh weight by UV-B irradiation in leaves of Morella rubra seedlings. MrERF34 was identified as an activator that can regulate the expression of MrFLS2, and promoted flavonol biosynthesis with activator MrMYB12 under UV-B treatment. Transient overexpression of MrERF34 resulted in higher flavonol accumulation, while virus-induced gene silencing of MrERF34 reduced the content of flavonols in bayberry leaves. We further demonstrated that a repressor MrERF4 inhibited the expression of MrERF34 and MrMYB12 as well as MrFLS2 via ERF-associated-amphiphilic repression motif. Exposure to UV-B reduced the promoter activity and transcription of MrERF4, which weakened the inhibitory effect of MrERF4 on MrERF34, MrMYB12, and MrFLS2, leading to a tremendous accumulation of flavonols. Such inhibitory roles of MrERF4 in regulation of flavonol biosynthesis were further validated by transient overexpression in leaves of Nicotiana benthamiana and M. rubra. These findings enrich the synergistical regulatory mechanisms between repressor and activators in flavonol biosynthesis, and provide new insights into photoprotectants biosynthesis to mitigate UV-B stress in plants.

Removal of toxic steroidal glycoalkaloids and bitterness in tomato is controlled by a complex epigenetic and genetic network

The steroidal glycoalkaloids (SGAs) produced in Solanaceae crops, including tomato, are antinutritional because of their cellular toxicity and resultant bitter taste to humans. To make fruits palatable, SGA profiles shift from bitter and toxic α-tomatine to nonbitter and nontoxic esculeoside A during the ripening process. However, the mechanisms regulating this conversion remain unclear. In this study, we showed that removal of toxic and bitter SGAs is under the control of DNA demethylation, ethylene, and key transcription factors by forming a feedback loop that governs the expression of key GLYCOALKALOID METABOLISM (GAME) genes during ripening. Moreover, the ethylene-inducible transcription factors NON-RIPENING, RIPENING INHIBITOR, and FRUITFULL1 coordinately regulate the expression of GAME31, GAME40, GAME5, and the glycoalkaloid transporter gene GORKY, whereas jasmonic acid-induced MYC2 modulates the transcription of GAME36. Furthermore, DNA demethylation mediated by the DEMETER-LIKE 2 drives SGA detoxification during tomato domestication.

Ethylene response factor SlERF.D6 promotes ripening in part through transcription factors SlDEAR2 and SlTCP12

Ripening is crucial for the development of fleshy fruits that release their seeds following consumption by frugivores and are important contributors to human health and nutritional security. Many genetic ripening regulators have been identified, especially in the model system tomato, yet more remain to be discovered and integrated into comprehensive regulatory models. Most tomato ripening genes have been studied in pericarp tissue, though recent evidence indicates that locule tissue is a site of early ripening-gene activities. Here, we identified and functionally characterized an Ethylene Response Factor (ERF) gene, SlERF.D6, by investigating tomato transcriptome data throughout plant development, emphasizing genes elevated in the locule during fruit development and ripening. SlERF.D6 loss-of-function mutants resulting from CRISPR/Cas9 gene editing delayed ripening initiation and carotenoid accumulation in both pericarp and locule tissues. Transcriptome analysis of lines altered in SlERF.D6 expression revealed multiple classes of altered genes including ripening regulators, in addition to carotenoid, cell wall, and ethylene pathway genes, suggesting comprehensive ripening control. Distinct regulatory patterns in pericarp versus locule tissues were observed, indicating tissue-specific activity of this transcription factor (TF). Analysis of SlERF.D6 interaction with target promoters revealed an APETALA 2/ETHYLENE RESPONSE FACTOR (AP2/ERF) TF (SlDEAR2) as a target of SlERF.D6. Furthermore, we show that a third TF gene, SlTCP12, is a target of SlDEAR2, presenting a tricomponent module of ripening control residing in the larger SlERF.D6 regulatory network.

The H2S-responsive transcription factor ERF.D3 regulates tomato abscisic acid metabolism, leaf senescence, and fruit ripening

Hydrogen sulfide (H2S) is a signaling molecule that regulates plant senescence. In this study, we found that H2S delays dark-induced senescence in tomato (Solanum lycopersicum) leaves. Transcriptome and reverse transcription quantitative PCR (RT-qPCR) analyses revealed an ethylene response factor ERF.D3 is quickly induced by H2S. H2S also persulfidated ERF.D3 at amino acid residues C115 and C118. CRISPR/Cas9-mediated gene editing, and gene overexpression analyses showed that ERF.D3 negatively regulates leaf senescence and fruit ripening. Abscisic acid (ABA) levels were reduced by ERF.D3 overexpression, suggesting ERF.D3 might regulate ABA metabolism. Additionally, the ABA 8'-hydroxylase-encoding gene CYP707A2, which is required for ABA degradation, was identified as an ERF.D3 target gene through transcriptome data, RT-qPCR, dual-luciferase reporter assays, and electrophoretic mobility shift assays. ERF.D3 persulfidation enhanced its transcriptional activity toward CYP707A2. Moreover, the E3 ligase RNF217 ubiquitinated ERF.D3, which may accelerate fruit ripening during the late stage of fruit development. Overall, our study provides valuable insights into the roles of a H2S-responsive ERF.D3 and its persulfidation state in delaying leaf senescence and fruit ripening and provides a link between H2S and ABA degradation.

CitGATA7 interact with histone acetyltransferase CitHAG28 to promote citric acid degradation by regulating the glutamine synthetase pathway in citrus

Organic acid is a crucial indicator of fruit quality traits. Citric acid, the predominant organic acid in citrus fruit, directly influences its edible quality and economic value. While the transcriptional regulatory mechanisms of citric acid metabolism have been extensively studied, the understanding about the transcriptional and epigenetic co-regulation mechanisms is limited. This study characterized a transcription factor, CitGATA7, which directly binds to and activates the expression of genes associated with the glutamine synthetase pathway regulating citric acid degradation. These genes include the aconitase encoding gene CitACO3, the isocitrate dehydrogenase encoding gene CitIDH1, and the glutamine synthetase encoding gene CitGS1. Furthermore, CitGATA7 physically interacts with the histone acetyltransferase CitHAG28 to enhance histone 3 acetylation levels near the transcription start site of CitACO3, CitIDH1, and CitGS1, thereby increasing their transcription and promoting citric acid degradation. The findings demonstrate that the CitGATA7-CitHAG28 protein complex transcriptionally regulate the expression of the GS pathway genes, i.e., CitACO3, CitIDH1, and CitGS1, via histone acetylation, thus promoting citric acid catabolism. This study establishes a direct link between transcriptional regulation and histone acetylation regarding citric acid metabolism, providing insights for strategies to manipulate organic acid accumulation in fruit.

Hydrogen sulfide interferes with ethylene biosynthesis and signaling pathway in tomato by the mediation of SlERF.D2 persulfidation

Hydrogen sulfide (H2S), as a signaling molecule, is found to delay fruit ripening and senescence by antagonizing the biosynthesis and signaling of ethylene, whereas the mechanism remains unclear. In the current work, exogenous H2S fumigation could alleviate tomato fruit ripening and an ethylene response factor SlERF.D2 was found to be persulfidated at Cys35 by mass spectrometry analysis. Meanwhile, ethylene biosynthesis related genes SlACS1 and SlACO3 were significantly downregulated at gene expression level in H2S-treated fruit. By CRISPR/Cas9 and gene overexpression, we showed that overexpression of SlERF.D2 promoted fruit ripening by accelerating chlorophyll degradation and carotenoid accumulation and upregulating the expression of ripening related genes SlPAO, SlPPH, SlSGR1, SlACS1, SlACS2, SlACS4, SlEIN2, SlACO1, and SlACO3, while the mutation of slerf.d2 delayed fruit ripening. Additionally, slerf.d2 mutant showed delayed ethylene production during tomato fruit ripening. Moreover, SlERF.D2 was found to interact with the kinase SlMAPK4 and was phosphorylated at Ser42 by yeast two-hybrid screening, pull down and LC-MS/MS. By cis-element analysis, electrophoretic mobility shift assay and dual-luciferase assay, SlERF.D2 could activate the transcription of the ethylene pathway-associated gene SlACO3 and SlEIN2. Besides, we provided evidence that SlERF.D2 persulfidation weakened the transcriptional activity of SlERF.D2 on the target gene SlACO3 and SlEIN2. In contrast, SlMAPK4-mediated phosphorylation enhanced SlERF.D2's transcriptional activation activity on SlACO3 and SlEIN2. Therefore, the present research provides insights into the mechanism of H2S in antagonizing the biosynthesis and signaling transduction of ethylene and reveals the importance of SlERF.D2 persulfidation and phosphorylation in dynamically regulating tomato fruit ripening.

Transcriptome analysis reveals the potential mechanism of methyl jasmonate alleviated ripening disorder in mango fruit at low temperature

High susceptibility of mangoes to low temperature leads to ripening failure that restricts the marketability of products. This study investigated the effect of methyl jasmonate (MeJA) on ripening disorder and mechanism involved in mangoes during refrigeration. Results showed that 50 μM MeJA ameliorated ripening disorder, as indicated by accelerated advancement of ripening-related parameters. Transcriptome analysis revealed that 17,414 significantly differentially expressed genes were mainly enriched in ethylene synthesis, cell wall degradation, starch degradation and sugar transport. Moreover, 8 AP2/ERF transcription factors and 12 ripening-related genes were characterized via qRT-PCR. Afterwards, through the analysis of transcription factor binding sites and cis-acting elements, a regulatory network of ERFs mediated alleviation of ripening disorder conferred by MeJA was constructed. Finally, the interactions between MiERFs and the promoters of target genes were verified by yeast one-hybrid assay. Our findings provide a theoretical basis for improving cold tolerance via counteracting ripening disorder in mangoes.

A vacuolar invertase gene SlVI modulates sugar metabolism and postharvest fruit quality and stress resistance in tomato

Sugars act as signaling molecules to modulate various growth processes and enhance plant tolerance to various abiotic and biotic stresses. Moreover, sugars contribute to the postharvest flavor in fleshy fruit crops. To date, the regulation of sugar metabolism and its effect in plant growth, fruit ripening, postharvest quality, and stress resistance remains not fully understood. In this study, we investigated the role of tomato gene encoding a vacuolar invertase, hydrolyzing sucrose to glucose and fructose. SlVI is specifically expressed during the tomato fruit ripening process. We found that overexpression of SlVI resulted in increased leaf size and early flowering, while knockout of SlVI led to increased fruit sucrose content, enhanced fruit firmness, and elevated resistance of postharvest fruit to Botrytis cinerea. Moreover, the content of naringenin and total soluble solids was significantly increased in SlVI knockout fruit at postharvest stage. Transcriptome analysis showed a negative feedback regulation triggered by sucrose accumulation in SlVI knockout fruit resulting in a downregulation of BAM3 and AMY2, which are critical for starch degradation. Moreover, genes associated with cell wall, cutin, wax, and flavonoid biosynthesis and pathogen resistance were upregulated in SlVI knockout fruit. Conversely, the expression levels of genes involved in cell wall degradation were decreased in knockout fruit. These results are consistent with the enhanced postharvest quality and resistance. Our findings not only provide new insights into the relationship between tomato fruit sucrose content and postharvest fruit quality, but also suggest new strategies to enhance fruit quality and extend postharvest shelf life.

An InDel variant in the promoter of the NAC transcription factor MdNAC18.1 plays a major role in apple fruit ripening

A complex regulatory network governs fruit ripening, but natural variations and functional differentiation of fruit ripening genes remain largely unknown. Utilizing a genome-wide association study (GWAS), we identified the NAC family transcription factor MdNAC18.1, whose expression is closely associated with fruit ripening in apple (Malus × domestica Borkh.). MdNAC18.1 activated the transcription of genes related to fruit softening (Polygalacturonase, PG) and ethylene biosynthesis (1-aminocyclopropane-1-carboxylic acid synthase, ACS), thereby promoting fruit ripening of apple and tomato (Solanum lycopersicum). There were two single-nucleotide polymorphisms (SNP-1,545 and SNP-2,002) and a 58-bp insertion-deletion (InDel-58) in the promoter region of MdNAC18.1. Among these, InDel-58 serves as the main effector in activating the expression of MdNAC18.1 and driving fruit ripening. InDel-58 determines the binding affinity of the class D MADS-box protein AGAMOUS-LIKE 11 (MdAGL11), a negative regulator of fruit ripening. The InDel-58 deletion in the early-ripening genotype reduces the inhibitory effect of MdAGL11 on MdNAC18.1. Moreover, MdNAC18.1 and its homologous genes originated from a common ancestor across 61 angiosperms, with functional diversification attributed to tandem replications that occurred in basal angiosperms. In summary, our study revealed how a set of natural variations influence fruit ripening and explored the functional diversification of MdNAC18.1 during evolution.

Protein phosphatase PP2C2 dephosphorylates transcription factor ZAT5 and modulates tomato fruit ripening

Although C2H2 zinc finger transcription factors are important in plant growth, development, and stress resistance, their specific roles in fruit ripening have been less explored. Here, we demonstrate that the C2H2 zinc finger transcription factor 5 (SlZAT5) regulates fruit ripening in tomato (Solanum lycopersicum L.). Overexpression of SlZAT5 delayed ripening, while its knockout accelerated it, confirming its role as a negative regulator. SlZAT5 functions as a transcriptional repressor by directly inhibiting ripening-related genes, including SlACS4, SlPL8, and SlGRAS38, thereby delaying ripening. Furthermore, SlZAT5 interacts with the type 2C protein phosphatase SlPP2C2, which regulates the repressor activity of SlZAT5 by dephosphorylating SlZAT5 at Ser-65. This interaction is crucial in modulating ethylene production, thereby influencing the ripening process. These findings reveal a regulatory function of SlZAT5 in tomato fruit development, offering insights into the SlZAT5-SlPP2C2 module and potential targets for genetic modification to improve fruit quality and extend fruit shelf life.

Red peel regulator 1 links ethylene response factor 25 and β-citraurin biosynthetic genes to regulate ethylene-induced peel reddening in citrus

The reddish apocarotenoid β-citraurin, produced by CAROTENOID CLEAVAGE DIOXYGENASE 4b (CsCCD4b), is responsible for peel reddening in citrus (Citrus spp.). Ethylene induces the characteristic red color of citrus peel, but the underlying molecular mechanism remains largely unclear. Here, we identified red peel regulator 1 (CsRP1), a trihelix transcriptional activator that regulates ethylene-induced peel reddening by directly binding to a key V-myb avian myeloblastosis viral oncogene homolog (MYB)-binding site in the CsCCD4b promoter, thus activating its transcription. Furthermore, 2 drought-responsive cis-elements in the CsRP1 promoter are bound by the ethylene response factor ethylene response factor 25 (CsERF25). We reconstructed the CsERF25-CsRP1-CsCCD4b transcriptional regulatory cascade through transient expression of CsERF25 and CsRP1 in citrus peel and via stable transformation of citrus calli. In this cascade, CsERF25 expression was induced by ethylene to activate CsRP1 expression, and then, CsRP1 directly induced CsCCD4b transcription to catalyze β-citraurin biosynthesis. CsRP1 and CsERF25 also bound to the promoters of other carotenogenic genes and induced their transcription, thereby promoting β-citraurin accumulation. Collectively, our findings reveal a complex regulatory network modulating ethylene-induced citrus peel reddening and provide innovative strategies for improving the nutritional and esthetic values of citrus and other fruit crops.

The histone deacetylase RhHDA15 represses petal senescence by epigenetically regulating reactive oxygen species homeostasis in rose

Epigenetic modifications play vital roles in many biological processes. Flower senescence involves epigenetic factors that influence the chromatin state and gene expression. However, the molecular mechanism underlying the role of histone deacetylation in regulating flower senescence has not been elucidated. Here, we demonstrate that histone deacetylation is involved in flower senescence by fine-tuning reactive oxygen species (ROS) homeostasis in rose (Rosa hybrida). Our data reveal that the histone lysine deacetyltransferase RhHDA15 inhibits ROS accumulation and petal senescence by downregulating the expression of NADPH OXIDASE/RESPIRATORY BURST OXIDASE HOMOLOG (RhRboh) genes. Furthermore, the transcription factor RELATED TO ABI3/VP1 2 (RhRAV2) recruits RhHDA15 and the co-repressor TOPLESS (RhTPL) to suppress flower senescence by reducing H3 lysine 9 acetylation (H3K9ac) at the RhRbohA1/2 promoter and thus directly inhibiting precocious RhRbohA1/2 expression. Our work sheds light on an epigenetic mechanism in which histone deacetylation plays a crucial role in controlling petal senescence by precisely fine-tuning ROS homeostasis, providing insights into the regulatory network of organ senescence.

MdWRKY31-MdNAC7 regulatory network: orchestrating fruit softening by modulating cell wall-modifying enzyme MdXTH2 in response to ethylene signalling

Softening in fruit adversely impacts their edible quality and commercial value, leading to substantial economic losses during fruit ripening, long-term storage, long-distance transportation, and marketing. As the apple fruit demonstrates climacteric respiration, its firmness decreases with increasing ethylene release rate during fruit ripening and postharvest storage. However, the molecular mechanisms underlying ethylene-mediated regulation of fruit softening in apple remain poorly understood. In this study, we identified a WRKY transcription factor (TF) MdWRKY31, which is repressed by ethylene treatment. Using transgenic approaches, we found that overexpression of MdWRKY31 delays softening by negatively regulating xyloglucan endotransglucosylase/hydrolases 2 (MdXTH2) expression. Yeast one-hybrid (Y1H), electrophoretic mobility shift (EMSA), and dual-luciferase assays further suggested that MdWRKY31 directly binds to the MdXTH2 promoter via a W-box element and represses its transcription. Transient overexpression of ethylene-induced MdNAC7, a NAC TF, in apple fruit promoted softening by decreasing cellulose content and increasing water-soluble pectin content in fruit. MdNAC7 interacted with MdWRKY31 to form a protein complex, and their interaction decreased the transcriptional repression of MdWRKY31 on MdXTH2. Furthermore, MdNAC7 does not directly regulate MdXTH2 expression, but the protein complex formed with MdWRKY31 hinders MdWRKY31 from binding to the promoter of MdXTH2. Our findings underscore the significance of the regulatory complex NAC7-WRKY31 in ethylene-responsive signalling, connecting the ethylene signal to XTH2 expression to promote fruit softening. This sheds light on the intricate mechanisms governing apple fruit firmness and opens avenues for enhancing fruit quality and reducing economic losses associated with softening.

Genome-wide survey and expression analysis of JAZ genes in watermelon (Citrullus lanatus)

BACKGROUND JAZ: (Jasmonate ZIM-domain) genes play important roles in plant growth and JA signaling pathway which is correlated with fruit ripening process. However, there have been few reports on the genome-wide identification of JAZ genes in watermelon and its relationship with fruit ripening. METHODS AND RESULTS: In this study, bioinformatics approaches were employed to identify ClaJAZ genes of watermelon at the genome-wide levels. Further exploration delved into the phylogenetic relationships, chromosomal mappings, promoter dynamics, expression, and architectural features of the JAZ genes. The results showed that a total of 9 ClaJAZ genes unevenly distributed across six chromosomes were identified in the watermelon genome, and they all have conserved Jas and TIFY domains. These JAZ genes were divided into four distinct groups with five genes involved in inter-chromosomal tandem duplication events, and members of the same subgroup exhibited a high degree of similarity in their gene structure and protein motif patterns. Analysis of the promoter regions of the ClaJAZ genes indicated the presence of cis-acting elements associated with hormonal responses, stress, and developmental processes. Gene expression analysis through real-time quantitative PCR (qRT-PCR) showed that there were spatiotemporal differences in the expression of ClaJAZ genes at various stages of fruit development. Among them, ClaJAZ7 has the highest level of transcriptional expression and showed strong promoter activity. CONCLUSIONS: This study conducted a comprehensive analysis of the ClaJAZ genes and provided insights into the role of ClaJAZ in the development and ripening of watermelon fruit.

The abscisic acid-responsive transcriptional regulatory module CsERF110-CsERF53 orchestrates citrus fruit coloration

Carotenoid biosynthesis is closely associated with abscisic acid (ABA) during the ripening process of non-climacteric fruits, but the regulatory mechanism that links ABA signaling to carotenoid metabolism remains largely unclear. Here, we identified two master regulators of ABA-mediated citrus fruit coloration, CsERF110 and CsERF53, which activate the expression of carotenoid metabolism genes (CsGGPPS, CsPSY, CsPDS, CsCRTISO, CsLCYB2, CsLCYE, CsHYD, CsZEP, and CsNCED2) to facilitate carotenoid accumulation. Further investigations showed that CsERF110 not only activates the expression of CsERF53 by binding to its promoter but also interacts with CsERF53 to form the transcriptional regulatory module CsERF110-CsERF53. We also discovered a positive feedback regulatory loop between the ABA signal and carotenoid metabolism regulated by the transcriptional regulatory module CsERF110-CsERF53. Our results reveal that the CsERF110-CsERF53 module responds to ABA signaling, thereby orchestrating citrus fruit coloration. Considering the importance of carotenoid content for citrus and many other carotenoid-rich crops, the revelation of molecular mechanisms that underlie ABA-mediated carotenoid biosynthesis in plants will facilitate the development of transgenic/gene-editing approaches, further contributing to improving the quality of citrus and other carotenoid-rich crops.

Histone deacetylase SlHDA7 impacts fruit ripening and shelf life in tomato

Fruit ripening depends on the accurate control of ripening-related genes expression, with histone deacetylases (HDACs) playing crucial roles in transcriptional regulation. However, the functions of HDACs in fruit maturation remain largely unexplored. Here, we show that SlHDA7 acts as a suppressor of fruit ripening and functions as an H4ac HDAC in tomato. Deletion of SlHDA7 accelerated fruit ripening, while overexpression of SlHDA7 delayed the maturation process. Additionally, ethylene production and carotenoid biosynthesis significantly increased in slhda7 mutant fruits but decreased in SlHDA7-overexpressing fruits. Furthermore, SlHDA7 repress the expression of ethylene production and signaling, carotenoid metabolism, cell wall modification, and transcriptional regulation-related genes. RT-qPCR and ChIP-qPCR analyses indicated that SlHDA7 may deacetylate H4ac, leading to reduced transcript levels of ACO1, GGPPS2, Z-ISO, EXP1, and XYL1 mRNA, consequently suppressing fruit ripening. Moreover, SlHDA7 suppresses fruit ripening by targeting specific ripening-associated transcription factors (TFs) like RIN, FUL1, and ERF.E1, ultimately leading to delayed ripening and prolonged fruit shelf life. In summary, our findings indicate that SlHDA7 negatively modulates tomato fruit maturation by adjusting H4ac levels of these ripening-associated genes and key TFs.

Effect of histone modifications on fruit ripening

Histone modifications are canonical epigenetic modifications mediating plant growth and development. Specially, histone modifications play important regulatory roles in plant fruit ripening, directly affecting fruit color changes, soluble sugar accumulation, and fruit softening. In this review, we focus on the effects of histone acetylation and methylation during fruit ripening. In particular, histone acetylation at H3 and H4 accelerates fruit ripening, whereas removal of histone acetylation via histone deacetylases (HDACs) inhibits or delays ripening by regulating the expression of carotenoid and anthocyanin production, glycometabolism, cell wall degradation, ethylene synthesis and signalling, and cell expansin-related genes. In addition, histone methylation is also involved in fruit ripening, in which the emergence of H3K27me3 modifications represses fruit ripening and H3K4me3 modifications promote fruit ripening by affecting multiple ripening-related pathways. However, the relationship between other histone modifications and fruit ripening is currently unclear. Here, we point out that accurate and comprehensive studies concerning the regulatory mechanism of histone modifications in fruit ripening are needed to facilitate the design of high-quality and high-yield fruit.

From non-coding RNAs to histone modification: The epigenetic mechanisms in tomato fruit ripening and quality regulation

Ripening is one of the most important stages of fruit development and determines the fruit quality. Various factors play a role in this process, with epigenetic mechanisms emerging as important players. Epigenetic regulation encompasses DNA methylation, histone modifications and variants, chromatin remodeling, RNA modifications, and non-coding RNAs. Over the past decade, studies using tomato as a model have made considerable progress in understanding the impact of epigenetic regulation on fleshy fruit ripening and quality. In this paper, we provide an overview of recent advancements in the epigenetic regulation of tomato fruit ripening and quality regulation, focusing on three main mechanisms: DNA/RNA modifications, non-coding RNAs, and histone modifications. Furthermore, we highlight the unresolved issues and challenges within this research field, offering perspectives for future investigations to drive agricultural innovation.

Inference of the genetic basis of fruit texture in highbush blueberries using genome-wide association analyses

The global production and consumption of blueberry (Vaccinium spp.), a specialty crop known for its abundant bioactive and antioxidant compounds, has more than doubled over the last decade. To hold this momentum, plant breeders have begun to use quantitative genetics and molecular breeding to guide their decisions and select new cultivars that are improved for fruit quality. In this study, we leveraged our inferences on the genetic basis of fruit texture and chemical components by surveying large breeding populations from northern highbush blueberries (NHBs) and southern highbush blueberries (SHBs), the two dominant cultivated blueberries. After evaluating 1065 NHB genotypes planted at the Oregon State University, and 992 SHB genotypes maintained at the University of Florida for 17 texture-related traits, evaluated over multiple years, our contributions consist of the following: (i) we drew attention to differences between NHB and SHB materials and showed that both blueberry types can be differentiated using texture traits; (ii) we computed genetic parameters and shed light on the genetic architecture of important texture attributes, indicating that most traits had a complex nature with low to moderate heritability; (iii) using molecular breeding, we emphasized that prediction could be performed across populations; and finally (iv) the genomic association analyses pinpointed some genomic regions harboring potential candidate genes for texture that could be used for further validation studies. Altogether, the methods and approaches used here can guide future breeding efforts focused on maximizing texture improvements in blueberries.

Fruit ripening and postharvest changes in very early-harvested tomatoes

It is well known that if a fruit is harvested extremely early its development and function are interrupted, and it may never attain full maturity and optimal quality. Reports revealing insights regarding the alterations of maturation, ripening and postharvest quality in very early picked fruits are rare. We examined the effects of early harvesting on tomatoes by characterizing different accessions at the molecular, physiological, and biochemical levels. We found that even very early-harvested fruits could achieve postharvest maturation and ripening though with some defects in pigment and cuticle formation, and seeds from very early-harvested fruits could still germinate and develop as normal and healthy plants. One critical regulator of tomato cuticle integrity, SlCER1-2, was shown to contribute to cuticle defects in very early-harvested fruits. Very early fruit harvest still allowing ripening and seed development indicate that the genetic and physiological programs of later maturation and ripening are set into motion early in fruit development and are not dependent on complete fruit expansion nor attachment to the plant.

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.

Ripening and rot: How ripening processes influence disease susceptibility in fleshy fruits

Fleshy fruits become more susceptible to pathogen infection when they ripen; for example, changes in cell wall properties related to softening make it easier for pathogens to infect fruits. The need for high-quality fruit has driven extensive research on improving pathogen resistance in important fruit crops such as tomato (Solanum lycopersicum). In this review, we summarize current progress in understanding how changes in fruit properties during ripening affect infection by pathogens. These changes affect physical barriers that limit pathogen entry, such as the fruit epidermis and its cuticle, along with other defenses that limit pathogen growth, such as preformed and induced defense compounds. The plant immune system also protects ripening fruit by recognizing pathogens and initiating defense responses involving reactive oxygen species production, mitogen-activated protein kinase signaling cascades, and jasmonic acid, salicylic acid, ethylene, and abscisic acid signaling. These phytohormones regulate an intricate web of transcription factors (TFs) that activate resistance mechanisms, including the expression of pathogenesis-related genes. In tomato, ripening regulators, such as RIPENING INHIBITOR and NON_RIPENING, not only regulate ripening but also influence fruit defenses against pathogens. Moreover, members of the ETHYLENE RESPONSE FACTOR (ERF) family play pivotal and distinct roles in ripening and defense, with different members being regulated by different phytohormones. We also discuss the interaction of ripening-related and defense-related TFs with the Mediator transcription complex. As the ripening processes in climacteric and non-climacteric fruits share many similarities, these processes have broad applications across fruiting crops. Further research on the individual contributions of ERFs and other TFs will inform efforts to diminish disease susceptibility in ripe fruit, satisfy the growing demand for high-quality fruit and decrease food waste and related economic losses.

Histone H3K27 demethylase SlJMJ3 modulates fruit ripening in tomato

The histone lysine (K) demethylase 4 (KDM4/JHDM3) subfamily of jumonji domain-containing demethylases (JMJs) has been implicated in various aspects of plant development. However, their involvement in regulating the ripening of fleshy fruits remains unclear. In this study, we identified SlJMJ3, a member of the KDM4/JHDM3 family, as an H3K27me3 demethylase in tomato (Solanum lycopersicum) that plays an important role in fruit ripening regulation. Overexpression of SlJMJ3 leads to accelerated fruit ripening, whereas loss of function of SlJMJ3 delays this process. Furthermore, we determined that SlJMJ3 exerts its regulatory function by modulating the expression of multiple ripening-related genes involved in ethylene biosynthesis and response, carotenoid metabolism, cell wall modification, transcriptional control, and DNA methylation modification. SlJMJ3 binds directly to the promoters of ripening-related genes harboring the CTCTGYTY motif and activates their expression. Additionally, SlJMJ3 reduces the levels of H3K27me3 at its target genes, thereby upregulating their expression. In summary, our findings highlight the role of SlJMJ3 in the regulation of fruit ripening in tomato. By removing the methyl group from trimethylated histone H3 lysine 27 at ripening-related genes, SlJMJ3 acts as an epigenetic regulator that orchestrates the complex molecular processes underlying fruit ripening.

Plant responses to abiotic stress regulated by histone acetylation

In eukaryotes, histone acetylation and deacetylation play an important role in the regulation of gene expression. Histone acetylation levels are reversibly regulated by histone acetyltransferases (HATs) and histone deacetylases (HDACs). Increasing evidence highlights histone acetylation plays essential roles in the regulation of gene expression in plant response to environmental stress. In this review, we discussed the recent advance of histone acetylation in the regulation of abiotic stress responses including temperature, light, salt and drought stress. This information will contribute to our understanding of how plants adapt to environmental changes. As the mechanisms of epigenetic regulation are conserved in many plants, research in this field has potential applications in improvement of agricultural productivity.

Genome-wide identification and expression analysis of histone deacetylase and histone acetyltransferase genes in response to drought in poplars

BACKGROUND

Histone deacetylases (HDACs) and histone acetyltransferases (HATs) are involved in plant growth and development as well as in response to environmental changes, by dynamically regulating gene acetylation levels. Although there have been numerous reports on the identification and function of HDAC and HAT in herbaceous plants, there are fewer report related genes in woody plants under drought stress.

RESULTS

In this study, we performed a genome-wide analysis of the HDAC and HAT families in Populus trichocarpa, including phylogenetic analysis, gene structure, conserved domains, and expression analysis. A total of 16 PtrHDACs and 12 PtrHATs were identified in P. trichocarpa genome. Analysis of cis-elements in the promoters of PtrHDACs and PtrHATs revealed that both gene families could respond to a variety of environmental signals, including hormones and drought. Furthermore, real time quantitative PCR indicated that PtrHDA906 and PtrHAG3 were significantly responsive to drought. PtrHDA906, PtrHAC1, PtrHAC3, PtrHAG2, PtrHAG6 and PtrHAF1 consistently responded to abscisic acid, methyl jasmonate and salicylic acid under drought conditions.

CONCLUSIONS

Our study demonstrates that PtrHDACs and PtrHATs may respond to drought through hormone signaling pathways, which helps to reveal the hub of acetylation modification in hormone regulation of abiotic stress.

Integrative Analysis of Metabolome and Transcriptome of Carotenoid Biosynthesis Reveals the Mechanism of Fruit Color Change in Tomato (Solanum lycopersicum)

Tomato fruit ripening is accompanied by carotenoid accumulation and color changes. To elucidate the regulatory mechanisms underlying carotenoid synthesis during fruit ripening, a combined transcriptomic and metabolomic analysis was conducted on red-fruited tomato (WP190) and orange-fruited tomato (ZH108). A total of twenty-nine (29) different carotenoid compounds were identified in tomato fruits at six different stages. The abundance of the majority of the carotenoids was enhanced significantly with fruit ripening, with higher levels of lycopene; (E/Z)-lycopene; and α-, β- and γ-carotenoids detected in the fruits of WP190 at 50 and 60 days post anthesis (DPA). Transcriptome analysis revealed that the fruits of two varieties exhibited the highest number of differentially expressed genes (DEGs) at 50 DPA, and a module of co-expressed genes related to the fruit carotenoid content was established by WGCNA. qRT-PCR analysis validated the transcriptome result with a significantly elevated transcript level of lycopene biosynthesis genes (including SlPSY2, SlZCIS, SlPDS, SlZDS and SlCRTSO2) observed in WP190 at 50 DPA in comparison to ZH108. In addition, during the ripening process, the expression of ethylene biosynthesis (SlACSs and SlACOs) and signaling (SlEIN3 and SlERF1) genes was also increased, and these mechanisms may regulate carotenoid accumulation and fruit ripening in tomato. Differential expression of several key genes in the fruit of two tomato varieties at different stages regulates the accumulation of carotenoids and leads to differences in color between the two varieties of tomato. The results of this study provide a comprehensive understanding of carotenoid accumulation and ethylene biosynthesis and signal transduction pathway regulatory mechanisms during tomato fruit development.

A transcriptional cascade mediated by two APETALA2 family members orchestrates carotenoid biosynthesis in tomato

Carotenoids are important nutrients for human health that must be obtained from plants since they cannot be biosynthesized by the human body. Dissecting the regulatory mechanism of carotenoid metabolism in plants represents the first step toward manipulating carotenoid contents in plants by molecular design breeding. In this study, we determined that SlAP2c, an APETALA2 (AP2) family member, acts as a transcriptional repressor to regulate carotenoid biosynthesis in tomato (Solanum lycopersicum). Knockout of SlAP2c in both the "MicroTom" and "Ailsa Craig" backgrounds resulted in greater lycopene accumulation, whereas overexpression of this gene led to orange-ripe fruit with significantly lower lycopene contents than the wild type. We established that SlAP2c represses the expression of genes involved in lycopene biosynthesis by directly binding to the cis-elements in their promoters. Moreover, SlAP2c relies on its EAR motif to recruit the co-repressors TOPLESS (TPL)2/4 and forms a complex with histone deacetylase (had)1/3, thereby reducing the histone acetylation levels of lycopene biosynthesis genes. Furthermore, SlAP2a, a homolog of SlAP2c, acts upstream of SlAP2c and alleviates the SlAP2c-induced repression of lycopene biosynthesis genes by inhibiting SlAP2c transcription during fruit ripening. Therefore, we identified a transcriptional cascade mediated by AP2 family members that regulates lycopene biosynthesis during fruit ripening in tomato, laying the foundation for the manipulation of carotenoid metabolism in plants.

Integrative analysis of the methylome and transcriptome of tomato fruit (Solanum lycopersicum L.) induced by postharvest handling

Tomato fruit ripening is triggered by the demethylation of key genes, which alters their transcriptional levels thereby initiating and propagating a cascade of physiological events. What is unknown is how these processes are altered when fruit are ripened using postharvest practices to extend shelf-life, as these practices often reduce fruit quality. To address this, postharvest handling-induced changes in the fruit DNA methylome and transcriptome, and how they correlate with ripening speed, and ripening indicators such as ethylene, abscisic acid, and carotenoids, were assessed. This study comprehensively connected changes in physiological events with dynamic molecular changes. Ripening fruit that reached 'Turning' (T) after dark storage at 20°C, 12.5°C, or 5°C chilling (followed by 20°C rewarming) were compared to fresh-harvest fruit 'FHT'. Fruit stored at 12.5°C had the biggest epigenetic marks and alterations in gene expression, exceeding changes induced by postharvest chilling. Fruit physiological and chronological age were uncoupled at 12.5°C, as the time-to-ripening was the longest. Fruit ripening to Turning at 12.5°C was not climacteric; there was no respiratory or ethylene burst, rather, fruit were high in abscisic acid. Clear differentiation between postharvest-ripened and 'FHT' was evident in the methylome and transcriptome. Higher expression of photosynthetic genes and chlorophyll levels in 'FHT' fruit pointed to light as influencing the molecular changes in fruit ripening. Finally, correlative analyses of the -omics data putatively identified genes regulated by DNA methylation. Collectively, these data improve our interpretation of how tomato fruit ripening patterns are altered by postharvest practices, and long-term are expected to help improve fruit quality.

Comparative population genomics reveals convergent and divergent selection in the apricot-peach-plum-mei complex

The economically significant genus Prunus includes fruit and nut crops that have been domesticated for shared and specific agronomic traits; however, the genomic signals of convergent and divergent selection have not been elucidated. In this study, we aimed to detect genomic signatures of convergent and divergent selection by conducting comparative population genomic analyses of the apricot-peach-plum-mei (APPM) complex, utilizing a haplotype-resolved telomere-to-telomere (T2T) genome assembly and population resequencing data. The haplotype-resolved T2T reference genome for the plum cultivar was assembled through HiFi and Hi-C reads, resulting in two haplotypes 251.25 and 251.29 Mb in size, respectively. Comparative genomics reveals a chromosomal translocation of ~1.17 Mb in the apricot genomes compared with peach, plum, and mei. Notably, the translocation involves the D locus, significantly impacting titratable acidity (TA), pH, and sugar content. Population genetic analysis detected substantial gene flow between plum and apricot, with introgression regions enriched in post-embryonic development and pollen germination processes. Comparative population genetic analyses revealed convergent selection for stress tolerance, flower development, and fruit ripening, along with divergent selection shaping specific crop, such as somatic embryogenesis in plum, pollen germination in mei, and hormone regulation in peach. Notably, selective sweeps on chromosome 7 coincide with a chromosomal collinearity from the comparative genomics, impacting key fruit-softening genes such as PG, regulated by ERF and RMA1H1. Overall, this study provides insights into the genetic diversity, evolutionary history, and domestication of the APPM complex, offering valuable implications for genetic studies and breeding programs of Prunus crops.

Bifunctional transcription factors SlERF.H5 and H7 activate cell wall and repress gibberellin biosynthesis genes in tomato via a conserved motif

The plant cell wall is a dynamic structure that plays an essential role in development, but the mechanism regulating cell wall formation remains poorly understood. We demonstrate that two transcription factors, SlERF.H5 and SlERF.H7, control cell wall formation and tomato fruit firmness in an additive manner. Knockout of SlERF.H5, SlERF.H7, or both genes decreased cell wall thickness, firmness, and cellulose contents in fruits during early development, especially in double-knockout lines. Overexpressing either gene resulted in thicker cell walls and greater fruit firmness with elevated cellulose levels in fruits but severely dwarf plants with lower gibberellin contents. We further identified that SlERF.H5 and SlERF.H7 activate the cellulose biosynthesis gene SlCESA3 but repress the gibberellin biosynthesis gene GA20ox1. Moreover, we identified a conserved LPL motif in these ERFs responsible for their activities as transcriptional activators and repressors, providing insight into how bifunctional transcription factors modulate distinct developmental processes.

ELONGATED HYPOCOTYL 5a modulates FLOWERING LOCUS T2 and gibberellin levels to control dormancy and bud break in poplar

Photoperiod is a crucial environmental cue for phenological responses, including growth cessation and winter dormancy in perennial woody plants. Two regulatory modules within the photoperiod pathway explain bud dormancy induction in poplar (Populus spp.): the circadian oscillator LATE ELONGATED HYPOCOTYL 2 (LHY2) and GIGANTEA-like genes (GIs) both regulate the key target for winter dormancy induction FLOWERING LOCUS T2 (FT2). However, modification of LHY2 and GIs cannot completely prevent growth cessation and bud set under short-day (SD) conditions, indicating that additional regulatory modules are likely involved. We identified PtoHY5a, an orthologs of the photomorphogenesis regulatory factor ELONGATED HYPOCOTYL 5 (HY5) in poplar (Populus tomentosa), that directly activates PtoFT2 expression and represses the circadian oscillation of LHY2, indirectly activating PtoFT2 expression. Thus, PtoHY5a suppresses SD-induced growth cessation and bud set. Accordingly, PtoHY5a knockout facilitates dormancy induction. PtoHY5a also inhibits bud-break in poplar by controlling gibberellic acid (GA) levels in apical buds. Additionally, PtoHY5a regulates the photoperiodic control of seasonal growth downstream of phytochrome PHYB2. Thus, PtoHY5a modulates seasonal growth in poplar by regulating the PtoPHYB2-PtoHY5a-PtoFT2 module to determine the onset of winter dormancy, and by fine-tuning GA levels to control bud-break.

iJAZ-based approach to engineer lepidopteran pest resistance in multiple crop species

The fall armyworm (FAW) poses a significant threat to global crop production. Here we showed that overexpression of jasmonate ZIM-domain (JAZ) protein GhJAZ24 confers resistance to cotton bollworm and FAW, while also causing sterility in transgenic cotton by recruiting TOPLESS and histone deacetylase 6. We identified the NGR motif of GhJAZ24 that recognizes and binds the aminopeptidase N receptor, enabling GhJAZ24 to enter cells and disrupt histone deacetylase 3, leading to cell death. To overcome plant sterility associated with GhJAZ24 overexpression, we developed iJAZ (i, induced), an approach involving damage-induced expression and a switch from intracellular to extracellular localization of GhJAZ24. iJAZ transgenic cotton maintained fertility and showed insecticidal activity against cotton bollworm and FAW. In addition, iJAZ transgenic rice, maize and tobacco plants showed insecticidal activity against their lepidopteran pests, resulting in an iJAZ-based approach for generating alternative insecticidal proteins with distinctive mechanisms of action, thus holding immense potential for future crop engineering.

Pyrus betulaefolia ERF3 interacts with HsfC1a to coordinately regulate aquaporin PIP1;4 and NCED4 for drought tolerance

Environmental disasters like drought reduce agricultural output and plant growth. Redox management significantly affects plant stress responses. An earlier study found that PbPIP1;4 transports H2O2 and promotes H2O2 downstream cascade signaling to restore redox equilibrium. However, this regulatory mechanism requires additional investigation. In this search, the AP2 domain-containing transcription factor was isolated by screening Y1H from the wild pear (Pyrus betulaefolia) cDNA library, named PbERF3. The overexpression of PbERF3 in pear callus and Arabidopsis enhanced plant resistance to drought and re-established redox balance. The transcripts of the NCEDs gene were upregulated under drought stress. The drought stress-related abscisic acid (ABA) signaling pathway modulates PbERF3. PbERF3 silencing lowered drought tolerance. Furthermore, yeast 2-hybrid, luciferase, bimolecular fluorescence complementation, and co-immunoprecipitation assays verified that PbERF3 physically interacted with PbHsfC1a. The PbERF3-PbHsfC1a heterodimer coordinately bound to PbPIP1;4 and PbNCED4 promoter, therefore activating both the H2O2 and the ABA signaling pathway. This work revealed a novel PbERF3-PbHsfC1a-PbNCED4-PbPIP1;4 regulatory module, in which PbERF3 interacts with PbHsfC1a to trigger the expression of target genes. This module establishes an interaction between the H2O2 signaling component PbPIP1;4 and the ABA pathways component PbNCED4, enabling a response to drought.

Promoter variations of ClERF1 gene determines flesh firmness in watermelon

BACKGROUND

Flesh firmness is a critical factor that influences fruit storability, shelf-life and consumer's preference as well. However, less is known about the key genetic factors that are associated with flesh firmness in fresh fruits like watermelon.

RESULTS

In this study, through bulk segregant analysis (BSA-seq), we identified a quantitative trait locus (QTL) that influenced variations in flesh firmness among recombinant inbred lines (RIL) developed from cross between the Citrullus mucosospermus accession ZJU152 with hard-flesh and Citrullus lanatus accession ZJU163 with soft-flesh. Fine mapping and sequence variations analyses revealed that ethylene-responsive factor 1 (ClERF1) was the most likely candidate gene for watermelon flesh firmness. Furthermore, several variations existed in the promoter region between ClERF1 of two parents, and significantly higher expressions of ClERF1 were found in hard-flesh ZJU152 compared with soft-flesh ZJU163 at key developmental stages. DUAL-LUC and GUS assays suggested much stronger promoter activity in ZJU152 over ZJU163. In addition, the kompetitive allele-specific PCR (KASP) genotyping datasets of RIL populations and germplasm accessions further supported ClERF1 as a possible candidate gene for fruit flesh firmness variability and the hard-flesh genotype might only exist in wild species C. mucosospermus. Through yeast one-hybrid (Y1H) and dual luciferase assay, we found that ClERF1 could directly bind to the promoters of auxin-responsive protein (ClAux/IAA) and exostosin family protein (ClEXT) and positively regulated their expressions influencing fruit ripening and cell wall biosynthesis.

CONCLUSIONS

Our results indicate that ClERF1 encoding an ethylene-responsive factor 1 is associated with flesh firmness in watermelon and provide mechanistic insight into the regulation of flesh firmness, and the ClERF1 gene is potentially applicable to the molecular improvement of fruit-flesh firmness by design breeding.

A distal enhancer guides the negative selection of toxic glycoalkaloids during tomato domestication

Steroidal glycoalkaloids (SGAs) are major plant defense metabolites against pests, while they are considered poisonous in food. The genetic basis that guides negative selection of SGAs production during tomato domestication remains poorly understood. Here, we identify a distal enhancer, GAME Enhancer 1 (GE1), as the key regulator of SGAs metabolism in tomato. GE1 recruits MYC2-GAME9 transcriptional complex to regulate the expression of GAME cluster genes via the formation of chromatin loops located in the neighboring DNA region. A naturally occurring GE176 allelic variant is found to be more active in stimulating GAME expression. We show that the weaker GE1 allele has been the main driver for selecting reduced SGAs levels during tomato domestication. Unravelling the "TFs-Enhancer-Promoter" regulatory mechanism operating in SGAs metabolism opens unprecedented prospects for SGAs manipulation in Solanaceae via precision breeding strategies.

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.

Ethylene-MPK8-ERF.C1-PR module confers resistance against Botrytis cinerea in tomato fruit without compromising ripening

The plant hormone ethylene plays a critical role in fruit defense against Botrytis cinerea attack, but the underlying mechanisms remain poorly understood. Here, we showed that ethylene response factor SlERF.C1 acts as a key regulator to trigger the ethylene-mediated defense against B. cinerea in tomato fruits without compromising ripening. Knockout of SlERF.C1 increased fruit susceptibility to B. cinerea with no effect on ripening process, while overexpression enhanced resistance. RNA-Seq, transactivation assays, EMSA and ChIP-qPCR results indicated that SlERF.C1 activated the transcription of PR genes by binding to their promoters. Moreover, SlERF.C1 interacted with the mitogen-activated protein kinase SlMPK8 which allowed SlMPK8 to phosphorylate SlERF.C1 at the Ser174 residue and increases its transcriptional activity. Knocking out of SlMPK8 increased fruit susceptibility to B. cinerea, whereas overexpression enhanced resistance without affecting ripening. Furthermore, genetic crosses between SlMPK8-KO and SlERF.C1-OE lines reduced the resistance to B. cinerea attack in SlERF.C1-OE fruits. In addition, B. cinerea infection induced ethylene production which in turn triggered SlMPK8 transcription and enhanced the phosphorylation of SlERF.C1. Overall, our findings reveal the regulatory mechanism of the 'Ethylene-MPK8-ERF.C1-PR' module in resistance against B. cinerea and provide new insight into the manipulation of gray mold disease in fruits.

The tomato EAR-motif repressor, SlERF36, accelerates growth transitions and reduces plant life cycle by regulating GA levels and responses

Faster vegetative growth and early maturity/harvest reduce plant life cycle time and are important agricultural traits facilitating early crop rotation. GA is a key hormone governing developmental transitions that determine growth speed in plants. An EAR-motif repressor, SlERF36 that regulates various growth transitions, partly through regulation of the GA pathway and GA levels, was identified in tomato. Suppression of SlERF36 delayed germination, slowed down organ growth and delayed the onset of flowering time, fruit harvest and whole-plant senescence by 10-15 days. Its over-expression promoted faster growth by accelerating all these transitions besides increasing organ expansion and plant height substantially. The plant life cycle and fruit harvest were completed 20-30 days earlier than control without affecting yield, in glasshouse as well as net-house conditions, across seasons and generations. These changes in life cycle were associated with reciprocal changes in expression of GA pathway genes and basal GA levels between suppression and over-expression lines. SlERF36 interacted with the promoters of two GA2 oxidase genes, SlGA2ox3 and SlGA2ox4, and the DELLA gene, SlDELLA, reducing their transcription and causing a 3-5-fold increase in basal GA3/GA4 levels. Its suppression increased SlGA2ox3/4 transcript levels and reduced GA3/GA4 levels by 30%-50%. SlERF36 is conserved across families making it an important candidate in agricultural and horticultural crops for manipulation of plant growth and developmental transitions to reduce life cycles for faster harvest.

Ethylene-responsive VviERF003 modulates glycosylated monoterpenoid synthesis by upregulating VviGT14 in grapes

Terpenoids are important contributors to the aroma of grapes and wines. Grapes contain terpenoids in both volatile free form and non-volatile glycosidic form, with the latter being more abundant. Glycosylated terpenoids are deemed as latent aromatic potentials for their essential role in adding to the flowery and fruity bouquet of wines. However, the transcriptional regulatory mechanism underlying glycosylated terpenoid biosynthesis remains poorly understood. Our prior study identified an AP2/ERF transcription factor, VviERF003, through DNA pull-down screening using the promoter of terpenoid glycosyltransferase VviGT14 gene. This study demonstrated that both genes were co-expressed and synchronized with the accumulation of glycosylated monoterpenoids during grape maturation. VviERF003 can bind to the VviGT14 promoter and promote its activity according to yeast one-hybrid and dual-luciferase assays. VviERF003 upregulated VviGT14 expression in vivo, leading to increased production of glycosylated monoterpenoids based on the evidence from overexpression or RNA interference in leaves, berry skins, and calli of grapes, as well as tomato fruits. Additionally, VviERF003 and VviGT14 expressions and glycosylated monoterpenoid levels were induced by ethylene in grapes. The findings suggest that VviERF003 is ethylene-responsive and stimulates glycosylated monoterpenoid biosynthesis through upregulating VviGT14 expression.

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.