The role of ethylene and cold temperature in the regulation of the apple POLYGALACTURONASE1 gene and fruit softening

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.

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.

Study on the Quality Change and Regulation Mechanism of 'Shannongsu' Pear Under Low-Temperature Storage

'Shannongsu' pear is a new high-quality cultivar. To ascertain the storage characteristics of 'Shannongsu' pears at low temperatures (0 ± 0.5 °C), the following parameters were determined: fruit firmness, ethylene, aromatic compounds, sugar content, acidity, ascorbic acid, and the expression levels of ethylene-related genes and texture-softening genes. The firmness of 'Shannongsu' pears changed less than that of the control, decreasing by only 18.8% after 170 days of storage. Low temperatures suppressed the expression of key genes associated with PbACS1a and PbACO1. Moreover, the expression of key genes related to fruit softening (PbPG1, PbXET, PbPME, and Pbα-L-Af) was suppressed during storage at low temperatures and remained at low levels. Therefore, the low levels of ethylene biosynthesis and the expression of key genes involved in fruit softening might play a major role in the excellent storage characteristics of the 'Shannongsu' cultivar. After 170 days of storage, 'Shannongsu' pears did not show significant changes in key quality dimensions such as firmness, sugar, acid, sugar-acid ratio, and ascorbic acid content. Therefore, low temperatures could help maintain the freshness, flavor, and nutritional quality of the 'Shannongsu' pear. Our findings reveal for the first time the low-temperature storage characteristics of 'Shannongsu' pears, providing a new scientific theoretical basis for pear production and marketing.

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.

Multiomics analyses of the effects of LED white light on the ripening of apricot fruits

INTRODUCTION

Apricot (Prunus armeniaca L.) fruits are highly perishable and prone to quality deterioration during storage and transportation.

OBJECTIVES

To investigate the effects of LED white light treatment on postharvest ripening of fruits using metabolomics, transcriptomics, and ATAC-Seq analysis.

METHODS

Fruits were exposed to 5 μmol m-2 s-1 LED white light for 12 h followed by 12 h of darkness at 20 °C daily for 12 days. The effects of the treatments on the physiological and nutritional quality of the fruits were evaluated. These data were combined with transcriptomic, metabolomic, and ATAC-Seq data from fruits taken on 8 d of treatment to provide insight into the potential mechanism by which LED treatment delays ripening.

RESULTS

LED treatment activated pathways involved in ascorbate and aldarate metabolism and flavonoid and phenylpropanoid biosynthesis. Specifically, LED treatment increased the expression of UDP-sugar pyrophosphorylase (USP), L-ascorbate peroxidase (AO), dihydroflavonol 4-reductase (DFR), chalcone synthase (CHS), and caffeoyl-CoA O-methyltransferase (CCOAOMT1), leading to the accumulation of caffeoyl quinic acid, epigallocatechin, and dihydroquercetin and the activation of anthocyanin biosynthesis. LED treatment also affected the expression of genes associated with plant hormone signal transduction, fruit texture and color transformation, and antioxidant activity. The notable genes affected by LED treatment included 1-aminocyclopropane-1-carboxylate synthase (ACS), 1-aminocyclopropane-1-carboxylate oxidase (ACO), hexokinase (HK), lipoxygenase (LOX), malate dehydrogenase (MDH), endoglucanase (CEL), various transcription factors (TCP, MYB, EFR), and peroxidase (POD). ATAC-Seq analysis further revealed that LED treatment primarily regulated phenylpropanoid biosynthesis.

CONCLUSION

The results obtained in this study provide insights into the effects of LED light exposure on apricot fruits ripening. LEDs offer a promising approach for extending the shelf life of other fruits and vegetables.

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.

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.

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.

Constitutive expression of apple endo-POLYGALACTURONASE1 in fruit induces early maturation, alters skin structure and accelerates softening

During fruit ripening, polygalacturonases (PGs) are key contributors to the softening process in many species. Apple is a crisp fruit that normally exhibits only minor changes to cell walls and limited fruit softening. Here, we explore the effects of PG overexpression during fruit development using transgenic apple lines overexpressing the ripening-related endo-POLYGALACTURONASE1 gene. MdPG1-overexpressing (PGox) fruit displayed early maturation/ripening with black seeds, conversion of starch to sugars and ethylene production occurring by 80 days after pollination (DAP). PGox fruit exhibited a striking, white-skinned phenotype that was evident from 60 DAP and most likely resulted from increased air spaces and separation of cells in the hypodermis due to degradation of the middle lamellae. Irregularities in the integrity of the epidermis and cuticle were also observed. By 120 DAP, PGox fruit cracked and showed lenticel-associated russeting. Increased cuticular permeability was associated with microcracks in the cuticle around lenticels and was correlated with reduced cortical firmness at all time points and extensive post-harvest water loss from the fruit, resulting in premature shrivelling. Transcriptomic analysis suggested that early maturation was associated with upregulation of genes involved in stress responses, and overexpression of MdPG1 also altered the expression of genes involved in cell wall metabolism (e.g. β-galactosidase, MD15G1221000) and ethylene biosynthesis (e.g. ACC synthase, MD14G1111500). The results show that upregulation of PG not only has dramatic effects on the structure of the fruit outer cell layers, indirectly affecting water status and turgor, but also has unexpected consequences for fruit development.

The apple transcription factor MdZF-HD11 regulates fruit softening by promoting Mdβ-GAL18 expression

Fruit ripening and the associated softening are major determinants of fruit quality and post-harvest shelf life. Although the mechanisms underlying fruit softening have been intensively studied, there are limited reports on the regulation of fruit softening in apples (Malus domestica). Here, we identified a zinc finger homeodomain transcription factor MdZF-HD11that trans-activates the promoter of Mdβ-GAL18, which encodes a pectin-degradation enzyme associated with cell wall metabolism. Both MdZF-HD11 and Mdβ-GAL18 genes were up-regulated by exogenous ethylene treatment and repressed by 1-methylcyclopropene treatment. Further experiments revealed that MdZF-HD11 binds directly to the Mdβ-GAL18 promoter and up-regulates its transcription. Moreover, using transgenic apple fruit calli, we found that overexpression of Mdβ-GAL18 or MdZF-HD11 significantly enhanced β-galactosidase activity, and overexpression of MdZF-HD11 induced the expression of Mdβ-GAL18. We also discovered that transient overexpression of Mdβ-GAL18 or MdZF-HD11 in 'Golden Delicious' apple significantly increased the release of ethylene, reduced fruit firmness, promoted the transformation of skin color from green to yellow, and accelerated ripening and softening of the fruit. Finally, the overexpression of MdZF-HD11 in tomato also promoted fruit softening. Collectively, these results indicate that ethylene-induced MdZF-HD11 interacts with Mdβ-GAL18 to promote the post-harvest softening of apple.

Two adjacent NAC transcription factors regulate fruit maturity date and flavor in peach

Although maturity date (MD) is an essential factor affecting fresh fruit marketing and has a pleiotropic effect on fruit taste qualities, the underlying mechanisms remain largely unclear. In this study, we functionally characterized two adjacent NAM-ATAF1/2-CUC2 (NAC) transcription factors (TFs), PpNAC1 and PpNAC5, both of which were associated with fruit MD in peach. PpNAC1 and PpNAC5 were found capable of activating transcription of genes associated with cell elongation, cell wall degradation and ethylene biosynthesis, suggesting their regulatory roles in fruit enlargement and ripening. Furthermore, PpNAC1 and PpNAC5 had pleiotropic effects on fruit taste due to their ability to activate transcription of genes for sugar accumulation and organic acid degradation. Interestingly, both PpNAC1 and PpNAC5 orthologues were found in fruit-producing angiosperms and adjacently arranged in all 91 tested dicots but absent in fruitless gymnosperms, suggesting their important roles in fruit development. Our results provide insight into the regulatory roles of NAC TFs in MD and fruit taste.

Low temperature inhibits pectin degradation by PpCBFs to prolong peach storage time

Low-temperature storage is a widely used method for peach fruit storage. However, the impact of PpCBFs on pectin degradation during low-temperature storage is unclear. As such, in this study, we stored the melting-flesh peach cultivar "Fuli" at low temperature (LT, 6°C) and room temperature (RT, 25°C) to determine the effect of different temperatures on its physiological and biochemical changes. Low-temperature storage can inhibit the softening of "Fuli" peaches by maintaining the stability of the cell wall. It was found that the contents of water-soluble pectin and ionic-soluble pectin in peach fruit stored at RT were higher than those stored at LT. The enzyme activities of polygalacturonase (PG), pectate lyase (PL), and pectin methylesterase (PME) were all inhibited by LT. The expressions of PpPME3, PpPL2, and PpPG were closely related to fruit firmness, but PpCBF2 and PpCBF3 showed higher expression levels at LT than RT. The promoters of PpPL2 and PpPG contain the DER motif, which suggested that PpCBF2 and PpCBF3 might negatively regulate their expression by directly binding to their promoters. These results indicated that LT may maintain firmness by activating PpCBFs to repress pectin-degradation-related enzyme genes during storage.

Ethylene enhances MdMAPK3-mediated phosphorylation of MdNAC72 to promote apple fruit softening

The phytohormone ethylene plays an important role in promoting the softening of climacteric fruits, such as apples (Malus domestica); however, important aspects of the underlying regulatory mechanisms are not well understood. In this study, we identified apple MITOGEN-ACTIVATED PROTEIN KINASE 3 (MdMAPK3) as an important positive regulator of ethylene-induced apple fruit softening during storage. Specifically, we show that MdMAPK3 interacts with and phosphorylates the transcription factor NAM-ATAF1/2-CUC2 72 (MdNAC72), which functions as a transcriptional repressor of the cell wall degradation-related gene POLYGALACTURONASE1 (MdPG1). The increase in MdMAPK3 kinase activity was induced by ethylene, which promoted the phosphorylation of MdNAC72 by MdMAPK3. Additionally, MdPUB24 functions as an E3 ubiquitin ligase to ubiquitinate MdNAC72, resulting in its degradation via the 26S proteasome pathway, which was enhanced by ethylene-induced phosphorylation of MdNAC72 by MdMAPK3. The degradation of MdNAC72 increased the expression of MdPG1, which in turn promoted apple fruit softening. Notably, using variants of MdNAC72 that were mutated at specific phosphorylation sites, we observed that the phosphorylation state of MdNAC72 affected apple fruit softening during storage. This study thus reveals that the ethylene-MdMAPK3-MdNAC72-MdPUB24 module is involved in ethylene-induced apple fruit softening, providing insights into climacteric fruit softening.

Polygalacturonase gene family analysis identifies FcPG12 as a key player in fig (Ficus carica L.) fruit softening

BACKGROUND

The fig (Ficus carica L.) tree has high economic value. However, its fruit have a short shelf life due to rapid softening. Polygalacturonases (PGs) are essential hydrolases, responsible for the pectin degradation that plays a key role in fruit softening. However, fig PG genes and their regulators have not yet been characterized.

RESULTS

In this study, 43 FcPGs were identified in the fig genome. They were non-uniformly distributed on 13 chromosomes, and tandem repeat PG gene clusters were found on chromosomes 4 and 5. Ka/Ks calculation and collinear analysis indicated negative selection as the main driver of FcPG family expansion. Fourteen FcPGs were found expressed in fig fruit with FPKM values > 10, of which seven were positively correlated, and three, negatively correlated with fruit softening. Eleven FcPGs were upregulated and two downregulated in response to ethephon treatment. FcPG12, a member of the tandem repeat cluster on chromosome 4, was selected for further analyses due to its sharp increment in transcript abundance during fruit softening and its response to ethephon treatment. Transient overexpression of FcPG12 led to decreased fig fruit firmness and increased PG enzyme activity in the tissue. Two ethylene response factor (ERF)-binding GCC-box sites were found on the FcPG12 promoter. Yeast one-hybrid and dual luciferase assays showed that FcERF5 binds directly to the FcPG12 promoter and upregulates its expression. Transient overexpression of FcERF5 upregulated FcPG12 expression, thereby increasing PG activity and fruit softening.

CONCLUSIONS

Our study identified FcPG12 as a key PG gene in fig fruit softening, and its direct positive regulation by FcERF5. The results provide new information on the molecular regulation of fig fruit softening.

The transcription factor CmERFI-2 represses CmMYB44 expression to increase sucrose levels in oriental melon fruit

Soluble sugar accumulation in fruit ripening determines fleshy fruit quality. However, the molecular mechanism for this process is not yet understood. Here, we showed a transcriptional repressor, CmMYB44 regulates sucrose accumulation and ethylene synthesis in oriental melon (Cucumis. melo var. makuwa Makino) fruit. Overexpressing CmMYB44 suppressed sucrose accumulation and ethylene production. Furthermore, CmMYB44 repressed the transcriptional activation of CmSPS1 (sucrose phosphate synthase 1) and CmACO1 (ACC oxidase 1), two key genes in sucrose and ethylene accumulation, respectively. During the later stages of fruit ripening, the repressive effect of CmMYB44 on CmSPS1 and CmACO1 could be released by overexpressing CmERFI-2 (ethylene response factor I-2) and exogenous ethylene in "HS" fruit (high sucrose accumulation fruit). CmERFI-2 acted upstream of CmMYB44 as a repressor by directly binding the CmMYB44 promoter region, indirectly stimulating the expression level of CmSPS1 and CmACO1. Taken together, we provided a molecular regulatory pathway mediated by CmMYB44, which determines the degree of sucrose and ethylene accumulation in oriental melon fruit and sheds light on transcriptional responses triggered by ethylene sensing that enable the process of fruit ripening.

Low temperatures inhibit the pectin degradation of 'Docteur Jules Guyot' pear (Pyrus communis L.)

The most remarkable characteristic of European pears is extremely perishable and difficult to store after postharvest softening. Low-temperature storage is one of the most commonly used methods to prolong the shelf life of European pears. However, the regulatory mechanism of the low-temperature delay of the softening of European pears is still unclear. In this study, the fruit firmness, pectin polysaccharide content, pectin-degrading enzyme activity, and pectin degradation gene expression of 'Docteur Jules Guyot' pears under low temperature (LT) and room temperature (RT) were analyzed. It was found that water-soluble pectin (WSP) was significantly negatively correlated with fruit flesh firmness, and the activities of several pectin-degrading enzymes were inhibited under LT storage conditions. In addition, it was also found that the gene expression patterns of PcPME2, PcPME3, PcPG1, PcPG2, PcPL, PcGAL1, PcGAL2, PcGAL4, and PcARF1 were inhibited by LT. The C-repeat binding factors PcCBF1 and PcCBF2 were also inhibited by long-term LT storage. Correlation analysis showed that the expression of PcCBFs was positively correlated with pectin-degradation enzyme genes, and we found that the promoters of many pectin-degradation enzyme genes contain the CRT/DRE motif, which CBF can directly bind. Therefore, it is speculated that long-term low-temperature conditions inhibit pectin degradation through PcCBFs.

Promoter Variation of the Key Apple Fruit Texture Related Gene MdPG1 and the Upstream Regulation Analysis

MdPG1 encoding polygalacturonase in apple (Malus × domestica) is a key gene associated with fruit firmness and texture variations among apple cultivars. However, the causative variants of MdPG1 are still not known. In this study, we identified a SNP^A/C variant within an ERF-binding element located in the promoter region of MdPG1. The promoter containing the ERF-binding element with SNP^A, rather than the SNP^C, could be strongly bound and activated by MdCBF2, a member of the AP2/ERF transcription factor family, as determined by yeast-one-hybrid and dual-luciferase reporter assays. We also demonstrated that the presence of a novel long non-coding RNA, lncRNA_PG1, in the promoter of MdPG1 was a causative variant. lncRNA_PG1 was specifically expressed in fruit tissues postharvest. lncRNA_PG1 could reduce promoter activity when it was fused to the promoter of MdPG1 and a tobacco gene encoding Mg-chelatase H subunit (NtCHLH) in transgenic tobacco cells but could not reduce promoter activity when it was supplied in a separate gene construct, indicating a cis-regulatory effect. Our results provide new insights into genetic regulation of MdPG1 allele expression and are also useful for the development of elite apple cultivars.

Ethylene inhibits malate accumulation in apple by transcriptional repression of aluminum-activated malate transporter 9 via the WRKY31-ERF72 network

Malic acid accumulation in the vacuole largely determines acidity and perception of sweetness of apple. It has long been observed that reduction in malate level is associated with increase in ethylene production during the ripening process of climacteric fruits, but the molecular mechanism linking ethylene to malate reduction is unclear. Here, we show that ethylene-modulated WRKY transcription factor 31 (WRKY31)-Ethylene Response Factor 72 (ERF72)-ALUMINUM ACTIVATED MALATE TRANSPORTER 9 (Ma1) network regulates malate accumulation in apple fruit. ERF72 binds to the promoter of ALMT9, a key tonoplast transporter for malate accumulation of apple, transcriptionally repressing ALMT9 expression in response to ethylene. WRKY31 interacts with ERF72, suppressing its transcriptional inhibition activity on ALMT9. In addition, WRKY31 directly binds to the promoters of ERF72 and ALMT9, transcriptionally repressing and activating ERF72 and ALMT9, respectively. The expression of WRKY31 decreases in response to ethylene, lowering the transcription of ALMT9 directly and via its interactions with ERF72. These findings reveal that the regulatory complex WRKY31 forms with ERF72 responds to ethylene, linking the ethylene signal to ALMT9 expression in reducing malate transport into the vacuole during fruit ripening.

Comparative transcriptomic profiling of peach and nectarine cultivars reveals cultivar-specific responses to chilled postharvest storage

INTRODUCTION

Peach (Prunus persica (L.) Batsch,) and nectarine fruits (Prunus persica (L.) Batsch, var nectarine), are characterized by a rapid deterioration at room temperature. Therefore, cold storage is widely used to delay fruit post-harvest ripening and extend fruit commercial life. Physiological disorders, collectively known as chilling injury, can develop typically after 3 weeks of low-temperature storage and affect fruit quality.

METHODS

A comparative transcriptomic analysis was performed to identify regulatory pathways that develop before chilling injury symptoms are detectable using next generation sequencing on the fruits of two contrasting cultivars, one peach (Sagittaria) and one nectarine, (Big Top), over 14 days of postharvest cold storage.

RESULTS

There was a progressive increase in the number of differentially expressed genes between time points (DEGs) in both cultivars. More (1264) time point DEGs were identified in 'Big Top' compared to 'Sagittaria' (746 DEGs). Both cultivars showed a downregulation of pathways related to photosynthesis, and an upregulation of pathways related to amino sugars, nucleotide sugar metabolism and plant hormone signal transduction with ethylene pathways being most affected. Expression patterns of ethylene related genes (including biosynthesis, signaling and ERF transcription factors) correlated with genes involved in cell wall modification, membrane composition, pathogen and stress response, which are all involved later during storage in development of chilling injury.

DISCUSSION

Overall, the results show that common pathways are activated in the fruit of 'Big Top' nectarine and 'Sagittaria' peach in response to cold storage but include also differences that are cultivar-specific responses.

Variation in Cell Wall Metabolism and Flesh Firmness of Four Apple Cultivars during Fruit Development

Fruit ripening and softening are highly complex processes, and there is an interplay and coordination between the metabolic pathways that are involved in the biological processes. In this study, we aimed to elucidate the variation in the characters and possible causes of cell wall materials and morphological structure during apple fruits development. We studied the cell wall material (CWM), structure, cellular morphology, hydrolase activity, and the transcriptional levels of the related genes in four apple varieties 'Ruixue' and 'Ruixianghong' and their parents ('Pink Lady' and 'Fuji') during fruit development. The decrease in the contents of CWMs, sodium carbonate soluble pectin, hemicellulose, and cellulose were positively correlated with the decline in the hardness during the fruit development. In general, the activities of polygalacturonase, β-galactosidase, and cellulase enzymes increased during the late developmental period. As the fruit grew, the fruit cells of all of the cultivars gradually became larger, and the cell arrangement became more relaxed, the fruit cell walls became thinner, and the intercellular space became larger. In conclusion, the correlation analysis indicated that the up-regulation of the relative expression levels of ethylene synthesis and cell wall hydrolase genes enhanced the activity of the cell wall hydrolase, resulting in the degradation of the CWMs and the depolymerization of the cell wall structure, which affected the final firmness of the apple cultivars in the mature period.

Transcriptional regulation of fleshy fruit texture

Fleshy fruit texture is a critically important quality characteristic of ripe fruit. Softening is an irreversible process which operates in most fleshy fruits during ripening which, together with changes in color and taste, contributes to improvements in mouthfeel and general attractiveness. Softening results mainly from the expression of genes encoding enzymes responsible for cell wall modifications but starch degradation and high levels of flavonoids can also contribute to texture change. Some fleshy fruit undergo lignification during development and post-harvest, which negatively affects eating quality. Excessive softening can also lead to physical damage and infection, particularly during transport and storage which causes severe supply chain losses. Many transcription factors (TFs) that regulate fruit texture by controlling the expression of genes involved in cell wall and starch metabolism have been characterized. Some TFs directly regulate cell wall targets, while others act as part of a broader regulatory program governing several aspects of the ripening process. In this review, we focus on advances in our understanding of the transcriptional regulatory mechanisms governing fruit textural change during fruit development, ripening and post-harvest. Potential targets for breeding and future research directions for the control of texture and quality improvement are discussed.

Examining the Role of Low Temperature in Satsuma Mandarin Fruit Peel Degreening via Comparative Physiological and Transcriptomic Analysis

Peel degreening is the most conspicuous aspect of fruit ripening in many citrus fruits because of its importance for marketability. In this study, peel degreening in response to propylene (an ethylene analog) and at varying storage temperatures was characterized in Satsuma mandarin (Citrus unshiu Marc.) fruit. Propylene treatment triggered rapid peel degreening (within 4-6 days), indicated by an increase in the citrus color index (CCI) and chlorophyll loss. Peel degreening was also observed in fruit at 10°C and 15°C after 28-42 days, with gradual CCI increase and chlorophyll reduction. However, fruit at 5°C, 20°C, and 25°C remained green, and no substantial changes in peel CCI and chlorophyll content were recorded during the 42-day storage duration. The transcriptomes of peels of fruit treated with propylene for 4 days and those stored at varying temperatures for 28 days were then analyzed by RNA-Seq. We identified three categories of differentially expressed genes that were regulated by (i) propylene (and by analogy, ethylene) alone, (ii) low temperature (5°C, 10°C, or 15°C vs. 25°C) alone, and (iii) either propylene or low temperature. Gene-encoding proteins associated with chlorophyll degradation (such as CuSGR1, CuNOL, CuACD2, CuCAB2, and CuLHCB2) and a transcription factor (CuERF114) were differentially expressed by propylene or low temperature. To further examine temperature-induced pathways, we also monitored gene expression during on-tree fruit maturation vs. postharvest. The onset of on-tree peel degreening coincided with autumnal drops in field temperatures, and it was accompanied by differential expression of low temperature-regulated genes. On the contrary, genes that were exclusively regulated by propylene (such as CuCOPT1 and CuPOX-A2) displayed insignificant expression changes during on-tree peel degreening. These findings indicate that low temperatures could be involved in the fruit ripening-related peel degreening independently of ethylene.

MaMYB4 is a negative regulator and a substrate of RING-type E3 ligases MaBRG2/3 in controlling banana fruit ripening

Fruit ripening is a complex developmental process, which is modulated by both transcriptional and post-translational events. Control of fruit ripening is important in maintaining moderate quality traits and minimizing postharvest deterioration. In this study, we discovered that the transcription factor MaMYB4 acts as a negative regulator of fruit ripening in banana. The protein levels of MaMYB4 decreased gradually with banana fruit ripening, paralleling ethylene production, and decline in firmness. DNA affinity purification sequencing combined with RNA-sequencing analyses showed that MaMYB4 preferentially binds to the promoters of various ripening-associated genes including ethylene biosynthetic and cell wall modifying genes. Furthermore, ectopic expression of MaMYB4 in tomato delayed tomato fruit ripening, which was accompanied by downregulation of ethylene biosynthetic and cell wall modifying genes. Importantly, two RING finger E3 ligases MaBRG2/3, whose protein accumulation increased progressively with fruit ripening, were found to interact with and ubiquitinate MaMYB4, contributing to decreased accumulation of MaMYB4 during fruit ripening. Transient overexpression of MaMYB4 and MaBRG2/3 in banana fruit ripening delayed or promoted fruit ripening by inhibiting or stimulating ethylene biosynthesis, respectively. Taken together, we demonstrate that MaMYB4 negatively modulates banana fruit ripening, and that MaMYB4 abundance could be regulated by protein ubiquitination, thus providing insights into the role of MaMYB4 in controlling fruit ripening at both transcriptional and post-translational levels.

Characterization and Identification of a Ripening-Related Gene AaPG18 in Actinidia arguta

Actinidia arguta (A. arguta) is a kind of climacteric fruit that quickly softens and limits fruit shelf-life and commercial value. Therefore, it is of great significance to develop kiwifruit genotypes with an extended shelf-life of fruit. However, the ripening and softening mechanisms remain unclear in A. arguta. Here, we demonstrated that a key polygalacturonase (PG)-encoding gene AaPG18 was involved in A. arguta ripening through the degradation of the cell wall. Fruits were harvested at three developmental stages (S1, S2, and S3) for high-throughput transcriptome sequencing, based on which two candidate transcripts c109562_g1 and c111961_g1 were screened. The genome-wide identification of the PG gene family assigned c109562_g1 and c111961_g1 to correspond to AaPG4 and AaPG18, respectively. The expression profiles of candidate genes at six preharvest stages of fruit showed significantly higher expression levels of AaPG18 than AaPG4, indicating AaPG18 might be a key gene during fruit ripening processes. The subcellular localization displayed AaPG18 was located at the cytoplasmic membrane. The transient overexpression of AaPG18 in strawberry and the following morphological observation suggested AaPG18 played a key role in maintaining the stability of cell morphology. The homologous transient transformation in A. arguta “RB-4” proved the crucial function of AaPG18 in fruit ripening processes by causing the rapid redness of the fruit, which was an indicator of fruit maturity. All in all, our results identified AaPG18 as a key candidate gene involved in cell wall degeneration, which provides a basis for the subsequent exploration of the molecular mechanisms underlying the ripening and softening of A. arguta fruit.

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.

Consensus co-expression network analysis identifies AdZAT5 regulating pectin degradation in ripening kiwifruit

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CCNA was advanced by introducing physiological traits.

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Six cell wall genes and four transcription factors were identified for pectin degradation.

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A series of experiments validated the regulations of AdZAT5 on AdPL5 and Adβ-Gal5.

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CCNA would be powerful for phishing the unknown regulators with higher efficiency and accuracy.

Introduction

Cell wall degradation and remodeling is the key factor causing fruit softening during ripening.

Objectives

To explore the mechanism underlying postharvest cell wall metabolism, a transcriptome analysis method for more precious prediction on functional genes was needed.

Methods

Kiwifruits treated by ethylene (a conventional and effective phytohormone to accelerate climacteric fruit ripening and softening as kiwifruits) or air were taken as materials. Here, Consensus Coexpression Network Analysis (CCNA), a procedure evolved from Weighted Gene Co-expression Network Analysis (WGCNA) package in R, was applied and generated 85 consensus clusters from twelve transcriptome libraries. Advanced and comprehensive modifications were achieved by combination of CCNA and WGCNA with introduction of physiological traits, including firmness, cell wall materials, cellulose, hemicellulose, water soluble pectin, covalent binding pectin and ionic soluble pectin.

Results

As a result, six cell wall metabolisms related structural genes AdGAL1, AdMAN1, AdPL1, AdPL5, Adβ-Gal5, AdPME1 and four transcription factors AdZAT5, AdDOF3, AdNAC083, AdMYBR4 were identified as hub candidate genes for pectin degradation. Dual-luciferase system and electrophoretic mobility shift assays validated that promoters of AdPL5 and Adβ-Gal5 were recognized and trans-activated by transcription factor AdZAT5. The relatively higher enzyme activities of PL and β-Gal were observed in ethylene treated kiwifruit, further emphasized the critical roles of these two pectin related genes for fruit softening. Moreover, stable transient overexpression AdZAT5 in kiwifruit significantly enhanced AdPL5 and Adβ-Gal5 expression, which confirmed the in vivo regulations between transcription factor and pectin related genes.

Conclusion

Thus, modification and application of CCNA would be powerful for the precious phishing the unknown regulators. It revealed that AdZAT5 is a key factor for pectin degradation by binding and regulating effector genes AdPL5 and Adβ-Gal5.

Development of potent promoters that drive the efficient expression of genes in apple protoplasts

Protoplast transient expression is a powerful strategy for gene functional characterization, especially in biochemical mechanism studies. We herein developed a highly efficient transient expression system for apple protoplasts. The abilities of the Arabidopsis thaliana and Malus domestica ubiquitin-10 (AtUBQ10 and MdUBQ10) promoters to drive the expression of multiple genes were compared with that of the CaMV 35S promoter, and the results revealed that the AtUBQ10 and MdUBQ10 promoters were more efficient in apple protoplasts. With this system, we demonstrated that active AtMKK7ac could activate MAPK6/3/4 signaling cascades, which further regulated MdWRKY33 phosphorylation and stability in apple. Furthermore, the ligand-induced interaction between the immune receptor AtFLS2 and the coreceptor AtBAK1 was reconstituted in apple protoplasts. We also found that the stability of the bacterial effector AvrRpt2 was regulated by feedback involving auxin and the immune regulator RIN4. The system established herein will serve as a useful tool for the molecular and biochemical analyses of apple genes.

The downregulation of PpPG21 and PpPG22 influences peach fruit texture and softening

The downregulation of PpPG21 and PpPG22 expression in melting-flesh peach delays fruit softening and hinders texture changes by influencing pectin solubilization and depolymerization. The polygalacturonase (PG)-catalyzed solubilization and depolymerization of pectin plays a central role in the softening and texture formation processes in peach fruit. In this study, the expression characteristics of 15 PpPG members in peach fruits belonging to the melting flesh (MF) and non-melting flesh (NMF) types were analyzed, and virus-induced gene silencing (VIGS) technology was used to identify the roles of PpPG21 (ppa006839m) and PpPG22 (ppa006857m) in peach fruit softening and texture changes. In both MF and NMF peaches, the expression of PpPG1, 10, 12, 23, and 25 was upregulated, whereas that of PpPG14, 24, 35, 38, and 39 was relatively stable or downregulated during shelf life. PpPG1 was highly expressed in NMF fruit, whereas PpPG21 and 22 were highly expressed in MF peaches. Suppressing the expression of PpPG21 and 22 by VIGS in MF peaches significantly reduced PG enzyme activity, maintained the firmness of the fruit during the late shelf life stage, and suppressed the occurrence of the "melting" stage compared with the control fruits. Moreover, the downregulation of PpPG21 and 22 expression also reduced the water-soluble pectin (WSP) content, increased the contents of ionic-soluble pectin (ISP) and covalent-soluble pectin (CSP) and affected the expression levels of ethylene synthesis- and pectin depolymerization-related genes in the late shelf life stage. These results indicate that PpPG21 and 22 play a major role in the development of the melting texture trait of peaches by depolymerizing cell wall pectin. Our results provide direct evidence showing that PG regulates peach fruit softening and texture changes.

Cold stress triggers premature fruit abscission through ABA-dependent signal transduction in early developing apple

Fruit abscission is a complex physiological process that is regulated by internal and environmental factors. During early development, apple fruit are exposed to extreme temperature fluctuations that are associated with premature fruit drop; however, their effect on fruit abscission is largely unknown. We hypothesized that fruit abscission is triggered by cold stress and investigated the molecular basis of premature fruit drop using RNA-Seq and metabolomics data from apple fruit undergoing abscission following cold stress in the field. Genes responsive to abscisic acid signaling and cell wall degradation were upregulated during abscission, consistent with the increased abscisic acid concentrations detected by liquid chromatography-mass spectrometry. We performed ex vivo cold shock experiments with excised tree subunits consisting of a branch, pedicel, and fruit. Abscission induction occurred in the cold-stressed subunits with concurrent upregulation of abscisic acid biosynthesis (MdNCED1) and metabolism (MdCYP707A) genes, and ethylene biosynthesis (MdACS1) and receptor (MdETR2) genes in the pedicel. Another key finding was the activation of cytoplasmic streaming in abscission-zone cells detected by electron microscopy. Our results provide a novel insight into the molecular basis of fruit abscission physiology in response to cold stress in apple.

Low temperature modulates natural peel degreening in lemon fruit independently of endogenous ethylene

Peel degreening is an important aspect of fruit ripening in many citrus fruit, and previous studies have shown that it can be advanced by ethylene treatment or by low-temperature storage. However, the important regulators and pathways involved in natural peel degreening remain largely unknown. To determine how natural peel degreening is regulated in lemon fruit (Citrus limon), we studied transcriptome and physiochemical changes in the flavedo in response to ethylene treatment and low temperatures. Treatment with ethylene induced rapid peel degreening, which was strongly inhibited by the ethylene antagonist, 1-methylcyclopropene (1-MCP). Compared with 25 ºC, moderately low storage temperatures of 5-20 °C also triggered peel degreening. Surprisingly, repeated 1-MCP treatments failed to inhibit the peel degreening induced by low temperature. Transcriptome analysis revealed that low temperature and ethylene independently regulated genes associated with chlorophyll degradation, carotenoid metabolism, photosystem proteins, phytohormone biosynthesis and signalling, and transcription factors. Peel degreening of fruit on trees occurred in association with drops in ambient temperature, and it coincided with the differential expression of low temperature-regulated genes. In contrast, genes that were uniquely regulated by ethylene showed no significant expression changes during on-tree peel degreening. Based on these findings, we hypothesize that low temperature plays a prominent role in regulating natural peel degreening independently of ethylene in citrus fruit.

High CO2/hypoxia-induced softening of persimmon fruit is modulated by DkERF8/16 and DkNAC9 complexes

Most persimmon (Diospyros kaki) cultivars are astringent and require post-harvest deastringency treatments such as 95% CO2 (high-CO2 treatment) to make them acceptable to consumers. High-CO2 treatment can, however, also induce excessive softening, which can be reduced by adding 1-methylcyclopropene (1-MCP). Previous studies have shown that genes encoding the ETHYLENE RESPONSE FACTORS (ERFs) DkERF8/16/19 can trans-activate xyloglucan endotransglycosylase/hydrolase (DkXTH9), which encodes the cell wall-degrading enzyme associated with persimmon fruit softening. In this study, RNA-seq data between three treatments were compared, namely high-CO2, high-CO2+1-MCP, and controls. A total of 227 differentially expressed genes, including 17 transcription factors, were predicted to be related to persimmon post-deastringency softening. Dual-luciferase assays indicated that DkNAC9 activated the DkEGase1 promoter 2.64-fold. Synergistic effects on transcription of DkEGase1 that involved DkNAC9 and the previously reported DkERF8/16 were identified. Electrophoretic mobility shift assay indicated that DkNAC9 could physically bind to the DkEGase1 promoter. Bimolecular fluorescence complementation and firefly luciferase complementation imaging assays indicated protein-protein interactions between DkNAC9 and DkERF8/16. Based on these findings, we conclude that DkNAC9 is a direct transcriptional activator of DkEGase1 that can co-operate with DkERF8/16 to enhance fruit post-deastringency softening.

Ethylene-responsive factor 4 is associated with the desirable rind hardness trait conferring cracking resistance in fresh fruits of watermelon

Fruit rind plays a pivotal role in alleviating water loss and disease and particularly in cracking resistance as well as the transportability, storability and shelf-life quality of the fruit. High susceptibility to cracking due to low rind hardness is largely responsible for severe annual yield losses of fresh fruits such as watermelon in the field and during the postharvest process. However, the candidate gene controlling the rind hardness phenotype remains unclear to date. Herein, we report, for the first time, an ethylene-responsive transcription factor 4 (ClERF4) associated with variation in rind hardness via a combinatory genetic map with bulk segregant analysis (BSA). Strikingly, our fine-mapping approach revealed an InDel of 11 bp and a neighbouring SNP in the ClERF4 gene on chromosome 10, conferring cracking resistance in F₂ populations with variable rind hardness. Furthermore, the concomitant kompetitive/competitive allele-specific PCR (KASP) genotyping data sets of 104 germplasm accessions strongly supported candidate ClERF4 as a causative gene associated with fruit rind hardness variability. In conclusion, our results provide new insight into the underlying mechanism controlling rind hardness, a desirable trait in fresh fruit. Moreover, the findings will further enable the molecular improvement of fruit cracking resistance in watermelon via precisely targeting the causative gene relevant to rind hardness, ClERF4.

Isolation, sequencing, and expression analysis of 30 AP2/ERF transcription factors in apple

BACKGROUND

AP2/ERF transcription factors are involved in the regulation of plant growth, development, and stress responses. Our research objective was to characterize novel apple (Malus × domestica Borkh.) genes encoding AP2/ERF transcription factors involved in regulation of plant growth, development, and stress response. The transcriptional level of apple AP2/ERF genes in different tissues and under various biotic and abiotic stress was determined to provide valuable insights into the function of AP2/ERF transcription factors in apple.

METHODS

Thirty full-length cDNA sequences of apple AP2/ERF genes were isolated from 'Zihong Fuji' apple (Malus × domestica cv. Zihong Fuji) via homologous comparison and RT-PCR confirmation, and the obtained cDNA sequences and the deduced amino acid sequences were analyzed with bioinformatics methods. Expression levels of apple AP2/ERF genes were detected in 16 different tissues using a known array. Expression patterns of apple AP2/ERF genes were detected in response to Alternaria alternata apple pathotype (AAAP) infection using RNA-seq with existing data, and the expression of apple AP2/ERF genes was analyzed under NaCl and mannitol treatments using qRT-PCR.

RESULTS

The sequencing results produced 30 cDNAs (designated as MdERF3-8, MdERF11, MdERF16-19, MdERF22-28, MdERF31-35, MdERF39, MdAP2D60, MdAP2D62-65, and MdRAV2). Phylogenetic analysis revealed that MdERF11/16, MdERF33/35, MdERF34/39, and MdERF18/23 belonged to groups A-2, A-4, A-5, and A-6 of the DREB subfamily, respectively; MdERF31, MdERF19, MdERF4/25/28/32, MdERF24, MdERF5/6/27, and MdERF3/7/8/17/22/26 belonged to groups B-1, B-2, B-3, B-4, B-5, and B-6 of the ERF subfamily, respectively; MdAP2D60 and MdAP2D62/63/64/65 belonged to the AP2 subfamily; and MdRAV2 belonged to the RAV subfamily. Array results indicated that 30 apple AP2/ERF genes were expressed in all examined tissues to different degrees. RNA-seq results using previously reported data showed that many members of the apple ERF and DREB subfamilies were induced by Alternaria alternate apple pathotype (AAAP) infection. Under salt treatment, many members in the apple ERF and DREB subfamilies were transcriptionally up or down-regulated. Under mannitol treatment, many members of the apple ERF, DREB, and AP2 subfamilies were induced at the transcriptional level. Taken together, the results indicated that the cloned apple AP2/ERF genes were expressed in all examined tissues. These genes were up-regulated or down-regulated in response to AAAP infection and to salt or mannitol treatment, which suggested they may be involved in regulating growth, development, and stress response in apple.

Cell type-specific gene expression underpins remodelling of cell wall pectin in exocarp and cortex during apple fruit development

In apple (Malus×domestica) fruit, the different layers of the exocarp (cuticle, epidermis, and hypodermis) protect and maintain fruit integrity, and resist the turgor-driven expansion of the underlying thin-walled cortical cells during growth. Using in situ immunolocalization and size exclusion epitope detection chromatography, distinct cell type differences in cell wall composition in the exocarp were revealed during apple fruit development. Epidermal cell walls lacked pectic (1→4)-β-d-galactan (associated with rigidity), whereas linear (1→5)-α-l-arabinan (associated with flexibility) was exclusively present in the epidermal cell walls in expanding fruit and then appeared in all cell types during ripening. Branched (1→5)-α-l-arabinan was uniformly distributed between cell types. Laser capture microdissection and RNA sequencing (RNA-seq) were used to explore transcriptomic differences controlling cell type-specific wall modification. The RNA-seq data indicate that the control of cell wall composition is achieved through cell-specific gene expression of hydrolases. In epidermal cells, this results in the degradation of galactan side chains by possibly five β-galactosidases (BGAL2, BGAL7, BGAL10, BGAL11, and BGAL103) and debranching of arabinans by α-arabinofuranosidases AF1 and AF2. Together, these results demonstrate that flexibility and rigidity of the different cell layers in apple fruit during development and ripening are determined, at least in part, by the control of cell wall pectin remodelling.

Characterization and Identification of PpEIN3 during the Modulation of Fruit Ripening Process by Ectopic Expressions in Tomato

First study of PpEIN3 by transgenic experiments to verify its function in the maturity process PpEIN3 is a positive regulator of ethylene signal transduction pathway to promote fruits ripening Ethylene is one of the most important phytohormone in plants and plays a critical role during growth, development, maturity, and aging. The framework of the ethylene signaling pathway is well reported. Nevertheless, studies on Ethylene Insensitive 3 (EIN3), the downstream regulator of the ethylene signaling pathway, need to be investigated, especially in peach [Prunus persica (L.) Batsch]. In this study, we cloned PpEIN3 from peach and characterized it in tomato (Solanum lycopersicum L.). Our results depicted that the open-reading frame of PpEIN3 was 1875 bp, encoding a protein with 624 amino acid residues that contained a conserved EIN3 domain, a highly conserved N-terminal region, and seven DNA-binding sites. PpEIN3 showed very close association with homologous EIN genes from apple (Malus domestica Borkh.) and grapevine (Vitis vinifera L.). All investigated EIN proteins shared similar domains and structures. The PpEIN3 promoter possessed several motifs related to hormones that affect fruit development and ripening. Spatial-temporal expression analysis revealed that PpEIN3 was expressed at high levels in the late stage of fruit development vs. the early stage. In transgenic tomato, PpEIIN3 showed overexpression and the key ethylene biosynthesis genes SlACO1, SlACS1, and SlSAMS1 were upregulated and promoted early maturation in fruit. By contrast, PpEIIN3 silencing delayed ripening and reduced SlEIN3 expression in tomato. The results confirmed that PpEIN3 is a positive regulator of the ethylene signal transduction pathway, which promoted fruit ripening. Our findings provide valuable insight to the roles in ethylene signal components in the modulation of peach fruit ripening.

Copy number variants in kiwifruit ETHYLENE RESPONSE FACTOR/APETALA2 (ERF/AP2)-like genes show divergence in fruit ripening associated cold and ethylene responses in C-REPEAT/DRE BINDING FACTOR-like genes

The ETYHLENE RESPONSE FACTOR/APETALA2 (ERF/AP2) transcription factors have been shown to control a wide range of developmental and environmental responses in plants. These include hormonal responses to ethylene and Abscisic Acid (ABA) as well as to cold and drought. In Actinidia chinensis (kiwifruit), ripening is unusual: although it is sometimes classed as a climacteric fruit (ethylene-associated ripening), much of fruit ripening occurs independently from autocatalytic ethylene production. Initiation of ripening appears to be strongly developmentally controlled and modulated by low temperature. In this study, fruit treated with different temperatures showed an increase in soluble sugar accumulation, and a corresponding increase in ß-AMYLASE (BAM) genes (predominantly BAM3.2 and BAM9) with lower temperatures. To investigate the potential role of the AP2/ERF gene family in the control of fruit ripening in kiwifruit this family was investigated further. Using the new genome annotation and further genome sequence analysis we identified 226 ERF-like genes, 10 AP2L/RAV-like genes and 32 AP2-like genes. An RNA-seq screen from kiwifruit of different maturities, and following treatment with ethylene and temperatures between 0 and 16°C, revealed 4%, 26% and 18% of the ERF-like genes were upregulated by maturation, ethylene and cold temperatures, respectively. Focusing on the C-REPEAT/DRE BINDING FACTOR (CBF) cold master regulators, nine potential genes were identified based on sequence similarity. Five of these CBF-like genes were found in a copy number variant (CNV) cluster of six genes on chromosome 14. Expression analysis showed that two homeologous genes (ERF41 and ERF180) increased in abundance with cold and ethylene, while the cluster of CNV CBF-like genes had lost the ability to respond to cold and increased only with ethylene, suggesting an evolutionary progression of function of these genes.

The control of endopolygalacturonase expression by the sugarcane RAV transcription factor during aerenchyma formation

The development of lysigenous aerenchyma starts with cell expansion and degradation of pectin from the middle lamella, leading to cell wall modification, and culminating with cell separation. Here we report that nutritional starvation of sugarcane induced gene expression along sections of the first 5 cm of the root and between treatments. We selected two candidate genes: a RAV transcription factor, from the ethylene response factors superfamily, and an endopolygalacturonase (EPG), a glycosyl hydrolase related to homogalacturonan hydrolysis from the middle lamella. epg1 and rav1 transcriptional patterns suggest they are essential genes at the initial steps of pectin degradation during aerenchyma development in sugarcane. Due to the high complexity of the sugarcane genome, rav1 and epg1 were sequenced from 17 bacterial artificial chromosome clones containing hom(e)ologous genomic regions, and the sequences were compared with those of Sorghum bicolor. We used one hom(e)olog sequence from each gene for transactivation assays in tobacco. rav1 was shown to bind to the epg1 promoter, repressing β-glucuronidase activity. RAV repression upon epg1 transcription is the first reported link between ethylene regulation and pectin hydrolysis during aerenchyma formation. Our findings may help to elucidate cell wall degradation in sugarcane and therefore contribute to second-generation bioethanol production.

Transcriptome Analysis Identifies a Zinc Finger Protein Regulating Starch Degradation in Kiwifruit

Ripening, including softening, is a critical factor in determining the postharvest shelf-life of fruit and is controlled by enzymes involved in cell wall metabolism, starch degradation, and hormone metabolism. Here, we used a transcriptomics-based approach to identify transcriptional regulatory components associated with texture, ethylene, and starch degradation in ripening kiwifruit (Actinidia deliciosa). Twelve differentially expressed structural genes, including seven involved in cell wall metabolism, four in ethylene biosynthesis, and one in starch degradation, and 14 transcription factors (TFs) induced by exogenous ethylene treatment and inhibited by the ethylene signaling inhibitor 1-methylcyclopropene were identified as changing in transcript levels during ripening. Moreover, analysis of the regulatory effects of differentially expressed genes identified a zinc finger TF, DNA BINDING WITH ONE FINGER (AdDof3), which showed significant transactivation on the AdBAM3L (β-amylase) promoter. AdDof3 interacted physically with the AdBAM3L promoter, and stable overexpression of AdBAM3L resulted in lower starch content in transgenic kiwifruit leaves, suggesting that AdBAM3L is a key gene for starch degradation. Moreover, transient overexpression analysis showed that AdDof3 up-regulated AdBAM3L expression in kiwifruit. Thus, transcriptomics analysis not only allowed the prediction of some ripening-regulating genes but also facilitated the characterization of a TF, AdDof3, and a key structural gene, AdBAM3L, in starch degradation.

The effect of 1-methylcyclopropene (1-MCP) on expression of ethylene receptor genes in durian pulp during ripening

Rapid fruit ripening is a significant problem that limits the shelf life of durian, with ethylene having a major impact on the regulation of this event. Durian treated with ethephon ripened 3 d after treatment with increased pulp total soluble solids, ethylene production of the whole fruit and decreased pulp firmness compared to the control fruit. 1-MCP treatment delayed ripening by up to 9 d with inhibited accumulation of total soluble solids, color change, softening and ethylene production. Genes related to ethylene perception (DzETR1 and DzETR2) and the signaling pathway (DzCTR1, DzEIL1 and DzEIL2) in the pulp were investigated during this process, using qPCR to quantify changes in gene transcription. All candidate genes were significantly up-regulated in ripening durian pulp. Ethephon treatment increased the expression of DzETR1 and DzETR2 genes, while expression of DzCTR1, DzEIL1 and DzEIL2 were slightly affected. 1-MCP treatment significantly inhibited the expression of the DzETR2 and DzEIL1 genes. The promoters of DzETR2 genes were isolated and their activation by fruit transcription factors studied using transient expression in tobacco leaves. It was found that members of the kiwifruit and apple EIL1, EIL2 and EIL3 genes strongly activated the DzETR2 promoter. These results suggest that ethylene-induced ripening of durian is via the regulation of DzETR2 by EIL transcription factors.

A Genome-Wide Association Study of Apple Quality and Scab Resistance

The apple ( × Borkh.) is an economically and culturally important crop grown worldwide. Growers of this long-lived perennial must produce fruit of adequate quality while also combatting abiotic and biotic stress. Traditional apple breeding can take up to 20 yr from initial cross to commercial release, but genomics-assisted breeding can help accelerate this process. To advance genomics-assisted breeding in apple, we performed genome-wide association studies (GWAS) and genomic prediction in a collection of 172 apple accessions by linking over 55,000 single nucleotide polymorphisms (SNPs) with 10 phenotypes collected over 2 yr. Genome-wide association studies revealed several known loci for skin color, harvest date and firmness at harvest. Several significant GWAS associations were detected for resistance to a major fungal pathogen, apple scab ( [Cke.] Wint.), but we demonstrate that these hits likely represent a single ancestral source. Using genomic prediction, we show that most phenotypes are sufficiently predictable using genome-wide SNPs to be candidates for genomic selection. Finally, we detect a signal for firmness retention after storage on chromosome 10 and show that it may not stem from variation in , a gene repeatedly identified in bi-parental mapping studies and widely believed to underlie a major QTL for firmness on chromosome 10. We provide evidence that this major QTL is more likely due to variation in a neighboring ethylene response factor (ERF) gene. The present study showcases the superior mapping resolution of GWAS compared to bi-parental linkage mapping by identifying a novel candidate gene underlying a well-studied, major QTL involved in apple firmness.

Malus sieversii: the origin, flavonoid synthesis mechanism, and breeding of red-skinned and red-fleshed apples

Flavonoids play essential roles in human health. Apple (Malus domestica Borkh.), one of the most widely produced and economically important fruit crops in temperate regions, is a significant source of flavonoids in the human diet and is among the top nutritionally rated and most widely consumed fruits worldwide. Epidemiological studies have shown that the consumption of apples, which are rich in a variety of free and easily absorbable flavonoids, is associated with a decreased risk of various diseases. However, apple production is challenged by serious inbreeding problems. The narrowing of the hereditary base has resulted in apples with poor nutritional quality and low flavonoid contents. Recently, there have been advances in our understanding of the roles that Malus sieversii (Ledeb.) M.Roem has played in the process of apple domestication and breeding. In this study, we review the origin of cultivated apples and red-fleshed apples, and discuss the genetic diversity and construction of the core collections of M. sieversii. We also discuss current research progress and breeding programs on red-skinned and red-fleshed apples and summarize the exploitation and utilization of M. sieversii in the breeding of high-flavonoid, and red-fleshed apples. This study highlights a valuable pattern of horticultural crop breeding using wild germplasm resources. The future challenges and directions of research on the molecular mechanisms of flavonoid accumulation and high-flavonoid apple breeding are discussed.

A Profusion of Molecular Scissors for Pectins: Classification, Expression, and Functions of Plant Polygalacturonases

In plants, the construction, differentiation, maturation, and degradation of the cell wall are essential for development. Pectins, which are major constituents of primary cell walls in eudicots, function in multiple developmental processes through their synthesis, modification, and degradation. Several pectin modifying enzymes regulate pectin degradation via different modes of action. Polygalacturonases (PGs), which function in the last step of pectin degradation, are a crucial class of pectin-modifying enzymes. Based on differences in their hydrolyzing activities, PGs can be divided into three main types: exo-PGs, endo-PGs, and rhamno-PGs. Their functions were initially investigated based on the expression patterns of PG genes and measurements of total PG activity in organs. In most plant species, PGs are encoded by a large, multigene family. However, due to the lack of genome sequencing data in early studies, the number of identified PG genes was initially limited. Little was initially known about the evolution and expression patterns of PG family members in different species. Furthermore, the functions of PGs in cell dynamics and developmental processes, as well as the regulatory pathways that govern these functions, are far from fully understood. In this review, we focus on how recent studies have begun to fill in these blanks. On the basis of identified PG family members in multiple species, we review their structural characteristics, classification, and molecular evolution in terms of plant phylogenetics. We also highlight the diverse expression patterns and biological functions of PGs during various developmental processes, as well as their mechanisms of action in cell dynamic processes. How PG functions are potentially regulated by hormones, transcription factors, environmental factors, pH and Ca²⁺ is discussed, indicating directions for future research into PG function and regulation.

Hypoxia-responsive ERFs involved in postdeastringency softening of persimmon fruit

Removal of astringency by endogenously formed acetaldehyde, achieved by postharvest anaerobic treatment, is of critical importance for many types of persimmon fruit. Although an anaerobic environment accelerates de-astringency, it also has the deleterious effect of promoting excessive softening, reducing shelf life and marketability. Some hypoxia-responsive ethylene response factors (ERFs) participate in anaerobic de-astringency, but their role in accelerated softening was unclear. Undesirable rapid softening induced by high CO₂ (95%) was ameliorated by adding the ethylene inhibitor 1-MCP (1 μL/L), resulting in reduced astringency while maintaining firmness, suggesting that CO₂ -induced softening involves ethylene signalling. Among the hypoxia-responsive genes, expression of eight involved in fruit cell wall metabolism (Dkβ-gal1/4, DkEGase1, DkPE1/2, DkPG1, DkXTH9/10) and three ethylene response factor genes (DkERF8/16/19) showed significant correlations with postdeastringency fruit softening. Dual-luciferase assay indicated that DkERF8/16/19 could trans-activate the DkXTH9 promoter and this interaction was abolished by a mutation introduced into the C-repeat/dehydration-responsive element of the DkXTH9 promoter, supporting the conclusion that these DkERFs bind directly to the DkXTH9 promoter and regulate this gene, which encodes an important cell wall metabolism enzyme. Some hypoxia-responsive ERF genes are involved in deastringency and softening, and this linkage was uncoupled by 1-MCP. Fruit of the Japanese cultivar 'Tonewase' provide a model for altered anaerobic response, as they lost astringency yet maintained firmness after CO₂ treatment without 1-MCP and changes in cell wall enzymes and ERFs did not occur.

Contrasting Transcriptional Programs Control Postharvest Development of Apples (Malus x domestica Borkh.) Submitted to Cold Storage and Ethylene Blockage

Apple is commercially important worldwide. Favorable genomic contexts and postharvest technologies allow year-round availability. Although ripening is considered a unidirectional developmental process toward senescence, storage at low temperatures, alone or in combination with ethylene blockage, is effective in preserving apple properties. Quality traits and genome wide expression were integrated to investigate the mechanisms underlying postharvest changes. Development and conservation techniques were responsible for transcriptional reprogramming and distinct programs associated with quality traits. A large portion of the differentially regulated genes constitutes a program involved in ripening and senescence, whereas a smaller module consists of genes associated with reestablishment and maintenance of juvenile traits after harvest. Ethylene inhibition was associated with a reversal of ripening by transcriptional induction of anabolic pathways. Our results demonstrate that the blockage of ethylene perception and signaling leads to upregulation of genes in anabolic pathways. We also associated complex phenotypes to subsets of differentially regulated genes.

'Bartlett' pear fruit (Pyrus communis L.) ripening regulation by low temperatures involves genes associated with jasmonic acid, cold response, and transcription factors

Low temperature (LT) treatments enhance ethylene production and ripening rate in the European pear (Pyrus communis L.). However, the underlying molecular mechanisms are not well understood. This study aims to identify genes responsible for ripening enhancement by LT. To this end, the transcriptome of 'Bartlett' pears treated with LT (0°C or 10°C for up to 14 d), which results in faster ripening, and control pears without conditioning treatment was analyzed. LT conditioned pears reached eating firmness (18N) in 6 d while control pears took about 12 d when left to ripen at 20°C. We identified 8,536 differentially expressed (DE) genes between the 0°C-treated and control fruit, and 7,938 DE genes between the 10°C-treated and control fruit. In an attempt to differentiate temperature-induced vs. ethylene-responsive pathways, we also monitored gene expression in fruit sequentially treated with 1-MCP then exposed to low temperature. This analysis revealed that genes associated with jasmonic acid biosynthesis and signaling, as well as the transcription factors TCP9a, TCP9b, CBF1, CBF4, AGL24, MYB1R1, and HsfB2b could be involved in the LT-mediated enhancement of ripening independently or upstream of ethylene.

Analysis about Heat Transfer of Vegetables during Cold Shock Treatment and Preservation Quality after Storage

This study investigated the heat transfer mechanism and preservation quality of axisymmetric vegetables during cold shock treatment (CST). A simulation model of heat transfer was developed based on geometrical and biological characteristics of the vegetables by finite element difference method. CST for cucumbers and carrots with cold water at 0°C (40 min), 2°C (20, 40 and 60 min) and 4°C (40 min) was conducted to evaluate the relationships between heat transfer characteristics and preservation quality. The comparative analysis shown that the simulated results agreed well with measured results. Meanwhile, in terms of weight loss, firmness and POD activity, CST with cold water at 2°C for 40 min could achieve the most positive effect on preserving cucumbers. The cucumber during treatment experienced whole variable temperature stage and appropriate constant temperature stage so as to reach optimal preservation quality.

Analysis of the Xyloglucan Endotransglucosylase/Hydrolase Gene Family during Apple Fruit Ripening and Softening

Ethylene and xyloglucan endotransglucosylase/hydrolase (XTH) genes were important for fruit ripening and softening in 'Taishanzaoxia' apple. In this study, we found it was ACS1-1/-1 homozygotes in 'Taishanzaoxia' apple, which determined the higher transcription activity of ACS1. XTH1, XTH3, XTH4, XTH5, and XTH9 were mainly involved in the early fruit softening independent of ethylene, while XTH2, XTH6, XTH7, XTH8, XTH10, and XTH11 were predominantly involved in the late fruit softening dependent on ethylene. Overexpression of XTH2 and XTH10 in tomato resulted in the elevated expression of genes involved in ethylene biosynthesis (ACS2, ACO1), signal transduction (ERF2), and fruit softening (XTHs, PG2A, Cel2, and TBG4). In summary, the burst of ethylene in 'Taishanzaoxia' apple was predominantly determined by ACS1-1/-1 genotype, and the differential expression of XTH genes dependent on and independent of ethylene played critical roles in the fruit ripening and softening. XTH2 and XTH10 may act as a signal switch in the feedback regulation of ethylene signaling and fruit softening.

Influence of 1-Methylcyclopropene Treatment on Postharvest Quality of Four Scab (Venturia inaequalis)-Resistant Apple Cultivars

Scab (Venturia inaequalis) is a very serious disease for apples causing up to 80% of loss in yield but there are only a few studies on postharvest quality of scab-resistant cultivars. In this study we evaluated the effect of 1-methylcyclopropene (1-MCP) on fruit quality, total phenolic content, and antioxidant capacity after storage of four scab-resistant cultivars and compared to a standard cultivar, “Golden Delicious.” In general, ethylene production and respiration rates significantly differed among cultivars, between control and 1-MCP-treated fruits, and between storage duration regimes. 1-MCP treatment retarded fruit softening and lowered juice pH but storage effect on soluble solids and acidity depended on cultivar and 1-MCP treatment. Total phenolic content was significantly affected by storage duration and 1-MCP treatment. Antioxidant capacity of the four scab-resistant cultivars was either similar to or significantly higher than that of “Golden Delicious” with the 1-MCP-treated fruits having significantly higher antioxidant capacity than the nontreated fruits after storage. Our results clearly show that the quality of four scab-resistant cultivars was comparable to that of “Golden Delicious” and 1-MCP effect differed among cultivars. These differences need to be considered in developing storage regime to minimize quality deterioration during long-term storage.