PpIAA1 and PpERF4 form a positive feedback loop to regulate peach fruit ripening by integrating auxin and ethylene signals

Unlocking the Growth Potential of Poplar: A Novel Transcriptomic-Metabolomic Approach to Evaluating the Impact of Divergent Pruning Strategies

Pruning is a common forest-tending method; its purpose is to promote growth and improve the overall stand quality. Poplar is a fast-growing, broad-leaved tree species with high ecological and economic value. It is a common management method to promote its growth by pruning and adjusting the spatial structure of the stand, but its potential regulatory mechanism remains unclear. In this study, transcriptome and metabolome data of different parts at all pruning intensities were determined and analyzed. The results showed that 7316 differentially expressed genes were identified in this study. In the plant hormone signal transduction pathway, candidate genes were found in eight kinds of plant hormones, among which the main expression was gibberellin, auxin, and brassinosteroid. Some candidate gene structures (beta-glucosidase, endoglucanase, hexokinase, glucan endo-1, 3-beta-D-glucosidase, beta-fructofuranosidase, fructokinase, maltase-glucoamylase, phosphoglucomutase, and sucrose) were specifically associated with starch and sucrose biosynthesis. In the starch and sucrose biosynthesis pathway, D-fructose 6-phosphate, D-glucose 1,6-bisphosphate, and glucose-1-phosphate were the highest in stems and higher in the first round of pruning than in no pruning. The bHLH plays a key role in the starch and sucrose synthetic pathway, and AP2/ERF-ERF is important in the plant hormone signal transduction pathway. These results laid a foundation for understanding the molecular mechanism of starch and sucrose biosynthesis and provided a theoretical basis for promoting tree growth through pruning.

Rational Design of High-Efficiency Synthetic Small Regulatory RNAs and Their Application in Robust Genetic Circuit Performance Through Tight Control of Leaky Gene Expression

Synthetic sRNAs show promise as tools for targeted and programmable gene expression manipulation. However, the design of high-efficiency synthetic sRNAs is a challenging task that necessitates careful consideration of multiple factors. Therefore, this study aims to investigate rational design strategies that significantly and robustly enhance the efficiency of synthetic sRNAs. This is achieved by optimizing the following parameters: the sRNA scaffold, mRNA binding affinity, Hfq protein expression level, and mRNA secondary structure. By utilizing optimized synthetic sRNAs within a positive feedback circuit, we effectively addressed the issue of gene expression leakage─an enduring challenge in synthetic biology that undermines the reliability of genetic circuits in bacteria. Our designed synthetic sRNAs successfully prevented gene expression leakage, thus averting unintended circuit activation caused by initial expression noise, even in the absence of signal molecules. This result shows that high-efficiency synthetic sRNAs not only enable precise gene knockdown for metabolic engineering but also ensure the robust performance of synthetic circuits. The strategies developed here hold significant promise for broad applications across diverse biotechnological fields, establishing synthetic sRNAs as pivotal tools in advancing synthetic biology and gene regulation.

Tandem transcription factors PpNAC1 and PpNAC5 synergistically activate the transcription of the PpPGF to regulate peach softening during fruit ripening

Peach fruit rapidly soften after harvest, a significant challenge for producers and marketers as it results in rotting fruit and significantly reduces shelf life. In this study, we identified two tandem genes, PpNAC1 and PpNAC5, within the sr (slow ripening) locus. Phylogenetic analysis showed that NAC1 and NAC5 are highly conserved in dicots and that PpNAC1 is the orthologous gene of Non-ripening (NOR) in tomato. PpNAC1 and PpNAC5 were highly expressed in peach fruit, with their transcript levels up-regulated at the onset of ripening. Yeast two-hybrid and bimolecular fluorescence complementation assays showed PpNAC1 interacting with PpNAC5 and this interaction occurs with the tomato and apple orthologues. Transient gene silencing experiments showed that PpNAC1 and PpNAC5 positively regulate peach fruit softening. Yeast one-hybrid and dual luciferase assays and LUC bioluminescence imaging proved that PpNAC1 and PpNAC5 directly bind to the PpPGF promoter and activate its transcription. Co-expression of PpNAC1 and PpNAC5 showed higher levels of PpPGF activation than expression of PpNAC1 or PpNAC5 alone. In summary, our findings demonstrate that the tandem transcription factors PpNAC1 and PpNAC5 synergistically activate the transcription of PpPGF to regulate fruit softening during peach fruit ripening.

Promoter variations of ClERF1 gene determines flesh firmness in watermelon

BACKGROUND

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

RESULTS

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

CONCLUSIONS

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

Banana MabHLH28 positively regulates the expression of softening-related genes to mediate fruit ripening independently or via cooperating with MaWRKY49/111

Texture softening is a physiological indicator of fruit ripening, which eventually contributes to fruit quality and the consumer's acceptance. Despite great progress having been made in identification of the genes related to fruit softening, the upstream transcriptional regulatory pathways of these softening-related genes are not fully elucidated. Here, a novel bHLH gene, designated as MabHLH28, was identified because of its significant upregulation in banana fruit ripening. DAP-Seq analysis revealed that MabHLH28 bound to the core sequence of 'CAYGTG' presented in promoter regions of fruit softening-associated genes, such as the genes related to cell wall modification (MaPG3, MaPE1, MaPL5, MaPL8, MaEXP1, MaEXP2, MaEXPA2, and MaEXPA15) and starch degradation (MaGWD1 and MaLSF2), and these bindings were validated by EMSA and DLR assays. Transient overexpression and knockdown of MabHLH28 in banana fruit resulted in up- and down-regulation of softening-related genes, thereby hastening and postponing fruit ripening. Furthermore, overexpression of MabHLH28 in tomato accelerated the ripening process by elevating the accumulation of softening-associated genes. In addition, MabHLH28 showed interaction withMaWRKY49/111 and itself to form protein complexes, which could combinatorically strengthen the transcription of softening-associated genes. Taken together, our findings suggest that MabHLH28 mediates fruit softening by upregulating the expression of softening-related genes either alone or in combination with MaWRKY49/111.

Genome-wide identification and expression analysis of the JMJ-C gene family in melon (Cucumis melo L.) reveals their potential role in fruit development

BACKGROUND

Proteins with the jumonji (JMJ)-C domain belong to the histone demethylase family and contribute to reverse histone methylation. Although JMJ-C family genes have an essential role in regulating plant growth and development, the characterization of the JMJ-C family genes in melon has not been uncovered.

RESULTS

In this study, a total of 17 JMJ-C proteins were identified in melon (Cucumis melo L.). CmJMJs were categorized into five subfamilies based on the specific conserved domain: KDM4/JHDM3, KDM5/JARID1, JMJD6, KDM3/JHDM2, and JMJ-C domain-only. The chromosome localization analyses showed that 17 CmJMJs were distributed on nine chromosomes. Cis-acting element analyses of the 17 CmJMJ genes showed numerous hormone, light, and stress response elements distributed in the promoter region. Covariance analysis revealed one pair of replicated fragments (CmJMJ3a and CmJMJ3b) in 17 CmJMJ genes. We investigated the expression profile of 17 CmJMJ genes in different lateral organs and four developmental stages of fruit by RNA-seq transcriptome analysis and RT-qPCR. The results revealed that most CmJMJ genes were prominently expressed in female flowers, ovaries, and developing fruits, suggesting their active role in melon fruit development. Subcellular localization showed that the fruit-related CmJMJ5a protein is specifically localized in the cell nucleus.

CONCLUSIONS

This study provides a comprehensive understanding of the gene structure, classification, and evolution of JMJ-C in melon and supports the clarification of the JMJ-C functions in further research.

A comprehensive investigation of the regulatory roles of OsERF096, an AP2/ERF transcription factor, in rice cold stress response

KEY MESSAGE

OsERF096 negatively regulates rice cold tolerance and mediates IAA biosynthesis and signaling under cold stress. The APETALA2/ethylene-responsive factor (AP2/ERF) transcription factors play important roles in regulating plant tolerance to abiotic stress. OsERF096 was previously identified as a direct target of miR1320, and was suggested to negatively regulate rice cold tolerance. In this study, we performed RNA-sequencing and targeted metabolomics assays to reveal the regulatory roles of OsERF096 in cold stress response. GO and KEGG analysis of differentially expressed genes showed that the starch and sucrose metabolism, plant-pathogen interaction, and plant hormone signal transduction pathways were significantly enriched. Quantification analysis confirmed a significant difference in sugar contents among WT and OsERF096 transgenic lines under cold treatment. Targeted metabolomics analysis uncovered that IAA accumulation and signaling were modified by OsERF096 in response to cold stress. Expectedly, qRT-PCR assays confirmed significant OsIAAs and OsARFs expression changes in OsERF096 transgenic lines. Finally, we identified three targets of OsERF096 based on RNA-seq, qRT-PCR, and dual-LUC assays. In summary, these results revealed the multiple regulatory roles of OsERF096 in cold stress response.

Bioinformatic Assessment and Expression Profiles of the AP2/ERF Superfamily in the Melastoma dodecandrum Genome

AP2/ERF transcription factors play crucial roles in various biological activities, including plant growth, development, and responses to biotic and abiotic stressors. However, limited research has been conducted on the AP2/ERF genes of Melastoma dodecandrum for breeding of this potential fruit crop. Leveraging the recently published whole genome sequence, we conducted a comprehensive assessment of this superfamily and explored the expression patterns of AP2/ERF genes at a genome-wide level. A significant number of genes, totaling 218, were discovered to possess the AP2 domain sequence and displayed notable structural variations among five subfamilies. An uneven distribution of these genes was observed on 12 pseudochromosomes as the result of gene expansion facilitated by segmental duplications. Analysis of cis-acting elements within promoter sites and 87.6% miRNA splicing genes predicted their involvement in multiple hormone responses and abiotic stresses through transcriptional and post-transcriptional regulations. Transcriptome analysis combined with qRT-PCR results indicated that certain candidate genes are involved in tissue formation and the response to developmental changes induced by IAA hormones. Overall, our study provides valuable insights into the evolution of ERF genes in angiosperms and lays a solid foundation for future breeding investigations aimed at improving fruit quality and enhancing adaptation to barren land environments.

Exogenous auxin regulates the growth and development of peach fruit at the expansion stage by mediating multiple-hormone signaling

BACKGROUND

Fruit expansion stage is crucial to fruit yield and quality formation, and auxin plays a significant role by mediating multi-hormone signals during fruit expansion. However, till now, it is still unclear of the molecular regulatory network during auxin-mediated peach fruit expansion.

RESULTS

Here, exogenous NAA application markedly increased IAA content and drastically decreased ABA content at the fruit expansion stage. Correspondingly, NAA mainly induced the auxin biosynthesis gene (1 PpYUCCA) and early auxin-responsive genes (7PpIAA, 3 PpGH3, and 14 PpSAUR); while NAA down-regulated ABA biosynthesis genes (2 PpNCED, 1 PpABA3, and 1 PpAAO3). In addition, many DEGs involved in other plant hormone biosynthesis and signal transduction were significantly enriched after NAA treatment, including 7 JA, 7 CTK, 6 ETH, and 3 GA. Furthermore, we also found that NAA treatment down-regulated most of genes involved in the growth and development of peach fruit, including the cell wall metabolism-related genes (PpEG), sucrose metabolism-related genes (PpSPS), phenylalanine metabolism-related genes (PpPAL, Pp4CL, and PpHCT), and transcription factors (PpNAC, PpMADS-box, PpDof, PpSBP, and PpHB).

CONCLUSION

Overall, NAA treatment at the fruit expansion stage could inhibit some metabolism processes involved in the related genes in the growth and development of peach fruit by regulating multiple-hormone signaling networks. These results help reveal the short-term regulatory mechanism of auxin at the fruit expansion stage and provide new insights into the multi-hormone cascade regulatory network of fruit growth and development.

PpARF6 acts as an integrator of auxin and ethylene signaling to promote fruit ripening in peach

Although auxin is known to induce ethylene biosynthesis in some Rosaceae fruit crops, the mechanisms underlying the auxin-ethylene interaction during fruit ripening remain largely unknown. Here, the regulatory role of an auxin response factor, PpARF6, in fruit ripening was investigated in peach. Peach fruits showed accelerated ripening after treatment with auxin and PpARF6 was found to be significantly induced. PpARF6 not only could induce ethylene synthesis by directly activating the transcription of ethylene biosynthetic genes, but also competed with EIN3-binding F-box proteins PpEBF1/2 for binding to ethylene-insensitive3-like proteins PpEIL2/3, thereby keeping PpEIL2/3 active. Moreover, PpARF6 showed an interaction with PpEIL2/3 to enhance the PpEIL2/3-activated transcription of ethylene biosynthetic genes. Additionally, ectopic overexpression of PpARF6 in tomato accelerated fruit ripening by promoting the expression of genes involved in ethylene synthesis and fruit texture. In summary, our results revealed a positive regulatory role of PpARF6 in peach fruit ripening via integrating auxin and ethylene signaling.

Auxin-responsive protein MaIAA17-like modulates fruit ripening and ripening disorders induced by cold stress in 'Fenjiao' banana

Cold stress severely affects the banana fruit softening and de-greening, significantly inhibiting the ripening processes. However, the mechanism of ripening disorder caused by chilling injury (CI) in banana fruit remains largely unknown. Herein, MaIAA17-like, an Auxin/Indole-3-Acetic Acid (Aux/IAA) family member, was found to be highly related to the softening and de-greening in 'Fenjiao' banana. Its expression was rapidly increased with fruit ripening and then gradually decreased under normal ripening conditions (22 °C). Notably, cold storage severely repressed MaIAA17-like expression but was rapidly increased following ethephon treatment for ripening in fruits without CI. However, the expression repression was not reverted in fruits with serious CI symptoms after 12 days of storage at 7 °C. AtMaIAA17-like bound and regulated the activities of promoters of chlorophyll (MaNOL and MaSGR1), starch (MaBAM6 and MaBAM8), and cell wall (MaSUR14 and MaPL8) degradation-related genes. MaIAA17-like also interacted with ethylene-insensitive 3-binding F-box protein (MaEBF1), further activating the expression of MaNOL, MaBAM8, MaPL8, and MaSUR14. Generally, the transient overexpression of MaIAA17-like promoted fruit ripening by inducing the expression of softening and de-greening related genes. However, silencing MaIAA17-like inhibited fruit ripening by reducing the expression of softening and de-greening related genes. These results imply that MaIAA17-like modulates fruit ripening by transcriptionally upregulating the key genes related to fruit softening and de-greening.

Comparative physiological and transcriptomic analyses provide insights into fruit softening in Chinese cherry [Cerasus pseudocerasus (Lindl.) G.Don]

Fruit softening is a complex, genetically programmed and environmentally regulated process, which undergoes biochemical and physiological changes during fruit development. The molecular mechanisms that determine these changes in Chinese cherry [Cerasus peseudocerasus (Lindl.) G.Don] fruits are still unknown. In the present study, fruits of hard-fleshed 'Hongfei' and soft-fleshed 'Pengzhoubai' varieties of Chinese cherry were selected to illustrate the fruit softening at different developmental stages. We analyzed physiological characteristics and transcriptome profiles to identify key cell wall components and candidate genes related to fruit softening and construct the co-expression networks. The dynamic changes of cell wall components (cellulose, hemicellulose, pectin, and lignin), the degrading enzyme activities, and the microstructure were closely related to the fruit firmness during fruit softening. A total of 6,757 and 3,998 differentially expressed genes (DEGs) were screened between stages and varieties, respectively. Comprehensive functional enrichment analysis supported that cell wall metabolism and plant hormone signal transduction pathways were involved in fruit softening. The majority of structural genes were significantly increased with fruit ripening in both varieties, but mainly down-regulated in Hongfei fruits compared with Pengzhoubai, especially DEGs related to cellulose and hemicellulose metabolism. The expression levels of genes involving lignin biosynthesis were decreased with fruit ripening, while mainly up-regulated in Hongfei fruits at red stage. These obvious differences might delay the cell all degrading and loosening, and enhance the cell wall stiffing in Hongfei fruits, which maintained a higher level of fruit firmness than Pengzhoubai. Co-expressed network analysis showed that the key structural genes were correlated with plant hormone signal genes (such as abscisic acid, auxin, and jasmonic acid) and transcription factors (MADS, bHLH, MYB, ERF, NAC, and WRKY). The RNA-seq results were supported using RT-qPCR by 25 selected DEGs that involved in cell wall metabolism, hormone signal pathways and TF genes. These results provide important basis for the molecular mechanism of fruit softening in Chinese cherry.

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

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

ETHYLENE-INSENSITIVE 3-LIKE 2 regulates β-carotene and ascorbic acid accumulation in tomatoes during ripening

ETHYLENE-INSENSITIVE 3/ETHYLENE-INSENSITIVE 3-LIKEs (EIN3/EILs) are important ethylene response factors during fruit ripening. Here, we discovered that EIL2 controls carotenoid metabolism and ascorbic acid (AsA) biosynthesis in tomato (Solanum lycopersicum). In contrast to the red fruits presented in the wild type (WT) 45 d after pollination, the fruits of CRISPR/Cas9 eil2 mutants and SlEIL2 RNA interference lines (ERIs) showed yellow or orange fruits. Correlation analysis of transcriptome and metabolome data for the ERI and WT ripe fruits revealed that SlEIL2 is involved in β-carotene and AsA accumulation. ETHYLENE RESPONSE FACTORs (ERFs) are the typical components downstream of EIN3 in the ethylene response pathway. Through a comprehensive screening of ERF family members, we determined that SlEIL2 directly regulates the expression of 4 SlERFs. Two of these, SlERF.H30 and SlERF.G6, encode proteins that participate in the regulation of LYCOPENE-β-CYCLASE 2 (SlLCYB2), encoding an enzyme that mediates the conversion of lycopene to carotene in fruits. In addition, SlEIL2 transcriptionally repressed L-GALACTOSE 1-PHOSPHATE PHOSPHATASE 3 (SlGPP3) and MYO-INOSITOL OXYGENASE 1 (SlMIOX1) expression, which resulted in a 1.62-fold increase of AsA via both the L-galactose and myoinositol pathways. Overall, we demonstrated that SlEIL2 functions in controlling β-carotene and AsA levels, providing a potential strategy for genetic engineering to improve the nutritional value and quality of tomato fruit.

Transcriptomic Analysis Reveals Genes Associated with the Regulation of Peach Fruit Softening and Senescence during Storage

Peach (Prunus persica (L.) Batsch) is a highly desirable fruit that is consumed around the world. However, the peach fruit is highly perishable after harvest, a characteristic that limits the distribution and supply to the market and causes heavy economic losses. Thus, peach fruit softening and senescence after harvest urgently need to be addressed. In the current study, transcriptomic analysis was performed to identify candidate genes associated with peach fruit softening and senescence, comparing peach fruit from cultivars with different flesh textures, namely melting and stony hard (SH) flesh textures during storage at room temperature. The mitogen-activated protein kinase signaling pathway-plant and plant hormone signal transduction pathways were associated with peach fruit softening and senescence according to the Venn diagram analysis and weighted gene co-expression network analysis. The expression levels of seven genes, including Prupe.1G034300, Prupe.2G176900, Prupe.3G024700, Prupe.3G098100, Prupe.6G226100, Prupe.7G234800, and Prupe.7G247500, were higher in melting peach fruit than in SH peach fruit during storage. Furthermore, the SH peach fruit softened rapidly after 1-naphthylacetic acid treatment, during which the levels of expression of these seven genes, determined by a quantitative reverse transcription polymerase chain reaction, were strongly induced and upregulated. Thus, these seven genes may play essential roles in regulating peach fruit softening and senescence.

Research Progress on Mango Post-Harvest Ripening Physiology and the Regulatory Technologies

Mango (Mangifera indica L.) is an important tropical fruit with a delicate taste, pleasant aroma, and high nutritional value. In recent years, with the promotion of the rural revitalization strategy and the development of the poverty alleviation industry, China has gradually become an important mango producer. However, the short shelf life of mango fruit, the difficulty in regulating the postharvest quality, and the lack of preservation technology are the main problems that need to be solved in China's mango industry. In this paper, the physiological changes and mechanisms of mango during postharvest ripening were summarized, including sugar and acid changes, pigment synthesis and accumulation, and aroma formation and accumulation. The physical, chemical, and biological technologies (such as endogenous phytohormones, temperature, light, chemical preservatives, and edible coatings) commonly used in the regulation of mango postharvest ripening and their action principles were emphatically expounded. The shortcomings of the existing mango postharvest ripening regulation technology and physiological mechanism research were analyzed in order to provide a reference for the industrial application and development of mango postharvest.

A tomato HD-zip I transcription factor, VAHOX1, acts as a negative regulator of fruit ripening

Homeodomain-leucine zipper (HD-Zip) transcription factors are only present in higher plants and are involved in plant development and stress responses. However, our understanding of their participation in the fruit ripening of economical plants, such as tomato (Solanum lycopersicum), remains largely unclear. Here, we report that VAHOX1, a member of the tomato HD-Zip I subfamily, was expressed in all tissues, was highly expressed in breaker+4 fruits, and could be induced by ethylene. RNAi repression of VAHOX1 (VAHOX1-RNAi) resulted in accelerated fruit ripening, enhanced sensitivity to ethylene, and increased total carotenoid content and ethylene production. Conversely, VAHOX1 overexpression (VAHOX1-OE) in tomato had the opposite effect. RNA-Seq results showed that altering VAHOX1 expression affected the transcript accumulation of a series of genes involved in ethylene biosynthesis and signal transduction and cell wall modification. Additionally, a dual-luciferase reporter assay, histochemical analysis of GUS activity and a yeast one-hybrid (Y1H) assay revealed that VAHOX1 could activate the expression of AP2a. Our findings may expand our knowledge about the physiological functions of HD-Zip transcription factors in tomato and highlight the diversities of transcriptional regulation during the fruit ripening process.

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.

PpTCP18 is upregulated by lncRNA5 and controls branch number in peach (Prunus persica) through positive feedback regulation of strigolactone biosynthesis

Branch number is an important agronomic trait in peach (Prunus persica) trees because plant architecture affects fruit yield and quality. Although breeders can select varieties with different tree architecture, the biological mechanisms underlying architecture remain largely unclear. In this study, a pillar peach ('Zhaoshouhong') and a standard peach ('Okubo') were compared. 'Zhaoshouhong' was found to have significantly fewer secondary branches than 'Okubo'. Treatment with the synthetic strigolactone (SL) GR24 decreased branch number. Transcriptome analysis indicated that PpTCP18 (a homologous gene of Arabidopsis thaliana BRC1) expression was negatively correlated with strigolactone synthesis gene expression, indicating that PpTCP18 may play an important role in peach branching. Yeast one-hybrid, electrophoretic mobility shift, dual-luciferase assays and PpTCP18-knockdown in peach leaf buds indicated that PpTCP18 could increase expression of PpLBO1, PpMAX1, and PpMAX4. Furthermore, transgenic Arabidopsis plants overexpressing PpTCP18 clearly exhibited reduced primary rosette-leaf branches. Moreover, lncRNA sequencing and transient expression analysis revealed that lncRNA5 targeted PpTCP18, significantly increasing PpTCP18 expression. These results provide insights into the mRNA and lncRNA network in the peach SL signaling pathway and indicate that PpTCP18, a transcription factor downstream of SL signaling, is involved in positive feedback regulation of SL biosynthesis. This role of PpTCP18 may represent a novel mechanism in peach branching regulation. Our study improves current understanding of the mechanisms underlying peach branching and provides theoretical support for genetic improvement of peach tree architecture.

1-Methylcyclopropene counteracts ethylene promotion of fruit softening and roles of MiERF2/8 and MiPG in postharvest mangoes

Ethylene burst is an important sign of the initiation of postharvest mango ripening and softening is a typical characteristic of fruit ripening. However, the intrinsic link between ethylene release and fruit softening during ripening of postharvest mangoes is still not clear. The aim of this study was to investigate the effects of ethylene and its action inhibitor 1-methylcyclopropene (1-MCP) on fruit softening and ripening and the underlying regulatory mechanisms. Results showed that ethephon (ETH) promoted ethylene release and enhanced MDA content and activities of cell wall degrading enzymes, whereas 1-MCP treatment exhibited an opposite effect. Moreover, real-time quantitative polymerase chain reaction indicated that the transcription levels of genes involved in cell wall degradation (MiPG, Miβ-GAL and MiPE), ethylene biosynthesis (MiACO1 and MiACS6) and ethylene response factor (MiERF8) were remarkably induced by ETH. Correlation analysis further revealed that the production of ethylene was significantly negatively correlated with firmness, but positively correlated with MDA content, activities of cell wall degrading enzymes and expressions of MiPG and Miβ-GAL. Furthermore, yeast one hybrid (Y1H) assay showed that MiERF2 and MiERF8 could directly bind to the promotor of MiPG and then regulate its transcription. These findings suggest that ethylene production is closely associated with fruit softening, and MiERF2 and MiERF8 and MiPG may play crucial roles in regulation of ripening and softening of postharvest mangoes.

Interaction between PpERF5 and PpERF7 enhances peach fruit aroma by upregulating PpLOX4 expression

Ethylene plays a critical role in peach (Prunus persica) fruit ripening; however, the molecular mechanism underlying ethylene-mediated aroma biosynthesis remains unclear. Here, we compared the difference in aroma-related volatiles and gene expression levels between melting-flesh (MF) and stony hard (SH) peach cultivars at S3, S4 I, S4 II, S4 III stages, and explored the relation between volatile biosynthesis related genes and ethylene response factor (ERF) genes. The concentration of fruity aromatic compounds such as lactones and terpenes increased significantly in MF peach during fruit ripening, while it was nearly undetectable in SH peach. LOX4 and FAD1 genes expressed concomitantly with ethylene emission and significantly downregulated by 1-MCP. Besides, 1-MCP treatment could sharply influence the fruity aromatic compounds, suggesting that these genes play key roles in volatile biosynthesis during fruit ripening. Furthermore, PpERF5 and PpERF7 could bind together to form a protein complex that enhanced the transcription of LOX4 more than each transcription factor individually. Overall, this work provides new insights into the transcriptional regulatory mechanisms associated with aroma formation during peach fruit ripening.

Transcriptome analysis of peach fruit under 1-MCP treatment provides insights into regulation network in melting peach softening

Peach (Prunus persica L.) displays distinguish texture phenotype during postharvest, which could be classified into three types, including melting flesh (MF), non-melting flesh (NMF) and stony-hard (SH). Of that MF peach would soften rapidly with an outbreak of ethylene production, which cause a huge waste during fruit transportation and storage. 1-methylcyclopropene (1-MCP) was used to alleviate fruit softening. In this study, we performed RNA-sequencing on two MF peach cultivars (‘YuLu’ and ‘Yanhong’) after 1-MCP treatment to identify the candidate genes participating in peach fruit softening. 167 genes were identified by WGCNA and correlation analysis, which could respond to 1-MCP treatment and might be related to softening. Among them, 5 auxin related genes including 2 IAAs, 1 ARF and 2 SAURs, and 4 cell wall modifying genes (PpPG1, PpPG2, PpPG24 and PpPMEI) were characterized as key genes participating in MF peach softening. Furthermore, 2 transcription factors, which belong to HD-ZIP and MYB were predicted as candidates regulating softening process by constructing transcriptional network of these 4 cell wall modifying genes combined with expression pattern analysis, of that the HD-ZIP could trans-activate promoter of PpPG1.

PpSAUR43, an Auxin-Responsive Gene, Is Involved in the Post-Ripening and Softening of Peaches

Auxin’s role in the post-ripening of peaches is widely recognized as important. However, little is known about the processes by which auxin regulates fruit post-ripening. As one of the early auxin-responsive genes, it is critical to understand the role of small auxin-up RNA (SAUR) genes in fruit post-ripening and softening. Herein, we identified 72 PpSAUR auxin-responsive factors in the peach genome and divided them into eight subfamilies based on phylogenetic analysis. Subsequently, the members related to peach post-ripening in the PpSAUR gene family were screened, and we targeted PpSAUR43. The expression of PpSAUR43 was decreased with fruit post-ripening in melting flesh (MF) fruit and was high in non-melting flesh (NMF) fruit. The overexpression of PpSAUR43 showed a slower rate of firmness decline, reduced ethylene production, and a delayed fruit post-ripening process. The MADS-box gene family plays an important regulatory role in fruit ripening. In this study, we showed with yeast two-hybrid (Y2H) and bimolecular fluorescence complementation (BIFC) experiments that PpSAUR43 can interact with the MADS-box transcription factor PpCMB1(PpMADS2), which indicates that PpSAUR43 may inhibit fruit ripening by suppressing the function of the PpCMB1 protein. Together, these results indicate that PpSAUR43 acts as a negative regulator involved in the peach post-ripening process.

APETALA2/ethylene responsive factor in fruit ripening: Roles, interactions and expression regulation

Insects and animals are attracted to, and feed on ripe fruit, thereby promoting seed dispersal. As a vital vitamin and nutrient source, fruit make up an indispensable and enjoyable component of the human diet. Fruit ripening involves a series of physiological and biochemical changes in, among others, pigmentation, chlorophyll (Chl) degradation, texture, sugar accumulation, and flavor. Growing evidence indicates that the coordinated and ordered trait changes during fruit ripening depend on a complex regulatory network consisting of transcription factors, co-regulators, hormonal signals, and epigenetic modifications. As one of the predominant transcription factor families in plants and a downstream component of ethylene signaling, more and more studies are showing that APETALA2/ethylene responsive factor (AP2/ERF) family transcription factors act as critical regulators in fruit ripening. In this review, we focus on the regulatory mechanisms of AP2/ERFs in fruit ripening, and in particular the recent results on their target genes and co-regulators. We summarize and discuss the role of AP2/ERFs in the formation of key fruit-ripening attributes, the enactment of their regulatory mechanisms by interaction with other proteins, their role in the orchestration of phytohormone-signaling networks, and the epigenetic modifications associated with their gene expression. Our aim is to provide a multidimensional perspective on the regulatory mechanisms of AP2/ERFs in fruit ripening, and a reference for understanding and furthering research on the roles of AP2/ERF in fruit ripening.