Comprehensive Analysis of ABA Effects on Ethylene Biosynthesis and Signaling during Tomato Fruit Ripening

Mechanism of abscisic acid in promoting softening of postharvest 'Docteur Jules Guyot' pear (Pyrus communis L.)

Abscisic acid (ABA) is a key hormone in plant growth and development, playing a central role in responses to various biotic and abiotic stresses as well as in fruit ripening. The present study examined the impact of ABA and nordihydroguaiaretic acid (NDGA) on various postharvest 'Docteur Jules Guyot' pear fruit characteristics, including firmness, pectinase activity, pectin content, volatile aromatic substances, and the expression of correlated genes. The results showed that ABA quickly reduced fruit firmness, increasing the activity of pectin degradation-related enzymes. The contents of water-soluble pectin (WSP) and ionic-soluble pectin (ISP) increased, and covalent binding pectin (CBP) decreased under ABA treatment. Among the detected volatile aromatic substances, the highest-level substance of the fruit was ester, and the ABA treatment significantly promoted the amount of ester substances. The cell wall disassembly-related genes PcPME3, PcPG1, PcPG2, PcPL, PcARF2, and PcGAL1, as well as ABA biosynthesis-related genes PcNCED1 and PcNCED2, were also significantly induced by ABA. Conversely, all these genes were repressed in the NDGA treatment group. Therefore, it was speculated that ABA may promote the softening of postharvest European pear fruit by affecting the activity of pectin degradation enzymes in fruit cell walls.

Abscisic acid and ethylene coordinating fruit ripening under abiotic stress

Fleshy fruit metabolism is intricately influenced by environmental changes, yet the hormonal regulations underlying these responses remain poorly elucidated. ABA and ethylene, pivotal in stress responses across plant vegetative tissues, play crucial roles in triggering fleshy fruit ripening. Their actions are intricately governed by complex mechanisms, influencing key aspects such as nutraceutical compound accumulation, sugar content, and softening parameters. Both hormones are essential orchestrators of significant alterations in fruit development in response to stressors like drought, salt, and temperature fluctuations. These alterations encompass colour development, sugar accumulation, injury mitigation, and changes in cell-wall degradation and ripening progression. This review provides a comprehensive overview of recent research progress on the roles of ABA and ethylene in responding to drought, salt, and temperature stress, as well as the molecular mechanisms controlling ripening in environmental cues. Additionally, we propose further studies aimed at genetic manipulation of ABA and ethylene signalling, offering potential strategies to enhance fleshy fruit resilience in the face of future climate change scenarios.

Identification of two postharvest ripening regulatory models in kiwifruit: based on plant hormones, physiology, and transcriptome analysis

Kiwifruit (Actinidia spp.), celebrated for its unique flavor and rich nutritional content, is a globally popular fruit. This fruit requires post-harvest ripening before consumption. However, the unpredictable ripening pace significantly impacts consumer acceptance and sales, thereby hindering the commercial growth of kiwifruit. To address this, understanding the key molecular mechanisms and metabolites governing postharvest ripening and senescence could offer valuable insights for developing storage strategies and breeding techniques in yellow-fleshed kiwifruits. We constructed two models that integrated these findings with existing theories. The first model suggests that, unlike the T6P-sucrose regulatory mechanism observed in plant leaves, the separation of harvested kiwifruit from the mother plant leads to an insufficient supply of T6P, which activates the SnRK1 kinase. This, in turn, inhibits the TOR kinase signaling pathway, regulating starch metabolism. The T6P-SnRK1-TOR-starch metabolism pathway plays a regulatory role during postharvest ripening, limiting excessive starch degradation that could accelerate aging and decay in yellow-fleshed kiwifruit. The second model highlights the role of abscisic acid (ABA), cytokinins (CKs), and ethylene in regulating the process, inducing the activation of ERFs and cell wall-degrading enzymes, promoting fruit postharvest softening. These findings indicate that at least two models, the T6P-SnRK1-TOR-starch metabolism model and the ABA-CKs-ethylene-cell wall degradation model, regulate postharvest fruit ripening, offering new insights into the artificial regulation of yellow-fleshed kiwifruit ripening speed.

From Regulation to Application: The Role of Abscisic Acid in Seed and Fruit Development and Agronomic Production Strategies

Abscisic acid (ABA) is a crucial plant hormone that plays a decisive role in regulating seed and fruit development and is becoming increasingly important in agricultural applications. This article delves into ABA's regulatory functions in plant growth, particularly during the stages of seed and fruit development. In the seed phase, elevated ABA levels help maintain seed dormancy, aiding seed survival under unfavorable conditions. During fruit development, ABA regulates pigment synthesis and sugar accumulation, influencing the nutritional value and market quality of the fruit. This article highlights three main strategies for applying ABA in agricultural production: the use of ABA analogs, the development of ABA signal modulators, and breeding techniques based on ABA signaling. ABA analogs can mimic the natural functions of ABA, while ABA signal modulators, including enhancers and inhibitors, are used to finely tune plant responses to ABA, optimizing crop performance under specific growth conditions. Furthermore, breeding strategies based on ABA signaling aim to select crop varieties that effectively utilize ABA pathways through genetic engineering and other technologies. ABA is not only a key regulator of plant growth and development but also holds great potential for modern agricultural practices.

Ethylene and its crosstalk with hormonal pathways in fruit ripening: mechanisms, modulation, and commercial exploitation

Ethylene is an important phytohormone that orchestrates a multitude of physiological and biochemical processes regulating fruit ripening, from early maturation to post-harvest. This review offers a comprehensive analysis of ethylene's multifaceted roles in climacteric fruit ripening, characterized by a pronounced increase in ethylene production and respiration rates. It explores potential genetic and molecular mechanisms underlying ethylene's action, focusing on key transcription factors, biosynthetic pathway genes, and signal transduction elements crucial for the expression of ripening-related genes. The varied sensitivity and dependency of ripening traits on ethylene are elucidated through studies employing genetic mutations and ethylene inhibitors such as AVG and 1-MCP. Additionally, the modulation of ripening traits by ethylene is influenced by its interaction with other phytohormones, including auxins, abscisic acid, gibberellins, jasmonates, brassinosteroids, and salicylic acid. Pre-harvest fruit drop is intricately linked to ethylene, which triggers enzyme activity in the abscission zone, leading to cell wall degradation and fruit detachment. This review also highlights the potential for applying ethylene-related knowledge in commercial contexts to enhance fruit quality, control pre-harvest drop, and extend shelf life. Future research directions are proposed, advocating for the integration of physiological, genetic, biochemical, and transcriptional insights to further elucidate ethylene's role in fruit ripening and its interaction with other hormonal pathways.

Development History, Structure, and Function of ASR (Abscisic Acid-Stress-Ripening) Transcription Factor

Abiotic and biotic stress factors seriously affect plant growth and development. The process of plant response to abiotic stress involves the synergistic action of multiple resistance genes. The ASR (Abscisic acid stress-ripening) gene is a plant-specific transcription factor that plays a central role in regulating plant senescence, fruit ripening, and response to abiotic stress. ASR family members are highly conserved in plant evolution and contain ABA/WBS domains. ASR was first identified and characterized in tomatoes (Solanum lycopersicum L.). Subsequently, the ASR gene has been reported in many plant species, extending from gymnosperms to monocots and dicots, but lacks orthologues in Arabidopsis (Arabidopsis thaliana). The promoter regions of ASR genes in most species contain light-responsive elements, phytohormone-responsive elements, and abiotic stress-responsive elements. In addition, ASR genes can respond to biotic stresses via regulating the expression of defense genes in various plants. This review comprehensively summarizes the evolutionary history, gene and protein structures, and functions of the ASR gene family members in plant responses to salt stress, low temperature stress, pathogen stress, drought stress, and metal ions, which will provide valuable references for breeding high-yielding and stress-resistant plant varieties.

REDUCED CHLOROPLAST COVERAGE proteins are required for plastid proliferation and carotenoid accumulation in tomato

Increasing the amount of cellular space allocated to plastids will lead to increases in the quality and yield of crop plants. However, mechanisms that allocate cellular space to plastids remain poorly understood. To test whether the tomato (Solanum lycopersicum L.) REDUCED CHLOROPLAST COVERAGE (SlREC) gene products serve as central components of the mechanism that allocates cellular space to plastids and contribute to the quality of tomato fruit, we knocked out the 4-member SlREC gene family. We found that slrec mutants accumulated lower levels of chlorophyll in leaves and fruits, accumulated lower levels of carotenoids in flowers and fruits, allocated less cellular space to plastids in leaf mesophyll and fruit pericarp cells, and developed abnormal plastids in flowers and fruits. Fruits produced by slrec mutants initiated ripening later than wild type and produced abnormal levels of ethylene and abscisic acid (ABA). Metabolome and transcriptome analyses of slrec mutant fruits indicated that the SlREC gene products markedly influence plastid-related gene expression, primary and specialized metabolism, and the response to biotic stress. Our findings and previous work with distinct species indicate that REC proteins help allocate cellular space to plastids in diverse species and cell types and, thus, play a central role in allocating cellular space to plastids. Moreover, the SlREC proteins are required for the high-level accumulation of chlorophyll and carotenoids in diverse organs, including fruits, promote the development of plastids and influence fruit ripening by acting both upstream and downstream of ABA biosynthesis in a complex network.

The ethylene response factor gene, ThDRE1A, is involved in abscisic acid- and ethylene-mediated cadmium accumulation in Tamarix hispida

Tamarix hispida is highly tolerant to salt, drought and heavy metal stress and is a potential material for the remediation of cadmium (Cd)-contaminated soil under harsh conditions. In this study, T. hispida growth and chlorophyll content decreased, whereas flavonoid and carotenoid contents increased under long-term Cd stress (25 d). The aboveground components of T. hispida were collected for RNA-seq to investigate the mechanism of Cd accumulation. GO and KEGG enrichment analyses revealed that the differentially expressed genes (DEGs) were significantly enriched in plant hormone-related pathways. Exogenous hormone treatment and determination of Cd2+ levels showed that ethylene (ETH) and abscisic acid (ABA) antagonists regulate Cd accumulation in T. hispida. Twenty-five transcription factors were identified as upstream regulators of hormone-related pathways. ThDRE1A, which was previously identified as an important regulatory factor, was selected for further analysis. The results indicated that ThABAH2.5 and ThACCO3.1 were direct target genes of ThDRE1A. The determination of Cd2+, ABA, and ETH levels indicated that ThDRE1A plays an important role in Cd accumulation through the antagonistic regulation of ABA and ETH. In conclusion, these results reveal the molecular mechanism underlying Cd accumulation in plants and identify candidate genes for further research.

Unveiling the molecular dynamics of low temperature preservation in postharvest lotus seeds: a transcriptomic perspective

BACKGROUND

Postharvest quality deterioration poses a significant challenge to the commercial value of fresh lotus seeds. Low temperature storage is widely employed as the primary method for preserving postharvest lotus seeds during storage and transportation.

RESULTS

This approach effectively extends the storage life of lotus seeds, resulting in distinct physiological changes compared to room temperature storage, including a notable reduction in starch, protein, H2O2, and MDA content. Here, we conducted RNA-sequencing to generate global transcriptome profiles of postharvest lotus seeds stored under room or low temperature conditions. Principal component analysis (PCA) revealed that gene expression in postharvest lotus seeds demonstrated less variability during low temperature storage in comparison to room temperature storage. A total of 14,547 differentially expressed genes (DEGs) associated with various biological processes such as starch and sucrose metabolism, energy metabolism, and plant hormone signaling response were identified. Notably, the expression levels of DEGs involved in ABA signaling were significantly suppressed in contrast to room temperature storage. Additionally, nine weighted gene co-expression network analysis (WGCNA)-based gene molecular modules were identified, providing insights into the co-expression relationship of genes during postharvest storage.

CONCLUSION

Our findings illuminate transcriptional differences in postharvest lotus seeds between room and low temperature storage, offering crucial insights into the molecular mechanisms of low temperature preservation in lotus seeds.

Transcriptomic and metabolomic analyses reveal the importance of ethylene networks in mulberry fruit ripening

Mulberry (Morus alba L.) is a climacteric and highly perishable fruit. Ethylene has been considered to be an important trigger of fruit ripening process. However, the role of ethylene in the mulberry fruit ripening process remains unclear. In this study, we performed a comprehensive analysis of metabolomic and transcriptomic data of mulberry fruit and the physiological changes accompanying the fruit ripening process. Our study revealed that changes in the accumulation of specific metabolites at different stages of fruit development and ripening were closely correlated to transcriptional changes as well as underlying physiological changes and the development of taste biomolecules. The ripening of mulberry fruits was highly associated with the production of endogenous ethylene, and further application of exogenous ethylene assisted the ripening process. Transcriptomic analysis revealed that differential expression of diverse ripening-related genes was involved in sugar metabolism, anthocyanin biosynthesis, and cell wall modification pathways. Network analysis of transcriptomics and metabolomics data revealed that many transcription factors and ripening-related genes were involved, among which ethylene-responsive transcription factor 3 (MaERF3) plays a crucial role in the ripening process. The role of MaERF3 in ripening was experimentally proven in a transient overexpression assay in apples. Our study indicates that ethylene plays a vital role in modulating mulberry fruit ripening. The results provide a basis for guiding the genetic manipulation of mulberry fruits towards sustainable agricultural practices and improve post-harvest management, potentially enhancing the quality and shelf life of mulberry fruits for sustainable agriculture and forestry.

Endophytic Microorganisms in Tomato Roots, Changes in the Structure and Function of the Community at Different Growing Stages

This study analyzed flower bud differentiation and fruiting stages to investigate how the structure of the plant endophytic microbial community in the roots of tomatoes changes with plant senescence. Based on high-throughput sequencing technology, the diversity and relative abundance of endophytic microorganisms (bacteria and fungi) in tomato stems at different growth stages were analyzed. At the same time, based on LEfSe analysis, the differences in endophytic microorganisms in tomato stems at different growth stages were studied. Based on PICRUSt2 function prediction and FUNGuild, we predicted the functions of endophytic bacterial and fungal communities in tomato stems at different growth stages to explore potential microbial functional traits. The results demonstrated that not only different unique bacterial genera but also unique fungal genera could be found colonizing tomato roots at different growth stages. In tomato seedlings, flower bud differentiation, and fruiting stages, the functions of colonizing endophytes in tomato roots could primarily contribute to the promotion of plant growth, stress resistance, and improvement in nutrient cycling, respectively. These results also suggest that different functional endophytes colonize tomato roots at different growth stages.

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.

Ethylene promotes fruit ripening initiation by downregulating photosynthesis, enhancing abscisic acid and suppressing jasmonic acid in blueberry (Vaccinium ashei)

BACKGROUND

Blueberry fruit exhibit atypical climacteric ripening with a non-auto-catalytic increase in ethylene coincident with initiation of ripening. Further, application of ethephon, an ethylene-releasing plant growth regulator, accelerates ripening by increasing the proportion of ripe (blue) fruit as compared to the control treatment. To investigate the mechanistic role of ethylene in regulating blueberry ripening, we performed transcriptome analysis on fruit treated with ethephon, an ethylene-releasing plant growth regulator.

RESULTS

RNA-Sequencing was performed on two sets of rabbiteye blueberry ('Powderblue') fruit: (1) fruit from divergent developmental stages; and (2) fruit treated with ethephon, an ethylene-releasing compound. Differentially expressed genes (DEGs) from divergent developmental stages clustered into nine groups, among which cluster 1 displayed reduction in expression during ripening initiation and was enriched with photosynthesis related genes, while cluster 7 displayed increased expression during ripening and was enriched with aromatic-amino acid family catabolism genes, suggesting stimulation of anthocyanin biosynthesis. More DEGs were apparent at 1 day after ethephon treatment suggesting its early influence during ripening initiation. Overall, a higher number of genes were downregulated in response to ethylene. Many of these overlapped with cluster 1 genes, indicating that ethylene-mediated downregulation of photosynthesis is an important developmental event during the ripening transition. Analyses of DEGs in response to ethylene also indicated interplay among phytohormones. Ethylene positively regulated abscisic acid (ABA), negatively regulated jasmonates (JAs), and influenced auxin (IAA) metabolism and signaling genes. Phytohormone quantification supported these effects of ethylene, indicating coordination of blueberry fruit ripening by ethylene.

CONCLUSION

This study provides insights into the role of ethylene in blueberry fruit ripening. Ethylene initiates blueberry ripening by downregulating photosynthesis-related genes. Also, ethylene regulates phytohormone-metabolism and signaling related genes, increases ABA, and decreases JA concentrations. Together, these results indicate that interplay among multiple phytohormones regulates the progression of ripening, and that ethylene is an important coordinator of such interactions during blueberry fruit ripening.

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.

Gibberellins involved in fruit ripening and softening by mediating multiple hormonal signals in tomato

The phytohormone ethylene is well known for its important role in the ripening of climacteric fruit, such as tomato (Solanum lycopersicum). However, the role and mode of action of other plant hormones in climacteric fruit ripening regulation are not fully understood. Here, we showed that exogenous GA treatment or increasing endogenous gibberellin content by overexpressing the gibberellin synthesis gene SlGA3ox2 specifically in fruit tissues delayed tomato fruit ripening, whereas treatment with the GA biosynthesis inhibitor paclobutrazol (PAC) accelerated fruit ripening. Moreover, exogenous ethylene treatment cannot completely reverse the delayed fruit ripening phenotype. Furthermore, exogenous GA treatment of ethylene signalling mutant Never ripe (Nr) or SlEBF3-overexpressing lines still delayed fruit ripening, suggesting that GA involved in fruit ripening partially depends on ethylene. Transcriptome profiling showed that gibberellin affect the ripening of fruits by modulating the metabolism and signal transduction of multiple plant hormones, such as auxin and abscisic acid, in addition to ethylene. Overall, the results of this study provide new insight into the regulation of gibberellin in fruit ripening through mediating multiple hormone signals.

Recent Advances in Studying the Regulation of Fruit Ripening in Tomato Using Genetic Engineering Approaches

Tomato (Solanum lycopersicum L.) is one of the most commercially essential vegetable crops cultivated worldwide. In addition to the nutritional value, tomato is an excellent model for studying climacteric fruits' ripening processes. Despite this, the available natural pool of genes that allows expanding phenotypic diversity is limited, and the difficulties of crossing using classical selection methods when stacking traits increase proportionally with each additional feature. Modern methods of the genetic engineering of tomatoes have extensive potential applications, such as enhancing the expression of existing gene(s), integrating artificial and heterologous gene(s), pointing changes in target gene sequences while keeping allelic combinations characteristic of successful commercial varieties, and many others. However, it is necessary to understand the fundamental principles of the gene molecular regulation involved in tomato fruit ripening for its successful use in creating new varieties. Although the candidate genes mediate ripening have been identified, a complete picture of their relationship has yet to be formed. This review summarizes the latest (2017-2023) achievements related to studying the ripening processes of tomato fruits. This work attempts to systematize the results of various research articles and display the interaction pattern of genes regulating the process of tomato fruit ripening.

Genome-wide analysis of carotenoid cleavage oxygenases and identification of ripening-associated DzNCED5a in durian (Durio zibethinus) fruit

Durian (Durio zibethinus L.), popularly known as the "King of fruits," holds significant economic importance in Southeast Asia, including Thailand. During its ripening process, the phytohormone abscisic acid (ABA) content has been reported to increase. However, a comprehensive understanding of ABA's specific role in durian fruit ripening remains elusive. Furthermore, little is known about the molecular aspects of the carotenoid cleavage pathway in this iconic fruit. Therefore, we performed genome-wide identification of the carotenoid cleavage oxygenase (CCO) family in durian. This family includes the nine-cis-epoxycarotenoid dioxygenases (NCEDs) responsible for ABA production and the carotenoid cleavage dioxygenases exhibiting diverse substrate specificities. Through phylogenetic analysis, we classified 14 CCOs in durian into 8 distinct subfamilies. Notably, each DzCCO subfamily displayed a conserved motif composition. Cis-acting element prediction showed that cis-elements related to plant hormones and environmental stress responses were distributed in the DzCCO promoter. In addition, transcriptome analysis was performed to examine the expression pattern during the fruit development and ripening stages. Interestingly, DzNCED5a, a ripening-associated gene, exhibited the highest expression level at the ripe stage, outperforming other CCOs. Its expression markedly correlated with increased ABA contents during the ripening stages of both the "Monthong" variety and other durian cultivars. Transiently expressed DzNCED5a in Nicotiana benthamiana leaves confirmed its function in ABA biosynthesis. These findings highlight the involvement of DzNCED5a in ABA production and its potential importance in durian fruit ripening. Overall, this study provides insights into the significance of CCOs in durian fruit ripening.

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.

Uncovering the Role of Hormones in Enhancing Antioxidant Defense Systems in Stressed Tomato (Solanum lycopersicum) Plants

Tomato is one of the most important fruits worldwide. It is widely consumed due to its sensory and nutritional attributes. However, like many other industrial crops, it is affected by biotic and abiotic stress factors, reducing its metabolic and physiological processes. Tomato plants possess different mechanisms of stress responses in which hormones have a pivotal role. They are responsible for a complex signaling network, where the antioxidant system (enzymatic and non-enzymatic antioxidants) is crucial for avoiding the excessive damage caused by stress factors. In this sense, it seems that hormones such as ethylene, auxins, brassinosteroids, and salicylic, jasmonic, abscisic, and gibberellic acids, play important roles in increasing antioxidant system and reducing oxidative damage caused by different stressors. Although several studies have been conducted on the stress factors, hormones, and primary metabolites of tomato plants, the effect of endogenous and/or exogenous hormones on the secondary metabolism is still poorly studied, which is paramount for tomato growing management and secondary metabolites production. Thus, this review offers an updated overview of both endogenous biosynthesis and exogenous hormone application in the antioxidant system of tomato plants as a response to biotic and abiotic stress factors.

Fruit ripening under heat stress: The intriguing role of ethylene-mediated signaling

Crop production is significantly influenced by climate, and even minor climate changes can have a substantial impact on crop yields. Rising temperature due to climate change can lead to heat stress (HS) in plants, which not only hinders plant growth and development but also result in significant losses in crop yields. To cope with the different stresses including HS, plants have evolved a variety of adaptive mechanisms. In response to these stresses, phytohormones play a crucial role by generating endogenous signals that regulate the plant's defensive response. Among these, Ethylene (ET), a key phytohormone, stands out as a major regulator of stress responses in plants and regulates many plant traits, which are critical for crop productivity and nutritional quality. ET is also known as a ripening hormone for decades in climacteric fruit and many studies are available deciphering the function of different ET biosynthesis and signaling components in the ripening process. Recent studies suggest that HS significantly affects fruit quality traits and perturbs fruit ripening by altering the regulation of many ethylene biosynthesis and signaling genes resulting in substantial loss of fruit yield, quality, and postharvest stability. Despite the significant progress in this field in recent years the interplay between ET, ripening, and HS is elusive. In this review, we summarized the recent advances and current understanding of ET in regulating the ripening process under HS and explored their crosstalk at physiological and molecular levels to shed light on intricate relationships.

The haplotype-resolved T2T reference genome highlights structural variation underlying agronomic traits of melon

Melon (Cucumis melo L.) is an important vegetable crop that has an extensive history of cultivation. However, the genome of wild and semi-wild melon types that can be used for the analysis of agronomic traits is not yet available. Here we report a chromosome-level T2T genome assembly for 821 (C. melo ssp. agrestis var. acidulus), a semi-wild melon with two haplotypes of ~373 Mb and ~364 Mb, respectively. Comparative genome analysis discovered a significant number of structural variants (SVs) between melo (C. melo ssp. melo) and agrestis (C. melo ssp. agrestis) genomes, including a copy number variation located in the ToLCNDV resistance locus on chromosome 11. Genome-wide association studies detected a significant signal associated with climacteric ripening and identified one candidate gene CM_ac12g14720.1 (CmABA2), encoding a cytoplasmic short chain dehydrogenase/reductase, which controls the biosynthesis of abscisic acid. This study provides valuable genetic resources for future research on melon breeding.

Combined transcriptome and metabolome analysis reveal that the white and yellow mango pulp colors are associated with carotenoid and flavonoid accumulation, and phytohormone signaling

Mango (Mangifera indica L.) is a widely appreciated tropical fruit for its rich color and nutrition. However, knowledge on the molecular basis of color variation is limited. Here, we studied HY3 (yellowish-white pulp) and YX4 (yellow pulp), reaped with 24 h gap from the standard harvesting time. The carotenoids and total flavonoids increased with the advance of harvest time (YX4 > HY34). Transcriptome sequencing showed that higher expressions of the core carotenoid biosynthesis genes and flavonoid biosynthesis genes are correlated to their respective contents. The endogenous indole-3-acetic acid and jasmonic acid contents decreased but abscisic acid and ethylene contents increased with an increase in harvesting time (YX4 > HY34). Similar trends were observed for the corresponding genes. Our results indicate that the color differences are related to carotenoid and flavonoid contents, which in turn are influenced by phytohormone accumulation and signaling.

ChIP-Seq Analysis of SlAREB1 Downstream Regulatory Network during Tomato Ripening

SlAREB1, a member of the abscisic acid (ABA) response element-binding factors (AREB/ABFs) family, was reported to play a crucial role in the expression of ABA-regulated downstream genes and affect the ripening of tomato fruit. However, the downstream genes of SlAREB1 are still unclear. Chromatin immunoprecipitation (ChIP) is a powerful tool and a standard method for studying the interactions between DNA and proteins at the genome-wide level. In the present study, SlAREB1 was proved to continually increase until the mature green stage and then decrease during the ripening period, and a total of 972 gene peaks were identified downstream of SlAREB1 by ChIP-seq analysis, mainly located in the intergenic and promoter regions. Further gene ontology (GO) annotation analysis revealed that the target sequence of SlAREB1 was the most involved in biological function. Kyoto Encylopaedia of Genes and Genomes (KEGG) pathway analysis showed that the identified genes were mainly involved in the oxidative phosphorylation and photosynthesis pathways, and some of them were associated with tomato phytohormone synthesis, the cell wall, pigment, and the antioxidant characteristic of the fruit as well. Based on these results, an initial model of SlAREB1 regulation on tomato fruit ripening was constructed, which provided a theoretical basis for further exploring the effects of the regulation mechanism of SlAREB1 and ABA on tomato fruit ripening.

Postharvest fruit quality of tomatoes influenced by an ethylene signaling component during long-term cold storage

Ethylene production is essential for improving cold resistance of postharvest tomatoes. However, the role of ethylene signaling pathway in maintaining fruit quality during long-term cold storage remains poorly understood. Here, we demonstrated that a partial loss of function in ethylene signaling by mutation of Ethylene Response Factor 2 (SlERF2), worsened fruit quality during cold storage, as determined by visual characterization, and physiological analyses of membrane damage and reactive oxygen species metabolism. In addition, the transcriptions of genes related to abscisic acid (ABA) biosynthesis and signaling were also altered by SlERF2 gene in response to cold storage. Furthermore, mutation of SlERF2 gene compromised cold-induced expression of genes in the C-repeat/dehydration-responsive binding factor (CBF) signaling pathway. Therefore, it's concluded that an ethylene signaling component, SlERF2 contributed to the regulations of ABA biosynthesis and signaling, as well as CBF cold signaling pathway, ultimately affecting the fruit quality during long-term cold storage of tomatoes.

Dissecting the effect of ethylene in the transcriptional regulation of chilling treatment in grapevine leaves

Ethylene (ETH) plays important roles in various development programs and stress responses in plants. In grapevines, ETH increased dramatically under chilling stress and is known to positively regulate cold tolerance. However, the role of ETH in transcriptional regulation during chilling stress of grapevine leaves is still not clear. To address this gap, targeted hormone profiling and transcriptomic analysis were performed on leaves of Vitis amurensis under chilling stress with and without aminoethoxyvinylglycine (AVG, a inhibitor of ETH synthesis) treatment. APETALA2/ETHYLENE RESPONSIVE FACTOR (AP2/ERF) and WRKY transcription factors (TF) were only the two highly enriched TF families that were consistently up-regulated during chilling stress but inhibited by AVG. The comparison of leaf transcriptomes between chilling treatment and chilling with AVG allowed the identification of potential ETH-regulated genes. Potential genes that are positively regulated by ETH are enriched in solute transport, protein biosynthesis, phytohormone action, antioxidant and carbohydrate metabolism. Conversely, genes related to the synthesis and signaling of ETH, indole-3-acetic acid (IAA), abscisic acid (ABA) were up-regulated by chilling treatment but inhibited by AVG. The contents of ETH, ABA and IAA also paralleled with the transcriptome data, which suggests that the response of ABA and IAA during chilling stress may regulate by ETH signaling, and together may belong to an integrated network of hormonal signaling pathways underpinning chilling stress response in grapevine leaves. Together, these findings provide new clues for further studying the complex regulatory mechanism of ETH under low-temperature stress in plants more generally and new opportunities for breeding cold-resilient grapevines.

Application of 5-aminolevulinic acid promotes ripening and accumulation of primary and secondary metabolites in postharvest tomato fruit

5-Aminolevulinic acid (ALA) plays a vital role in promoting plant growth, enhancing stress resistance, and improving fruit yield and quality. In the present study, tomato fruits were harvested at mature green stage and sprayed with 200 mg L-1 ALA on fruit surface. During ripening, the estimation of primary and secondary metabolites, carotenoids, and chlorophyll contents, and the expression levels of key genes involved in their metabolism were carried out. The results showed that ALA significantly promoted carotenoids accumulation by upregulating the gene expression levels of geranylgeranyl diphosphate synthase (GGPPS, encoding geranylgeranyl diphosphate synthase), phytoene synthase 1 (PSY1, encoding phytoene synthase), phytoene desaturase (PDS, encoding phytoene desaturase), and lycopeneβ-cyclase (LCYB, encoding lycopene β-cyclase), whereas chlorophyll content decreased by downregulating the expression levels of Mg-chelatase (CHLH, encoding Mg-chelatase) and protochlorophyllide oxidoreductase (POR, encoding protochlorophyllide oxidoreductase). Besides, the contents of soluble solids, vitamin C, soluble protein, free amino acids, total soluble sugar, organic acid, total phenol, and flavonoid were increased in ALA-treated tomato fruit, but the fruit firmness was decreased. These results indicated that the exogenous ALA could not only promote postharvest tomato fruit ripening but also improve the internal nutritional and flavor quality of tomato fruit.

Molecular and Genetic Events Determining the Softening of Fleshy Fruits: A Comprehensive Review

Fruit softening that occurs during fruit ripening and postharvest storage determines the fruit quality, shelf life and commercial value and makes fruits more attractive for seed dispersal. In addition, over-softening results in fruit eventual decay, render fruit susceptible to invasion by opportunistic pathogens. Many studies have been conducted to reveal how fruit softens and how to control softening. However, softening is a complex and delicate life process, including physiological, biochemical and metabolic changes, which are closely related to each other and are affected by environmental conditions such as temperature, humidity and light. In this review, the current knowledge regarding fruit softening mechanisms is summarized from cell wall metabolism (cell wall structure changes and cell-wall-degrading enzymes), plant hormones (ETH, ABA, IAA and BR et al.), transcription factors (MADS-Box, AP2/ERF, NAC, MYB and BZR) and epigenetics (DNA methylation, histone demethylation and histone acetylation) and a diagram of the regulatory relationship between these factors is provided. It will provide reference for the cultivation of anti-softening fruits.

Different rhizosphere soil microbes are recruited by tomatoes with different fruit color phenotypes

Background

To explore and utilize abundant soil microbes and their beneficial functions, the bacterial and fungal compositions in rhizospheres between red- and yellow-fruited tomato varieties were analyzed using high-throughput sequencing technique.

Result

Our results indicated that different soil microbes in rhizospheres of tomatoes were exactly recruited by different color fruit tomatoes. For the reasons as not only soil bacterial community, but also soil fungal compositions were all different between red and yellow fruit tomatoes. For example, Nocardioides, norank_f_norank_o_Vicinamibacterales, norank_f_norank_o_norank_c_KD4-96, norank_f_Birii41, norank_f_norank_o_S085 and Bradyrhizobium were the specific dominant soil bacterial genera, and Lecythophora, Derxomyces and unclassified_f_Pyronemataceae were the dominant soil fungal genera in the rhizospheres of red tomato varieties. By contrast, unclassified_f__Micromonsporaceae, Acidipila, Roseisolibacter, Gaiella and norank_f_Xanthobacteraceae were the unique dominant soil bacterial genera in the rhizospheres of yellow tomato varieties. And unclassified_o__Onygenales, Trichocladium, unclassified_c__Sordariomycetes, Pseudogymnoascus, Acremonium, Oidiodendron, Phialemonium, Penicillium, Phialosimplex were the unique dominant soil fungal genera in rhizospheres of yellow tomato varieties. Moreover, a higher abundance of specific soil bacterial and fungal genera in the rhizosphere was found in rhizospheres of the yellow than those of the red tomato varieties.

Conclusion

Soil bacterial and fungal compositions in rhizospheres between red- and yellow-fruited tomato varieties were found significantly different which growing in the same environment under the identical managements. It suggested that different soil microbes in rhizospheres exactly were recruited by different phenotypes tomato varieties related to fruit color formation.

The molecular mechanism on suppression of climacteric fruit ripening with postharvest wax coating treatment via transcriptome

Wax coating is an important means to maintain fruit quality and extend fruit shelf life, especially for climacteric fruits, such as apples (Malus domestica). Here, we found that wax coating could inhibit ethylene production, chlorophyll degradation, and carotenoid synthesis, but the molecular mechanism remains unclear. The regulatory mechanism of wax coating on apple fruit ripening was determined by subjecting wax-treated apple fruits to transcriptome analysis. RNA-seq revealed that 1,137 and 1,398 genes were upregulated and downregulated, respectively. These differentially expressed genes (DEGs) were shown to be related to plant hormones, such as ethylene, auxin, abscisic acid, and gibberellin, as well as genes involved in chlorophyll degradation and carotenoid biosynthesis. Moreover, we found that some genes related to the wax synthesis process also showed differential expression after the wax coating treatment. Among the DEGs obtained from RNA-seq analysis, 15 were validated by quantitative RT-PCR, confirming the results from RNA-seq analysis. RNA-seq and qRT-PCR of pear (Pyrus ussuriensis) showed similar changes after wax treatment. Our data suggest that wax coating treatment inhibits fruit ripening through ethylene synthesis and signal transduction, chlorophyll metabolism, and carotenoid synthesis pathways and that waxing inhibits endogenous wax production. These results provide new insights into the inhibition of fruit ripening by wax coating.

Co-silencing of ABA receptors (SlRCAR) reveals interactions between ABA and ethylene signaling during tomato fruit ripening

The ripening of fleshy fruits is highly dependent on the regulation of endogenous hormones, including ethylene, abscisic acid (ABA) and other phytohormones. However, the regulatory mechanism of ABA signaling and its interaction with ethylene signaling in fruit ripening are still unclear. In this study, multi-gene interference (RNAi) was applied to silence the ABA receptor genes in tomato for screening the specific receptors that mediate ABA signaling during fruit ripening. The results indicated that the ABA receptors, including SlRCAR9, SlRCAR12, SlRCAR11, and SlRCAR13, participate in the regulation of tomato fruit ripening. Comparative analysis showed that SlRCAR11 and SlRCAR13 play more important roles in mediating ABA signaling during tomato fruit ripening. Co-silencing of the four genes encoding these receptors could weaken the ethylene biosynthesis and signaling pathway at the early stage of tomato fruit ripening, leading to delayed fruit ripening. Meanwhile, co-silencing enhanced fruit firmness, and altered the shelf-life and susceptibility to Botrytis cinerea of the transgenic fruits. Furthermore, blocking ABA signaling did not affect the ability of ethylene to induce fruit ripening, whereas the block may inhibit the effectiveness of ABA in promoting fruit ripening. These results suggested that ABA signaling may be located upstream of ethylene signaling in regulating fruit ripening. Our findings provide a new insight into the complex regulatory network of phytohormones in regulating fruit ripening in tomato.

Regulation of fleshy fruit ripening: From transcription factors to epigenetic modifications

Fleshy fruits undergo a complex ripening process, developing organoleptic fruit traits that attract herbivores and maximize seed dispersal. Ripening is the terminal stage of fruit development and involves a series of physiological and biochemical changes. In fleshy fruits, ripening always involves a drastic color change triggered by the accumulation of pigments and degradation of chlorophyll, softening caused by cell wall remodeling, and flavor formation as acids and sugars accumulate alongside volatile compounds. The mechanisms underlying fruit ripening rely on the orchestration of ripening-related transcription factors, plant hormones, and epigenetic modifications. In this review, we discuss current knowledge of the transcription factors that regulate ripening in conjunction with ethylene and environmental signals (light and temperature) in the model plant tomato (Solanum lycopersicum) and other fleshy fruits. We emphasize the critical roles of epigenetic regulation, including DNA methylation and histone modification as well as RNA m6A modification, which has been studied intensively. This detailed review was compiled to provide a comprehensive description of the regulatory mechanisms of fruit ripening and guide new strategies for its effective manipulation.

Molecular and biochemical basis of softening in tomato

We review the latest information related to the control of fruit softening in tomato and where relevant compare the events with texture changes in other fleshy fruits. Development of an acceptable texture is essential for consumer acceptance, but also determines the postharvest life of fruits. The complex modern supply chain demands effective control of shelf life in tomato without compromising colour and flavour.The control of softening and ripening in tomato (Solanum lycopersicum) are discussed with respect to hormonal cues, epigenetic regulation and transcriptional modulation of cell wall structure-related genes. In the last section we focus on the biochemical changes closely linked with softening in tomato including key aspects of cell wall disassembly. Some important elements of the softening process have been identified, but our understanding of the mechanistic basis of the process in tomato and other fruits remains incomplete, especially the precise relationship between changes in cell wall structure and alterations in fruit texture.

Potential Carbohydrate Regulation Mechanism Underlying Starvation-Induced Abscission of Tomato Flower

Tomato flower abscission is a critical agronomic problem directly affecting yield. It often occurs in greenhouses in winter, with the weak light or hazy weather leading to insufficient photosynthates. The importance of carbohydrate availability in flower retention has been illustrated, while relatively little is understood concerning the mechanism of carbohydrate regulation on flower abscission. In the present study, we analyzed the responding pattern of nonstructural carbohydrates (NSC, including total soluble sugars and starch) and the potential sugar signal pathway involved in abscission regulation in tomato flowers under shading condition, and their correlations with flower abscission rate and abscission-related hormones. The results showed that, when plants suffer from short-term photosynthesis deficiency, starch degradation in flower organs acts as a self-protection mechanism, providing a carbon source for flower growth and temporarily alleviating the impact on flower development. Trehalose 6-phosphate (T6P) and sucrose non-fermenting-like kinase (SnRK1) signaling seems to be involved in adapting the metabolism to sugar starvation stress through regulating starch remobilization and crosstalk with IAA, ABA, and ethylene in flowers. However, a continuous limitation of assimilating supply imposed starch depletion in flowers, which caused flower abscission.

Interaction between fructan metabolism and plant growth regulators

The relationship of fructan to plant growth regulators is clearly more complicated than it looks and is likely related to differences between fructan molecules in size and structure as well as localization. Fructans are a complex group of carbohydrates composed mainly of fructose units linked to a sucrose molecule. Fructans are present in plants as heterogeneous mixtures with diverse molecular structures and mass, different polymerization degrees, and linkage types between fructosyl residues. Like sucrose, they are frequently stored in leaves and other organs, acting as carbohydrate reserves. Fructans are synthesized in the cell vacuole by fructosyltransferase enzymes and catabolized by fructan exohydrolase enzymes. Several publications have shown that fructan metabolism varies with the stage of plant development and in response to the environment. Recent studies have shown a correlation between plant growth regulators (PGR), fructan metabolism, and tolerance to drought and cold. PGR are compounds that profoundly influence the growth and differentiation of plant cells, tissues, and organs. They play a fundamental role in regulating plant responses to developmental and environmental signals. In this review, we summarize the most up-to-date knowledge on the metabolism of fructans and their crosstalk with PGR signaling pathways. We identify areas that require more research to complete our understanding of the role of fructans in plants.

Multi-omics data integration provides insights into the post-harvest biology of a long shelf-life tomato landrace

In this study we investigated the transcriptome and epigenome dynamics of the tomato fruit during post-harvest in a landrace belonging to a group of tomatoes (Solanum lycopersicum L.) collectively known as "Piennolo del Vesuvio", all characterized by a long shelf-life. Expression of protein-coding genes and microRNAs as well as DNA methylation patterns and histone modifications were analysed in distinct post-harvest phases. Multi-omics data integration contributed to the elucidation of the molecular mechanisms underlying processes leading to long shelf-life. We unveiled global changes in transcriptome and epigenome. DNA methylation increased and the repressive histone mark H3K27me3 was lost as the fruit progressed from red ripe to 150 days post-harvest. Thousands of genes were differentially expressed, about half of which were potentially epi-regulated as they were engaged in at least one epi-mark change in addition to being microRNA targets in ~5% of cases. Down-regulation of the ripening regulator MADS-RIN and of genes involved in ethylene response and cell wall degradation was consistent with the delayed fruit softening. Large-scale epigenome reprogramming that occurred in the fruit during post-harvest likely contributed to delayed fruit senescence.

Abscisic Acid: Role in Fruit Development and Ripening

Abscisic acid (ABA) is a plant growth regulator known for its functions, especially in seed maturation, seed dormancy, adaptive responses to biotic and abiotic stresses, and leaf and bud abscission. ABA activity is governed by multiple regulatory pathways that control ABA biosynthesis, signal transduction, and transport. The transport of the ABA signaling molecule occurs from the shoot (site of synthesis) to the fruit (site of action), where ABA receptors decode information as fruit maturation begins and is significantly promoted. The maximum amount of ABA is exported by the phloem from developing fruits during seed formation and initiation of fruit expansion. In the later stages of fruit ripening, ABA export from the phloem decreases significantly, leading to an accumulation of ABA in ripening fruit. Fruit growth, ripening, and senescence are under the control of ABA, and the mechanisms governing these processes are still unfolding. During the fruit ripening phase, interactions between ABA and ethylene are found in both climacteric and non-climacteric fruits. It is clear that ABA regulates ethylene biosynthesis and signaling during fruit ripening, but the molecular mechanism controlling the interaction between ABA and ethylene has not yet been discovered. The effects of ABA and ethylene on fruit ripening are synergistic, and the interaction of ABA with other plant hormones is an essential determinant of fruit growth and ripening. Reaction and biosynthetic mechanisms, signal transduction, and recognition of ABA receptors in fruits need to be elucidated by a more thorough study to understand the role of ABA in fruit ripening. Genetic modifications of ABA signaling can be used in commercial applications to increase fruit yield and quality. This review discusses the mechanism of ABA biosynthesis, its translocation, and signaling pathways, as well as the recent findings on ABA function in fruit development and ripening.

Genome-wide identification and expression profiling of durian CYPome related to fruit ripening

Durian (Durio zibethinus L.) is a major economic crop native to Southeast Asian countries, including Thailand. Accordingly, understanding durian fruit ripening is an important factor in its market worldwide, owing to the fact that it is a climacteric fruit with a strikingly limited shelf life. However, knowledge regarding the molecular regulation of durian fruit ripening is still limited. Herein, we focused on cytochrome P450, a large enzyme family that regulates many biosynthetic pathways of plant metabolites and phytohormones. Deep mining of the durian genome and transcriptome libraries led to the identification of all P450s that are potentially involved in durian fruit ripening. Gene expression validation by RT-qPCR showed a high correlation with the transcriptome libraries at five fruit ripening stages. In addition to aril-specific and ripening-associated expression patterns, putative P450s that are potentially involved in phytohormone metabolism were selected for further study. Accordingly, the expression of CYP72, CYP83, CYP88, CYP94, CYP707, and CYP714 was significantly modulated by external treatment with ripening regulators, suggesting possible crosstalk between phytohormones during the regulation of fruit ripening. Interestingly, the expression levels of CYP88, CYP94, and CYP707, which are possibly involved in gibberellin, jasmonic acid, and abscisic acid biosynthesis, respectively, were significantly different between fast- and slow-post-harvest ripening cultivars, strongly implying important roles of these hormones in fruit ripening. Taken together, these phytohormone-associated P450s are potentially considered additional molecular regulators controlling ripening processes, besides ethylene and auxin, and are economically important biological traits.

Rose (Rosa hybrida) Ethylene Responsive Factor 3 Promotes Rose Flower Senescence via Direct Activation of the Abscisic Acid Synthesis-Related 9-CIS-EPOXYCAROTENOID DIOXYGENASE Gene

During plant senescence, energy and nutrients are transferred to young leaves, fruits or seeds. However, senescence reduces flower quality, which leads to huge economic losses in flower production. Ethylene is an important factor affecting the quality of cut roses during transportation and storage. Ethylene-responsive factors (ERFs) are key nodes in ethylene signaling, but the molecular mechanism underlying ERFs regulated flower senescence is not well understood. We addressed this issue in the present study by focusing on RhERF3 from Rosa hybrida, an ERF identified in a previous transcriptome analysis of ethylene-treated rose flowers. Expression of RhERF3 was strongly induced by ethylene during rose flower senescence. Transient silencing of RhERF3 delayed flower senescence, whereas overexpression (OE) accelerated the process. RNA sequencing analysis of RhERF3 OE and pSuper vector control samples identified 13,214 differentially expressed genes that were mostly related to metabolic process and plant hormone signal transduction. Transient activation and yeast one-hybrid assays demonstrated that RhERF3 directly bound the promoter of the 9-cis-epoxycarotenoid dioxygenase (RhNCED1) gene and activated gene expression. Thus, a RhERF3/RhNCED1 axis accelerates rose flower senescence.

Gene regulation in climacteric fruit ripening

Seed dispersion and consequent plant propagation depend on the success of fruit ripening. Thus, ripening is a highly regulated developmental process aiming to maximize fruit organoleptic traits to attract herbivores. During ripening, the developing fruit experiences dramatic modifications, including color change, flavor improvement, and loss of firmness that are remarkably coordinated. Dynamic interactions between multiple hormones, transcription factors, and epigenetic modifications establish the complex regulatory network that controls the expression levels of ripening-related genes. Tomato, as a climacteric fruit, displays a burst of respiration once the seeds mature, followed by an increase in ethylene that regulates ripening. The accepted paradigm of the ripening transcriptional regulation has been recently challenged by the generation of true-null mutants of the previously considered master regulators of ripening. In addition to hormonal and transcriptional control, epigenetic shifts regulate the ripening process. Future research will contribute to better understanding the factors regulating fruit ripening.

Effects of Light Intensity and Spectral Composition on the Transcriptome Profiles of Leaves in Shade Grown Tea Plants (Camellia sinensis L.) and Regulatory Network of Flavonoid Biosynthesis

Black net shade treatment attenuates flavonoid biosynthesis in tea plants, while the effect of light quality is still unclear. We investigated the flavonoid and transcriptome profiles of tea leaves under different light conditions, using black nets with different shade percentages, blue, yellow and red nets to alter the light intensity and light spectral composition in the fields. Flavonol glycosides are more sensitive to light intensity than catechins, with a reduction percentage of total flavonol glycosides up to 79.6% compared with 38.7% of total catechins under shade treatment. A total of 29,292 unigenes were identified, and the KEGG result indicated that flavonoid biosynthesis was regulated by both light intensity and light spectral composition while phytohormone signal transduction was modulated under blue net shade treatment. PAL, CHS, and F3H were transcriptionally downregulated with light intensity. Co-expression analysis showed the expressions of key transcription factors MYB12, MYB86, C1, MYB4, KTN80.4, and light signal perception and signaling genes (UVR8, HY5) had correlations with the contents of certain flavonoids (p < 0.05). The level of abscisic acid in tea leaves was elevated under shade treatment, with a negative correlation with TFG content (p < 0.05). This work provides a potential route of changing light intensity and spectral composition in the field to alter the compositions of flavor substances in tea leaves and regulate plant growth, which is instructive to the production of summer/autumn tea and matcha.

Transcriptomics of Improved Fruit Retention by Hexanal in 'Honeycrisp' Reveals Hormonal Crosstalk and Reduced Cell Wall Degradation in the Fruit Abscission Zone

Apples (Malus&nbsp;domestica Borkh) are prone to preharvest fruit drop, which is more pronounced in 'Honeycrisp'. Hexanal is known to improve fruit retention in several economically important crops. The effects of hexanal on the fruit retention of 'Honeycrisp' apples were assessed using physiological, biochemical, and transcriptomic approaches. Fruit retention and fruit firmness were significantly improved by hexanal, while sugars and fresh weight did not show a significant change in response to hexanal treatment. At commercial maturity, abscisic acid and melatonin levels were significantly lower in the treated fruit abscission zone (FAZ) compared to control. At this stage, a total of 726 differentially expressed genes (DEGs) were identified between treated and control FAZ. Functional classification of the DEGs showed that hexanal downregulated ethylene biosynthesis genes, such as S-adenosylmethionine synthase (SAM2) and 1-aminocyclopropane-1-carboxylic acid oxidases (ACO3, ACO4, and ACO4-like), while it upregulated the receptor genes ETR2 and ERS1. Genes related to ABA biosynthesis (FDPS and CLE25) were also downregulated. On the contrary, key genes involved in gibberellic acid biosynthesis (GA20OX-like and KO) were upregulated. Further, hexanal downregulated the expression of genes related to cell wall degrading enzymes, such as polygalacturonase (PG1), glucanases (endo-β-1,4-glucanase), and expansins (EXPA1-like, EXPA6, EXPA8, EXPA10-like, EXPA16-like). Our findings reveal that hexanal reduced the sensitivity of FAZ cells to ethylene and ABA. Simultaneously, hexanal maintained the cell wall integrity of FAZ cells by regulating genes involved in cell wall modifications. Thus, delayed fruit abscission by hexanal is most likely achieved by minimizing ABA through an ethylene-dependent mechanism.

Exogenous Application of 5-Aminolevulinic Acid Promotes Coloration and Improves the Quality of Tomato Fruit by Regulating Carotenoid Metabolism

5-Aminolevulinic acid (ALA) plays an important role in plant growth and development. It can also be used to enhance crop resistance to environmental stresses and improve the color and internal quality of fruits. However, there are limited reports regarding the effects of ALA on tomato fruit color and its regulatory mechanisms. Therefore, in this study, the effects of exogenous ALA on the quality and coloration of tomato fruits were examined. Tomato (Solanum lycopersicum "Yuanwei No. 1") fruit surfaces were treated with different concentrations of ALA (0, 100, and 200 mg⋅L-1) on the 24th day after fruit setting (mature green fruit stage), and the content of soluble sugar, titratable acid, soluble protein, vitamin C, and total free amino acids, as well as amino acid components, intermediates of lycopene synthetic and metabolic pathways, and ALA metabolic pathway derivatives were determined during fruit ripening. The relative expression levels of genes involved in lycopene synthesis and metabolism and those involved in ALA metabolism were also analyzed. The results indicated that exogenous ALA (200 mg⋅L-1) increased the contents of soluble sugars, soluble proteins, total free amino acids, and vitamin C as well as 11 kinds of amino acid components in tomato fruits and reduced the content of titratable acids, thus improving the quality of tomato fruits harvested 4 days earlier than those of the control plants. In addition, exogenous ALA markedly improved carotenoid biosynthesis by upregulating the gene expression levels of geranylgeranyl diphosphate synthase, phytoene synthase 1, phytoene desaturase, and lycopene β-cyclase. Furthermore, exogenous ALA inhibited chlorophyll synthesis by downregulating the genes expression levels of Mg-chelatase and protochlorophyllide oxidoreductase. These findings suggest that supplementation with 200 mg⋅L-1 ALA not only enhances the nutritional quality and color of the fruit but also promotes early fruit maturation in tomato.

The interplay between ABA/ethylene and NAC TFs in tomato fruit ripening: a review

This review contains functional roles of NAC transcription factors in the transcriptional regulation of ripening in tomato fruit, describes the interplay between ABA/ethylene and NAC TFs in tomato fruit ripening. Fruit ripening is regulated by a complex network of transcription factors (TFs) and genetic regulators in response to endogenous hormones and external signals. Studying the regulation of fruit ripening has important significance for controlling fruit quality, enhancing nutritional value, improving storage conditions and extending shelf-life. Plant-specific NAC (named after no apical meristem (NAM), Arabidopsis transcription activator factor 1/2 (ATAF1/2) and Cup-shaped cotyledon (CUC2)) TFs play essential roles in plant development, ripening and stress responses. In this review, we summarize the recent progress on the regulation of NAC TFs in fruit ripening, discuss the interactions between NAC and other factors in controlling fruit development and ripening, and emphasize how NAC TFs are involved in tomato fruit ripening through the ethylene and abscisic acid (ABA) pathways. The signaling network regulating ripening is complex, and both hormones and individual TFs can affect the status or activity of other network participants, which can alter the overall ripening network regulation, including response signals and fruit ripening. Our review helps in the systematic understanding of the regulation of NAC TFs involved in fruit ripening and provides a basis for the development or establishment of complex ripening regulatory network models.

Molecular and Hormonal Mechanisms Regulating Fleshy Fruit Ripening

This article focuses on the molecular and hormonal mechanisms underlying the control of fleshy fruit ripening and quality. Recent research on tomato shows that ethylene, acting through transcription factors, is responsible for the initiation of tomato ripening. Several other hormones, including abscisic acid (ABA), jasmonic acid (JA) and brassinosteroids (BR), promote ripening by upregulating ethylene biosynthesis genes in different fruits. Changes to histone marks and DNA methylation are associated with the activation of ripening genes and are necessary for ripening initiation. Light, detected by different photoreceptors and operating through ELONGATED HYPOCOTYL 5(HY5), also modulates ripening. Re-evaluation of the roles of 'master regulators' indicates that MADS-RIN, NAC-NOR, Nor-like1 and other MADS and NAC genes, together with ethylene, promote the full expression of genes required for further ethylene synthesis and change in colour, flavour, texture and progression of ripening. Several different types of non-coding RNAs are involved in regulating expression of ripening genes, but further clarification of their diverse mechanisms of action is required. We discuss a model that integrates the main hormonal and genetic regulatory interactions governing the ripening of tomato fruit and consider variations in ripening regulatory circuits that operate in other fruits.

Proteomic analysis reveals key proteins involved in ethylene-induced adventitious root development in cucumber (Cucumis sativus L.)

The mechanisms involved in adventitious root formation reflect the adaptability of plants to the environment. Moreover, the rooting process is regulated by endogenous hormone signals. Ethylene, a signaling hormone molecule, has been shown to play an essential role in the process of root development. In the present study, in order to explore the relationship between the ethylene-induced adventitious rooting process and photosynthesis and energy metabolism, the iTRAQ technique and proteomic analysis were employed to ascertain the expression of different proteins that occur during adventitious rooting in cucumber (Cucumis sativus L.) seedlings. Out of the 5,014 differentially expressed proteins (DEPs), there were 115 identified DEPs, among which 24 were considered related to adventitious root development. Most of the identified proteins were related to carbon and energy metabolism, photosynthesis, transcription, translation and amino acid metabolism. Subsequently, we focused on S-adenosylmethionine synthase (SAMS) and ATP synthase subunit a (AtpA). Our findings suggest that the key enzyme, SAMS, upstream of ethylene synthesis, is directly involved in adventitious root development in cucumber. Meanwhile, AtpA may be positively correlated with photosynthetic capacity during adventitious root development. Moreover, endogenous ethylene synthesis, photosynthesis, carbon assimilation capacity, and energy material metabolism were enhanced by exogenous ethylene application during adventitious rooting. In conclusion, endogenous ethylene synthesis can be improved by exogenous ethylene additions to stimulate the induction and formation of adventitious roots. Moreover, photosynthesis and starch degradation were enhanced by ethylene treatment to provide more energy and carbon sources for the rooting process.

Foes or Friends: ABA and Ethylene Interaction under Abiotic Stress

Due to their sessile nature, plants constantly adapt to their environment by modulating various internal plant hormone signals and distributions, as plants perceive environmental changes. Plant hormones include abscisic acid (ABA), auxins, brassinosteroids, cytokinins, ethylene, gibberellins, jasmonates, salicylic acid, and strigolactones, which collectively regulate plant growth, development, metabolism, and defense. Moreover, plant hormone crosstalk coordinates a sophisticated plant hormone network to achieve specific physiological functions, on both a spatial and temporal level. Thus, the study of hormone–hormone interactions is a competitive field of research for deciphering the underlying regulatory mechanisms. Among plant hormones, ABA and ethylene present a fascinating case of interaction. They are commonly recognized to act antagonistically in the control of plant growth, and development, as well as under stress conditions. However, several studies on ABA and ethylene suggest that they can operate in parallel or even interact positively. Here, an overview is provided of the current knowledge on ABA and ethylene interaction, focusing on abiotic stress conditions and a simplified hypothetical model describing stomatal closure / opening, regulated by ABA and ethylene.

Single and Double Mutations in Tomato Ripening Transcription Factors Have Distinct Effects on Fruit Development and Quality Traits

Spontaneous mutations associated with the tomato transcription factors COLORLESS NON-RIPENING (SPL-CNR), NON-RIPENING (NAC-NOR), and RIPENING-INHIBITOR (MADS-RIN) result in fruit that do not undergo the normal hallmarks of ripening but are phenotypically distinguishable. Here, we expanded knowledge of the physiological, molecular, and genetic impacts of the ripening mutations on fruit development beyond ripening. We demonstrated through phenotypic and transcriptome analyses that Cnr fruit exhibit a broad range of developmental defects before the onset of fruit ripening, but fruit still undergo some ripening changes similar to wild type. Thus, Cnr should be considered as a fruit developmental mutant and not just a ripening mutant. Additionally, we showed that some ripening processes occur during senescence in the nor and rin mutant fruit, indicating that while some ripening processes are inhibited in these mutants, others are merely delayed. Through gene expression analysis and direct measurement of hormones, we found that Cnr, nor, and rin have alterations in the metabolism and signaling of plant hormones. Cnr mutants produce more than basal levels of ethylene, while nor and rin accumulate high concentrations of abscisic acid. To determine genetic interactions between the mutations, we created for the first time homozygous double mutants. Phenotypic analyses of the double ripening mutants revealed that Cnr has a strong influence on fruit traits and that combining nor and rin leads to an intermediate ripening mutant phenotype. However, we found that the genetic interactions between the mutations are more complex than anticipated, as the Cnr/nor double mutant fruit has a Cnr phenotype but displayed inhibition of ripening-related gene expression just like nor fruit. Our reevaluation of the Cnr, nor, and rin mutants provides new insights into the utilization of the mutants for studying fruit development and their implications in breeding for tomato fruit quality.

Transcriptome Analysis Identified Coordinated Control of Key Pathways Regulating Cellular Physiology and Metabolism upon Aspergillus flavus Infection Resulting in Reduced Aflatoxin Production in Groundnut

Aflatoxin-affected groundnut or peanut presents a major global health issue to both commercial and subsistence farming. Therefore, understanding the genetic and molecular mechanisms associated with resistance to aflatoxin production during host–pathogen interactions is crucial for breeding groundnut cultivars with minimal level of aflatoxin contamination. Here, we performed gene expression profiling to better understand the mechanisms involved in reduction and prevention of aflatoxin contamination resulting from Aspergillus flavus infection in groundnut seeds. RNA sequencing (RNA-Seq) of 16 samples from different time points during infection (24 h, 48 h, 72 h and the 7th day after inoculation) in U 4-7-5 (resistant) and JL 24 (susceptible) genotypes yielded 840.5 million raw reads with an average of 52.5 million reads per sample. A total of 1779 unique differentially expressed genes (DEGs) were identified. Furthermore, comprehensive analysis revealed several pathways, such as disease resistance, hormone biosynthetic signaling, flavonoid biosynthesis, reactive oxygen species (ROS) detoxifying, cell wall metabolism and catabolizing and seed germination. We also detected several highly upregulated transcription factors, such as ARF, DBB, MYB, NAC and C2H2 in the resistant genotype in comparison to the susceptible genotype after inoculation. Moreover, RNA-Seq analysis suggested the occurrence of coordinated control of key pathways controlling cellular physiology and metabolism upon A. flavus infection, resulting in reduced aflatoxin production.