Down-Regulation of PpBGAL10 and PpBGAL16 Delays Fruit Softening in Peach by Reducing Polygalacturonase and Pectin Methylesterase Activity

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.

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.

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.

Genome-wide characterization of the cellulose synthase gene family in Ziziphus jujuba reveals its function in cellulose biosynthesis during fruit development

The cellulose synthase (Ces/Csl) is a key enzyme in plant cellulose synthesis. Jujube fruits are rich in cellulose. 29 ZjCesA/Csl genes were identified in jujube genome and showed tissue-specific expression. 13 genes highly expressed in jujube fruit exhibited obviously sequential expressions during the fruit development, indicating that they might play distinct roles during the process. Meanwhile, the correlation analysis showed the expressions of ZjCesA1 and ZjCslA1 were significant positive related to the cellulose synthase activities. Furthermore, transient overexpressions of ZjCesA1 or ZjCslA1 in jujube fruits significantly increased cellulose synthase activities and contents, whereas silencing of ZjCesA1 or ZjCslA1 in jujube seedlings obviously reduced cellulose levels. Moreover, the Y2H assays verified that ZjCesA1 and ZjCslA1 may participate in cellulose synthesis by forming protein complexes. The study not only reveals the bioinformatics characteristics and functions of cellulose synthase genes in jujube, but also provides clues for studying cellulose synthesis in other fruits.

Transgene-free genome editing and RNAi ectopic application in fruit trees: Potential and limitations

For the past fifteen years, significant research advances in sequencing technology have led to a substantial increase in fruit tree genomic resources and databases with a massive number of OMICS datasets (transcriptomic, proteomics, metabolomics), helping to find associations between gene(s) and performance traits. Meanwhile, new technology tools have emerged for gain- and loss-of-function studies, specifically in gene silencing and developing tractable plant models for genetic transformation. Additionally, innovative and adapted transformation protocols have optimized genetic engineering in most fruit trees. The recent explosion of new gene-editing tools allows for broadening opportunities for functional studies in fruit trees. Yet, the fruit tree research community has not fully embraced these new technologies to provide large-scale genome characterizations as in cereals and other staple food crops. Instead, recent research efforts in the fruit trees appear to focus on two primary translational tools: transgene-free gene editing via Ribonucleoprotein (RNP) delivery and the ectopic application of RNA-based products in the field for crop protection. The inherent nature of the propagation system and the long juvenile phase of most fruit trees are significant justifications for the first technology. The second approach might have the public favor regarding sustainability and an eco-friendlier environment for a crop production system that could potentially replace the use of chemicals. Regardless of their potential, both technologies still depend on the foundational knowledge of gene-to-trait relationships generated from basic genetic studies. Therefore, we will discuss the status of gene silencing and DNA-based gene editing techniques for functional studies in fruit trees followed by the potential and limitations of their translational tools (RNP delivery and RNA-based products) in the context of crop production.

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.

PpePL1 and PpePL15 Are the Core Members of the Pectate Lyase Gene Family Involved in Peach Fruit Ripening and Softening

Pectin is the major component in the primary cell wall and middle lamella, maintaining the physical stability and mechanical strength of the cell wall. Pectate lyase (PL), a cell wall modification enzyme, has a major influence on the structure of pectin. However, little information and no comprehensive analysis is available on the PL gene family in peach (Prunus persica L. Batsch). In this study, 20 PpePL genes were identified in peach. We characterized their physicochemical characteristics, sequence alignments, chromosomal locations, and gene structures. The PpePL family members were classified into five groups based on their phylogenetic relationships. Among those, PpePL1, 9, 10, 15, and 18 had the higher expression abundance in ripe fruit, and PpePL1, 15, and 18 were upregulated during storage. Detailed RT-qPCR analysis revealed that PpePL1 and PpePL15 were responsive to ETH treatment (1 g L^-1 ethephon) with an abundant transcript accumulation, which suggested these genes were involved in peach ripening and softening. In addition, virus-induced gene silencing (VIGS) technology was used to identify the roles of PpePL1 and PpePL15. Compared to controls, the RNAi fruit maintained greater firmness in the early storage stage, increased acid-soluble pectin (ASP), and reduced water-soluble pectin (WSP). Moreover, transmission electron microscopy (TEM) showed that cell wall degradation was reduced in the fruit of RNAi-1 and RNAi-15, which indicated that softening of the RNAi fruit has been delayed. Our results indicated that PpePL1 and PpePL15 play an important role in peach softening by depolymerizing pectin and degrading cell wall.

Acceleration of Aril Cracking by Ethylene in Torreya grandis During Nut Maturation

Torreya grandis 'Merrillii' is a famous nut with great nutritional value and high medicinal value. Aril cracking is an important process for seed dispersal, which is also an indicator of seed maturation. However, the cracking mechanism of T. grandis aril during the maturation stage remains largely unknown. Here, we provided a comprehensive view of the physiological and molecular levels of aril cracking in T. grandis by systematically analyzing its anatomical structure, physiological parameters, and transcriptomic response during the cracking process. These results showed that the length of both epidermal and parenchymatous cell layers significantly increased from 133 to 144 days after seed protrusion (DASP), followed by a clear separation between parenchymatous cell layers and kernel, which was accompanied by a breakage between epidermal and parenchymatous cell layers. Moreover, analyses of cell wall composition showed that a significant degradation of cellular wall polysaccharides occurred during aril cracking. To examine the global gene expression changes in arils during the cracking process, the transcriptomes (96 and 141 DASP) were analyzed. KEGG pathway analysis of DEGs revealed that 4 of the top 10 enriched pathways were involved in cell wall modification and 2 pathways were related to ethylene biosynthesis and ethylene signal transduction. Furthermore, combining the analysis results of co-expression networks between different transcription factors, cell wall modification genes, and exogenous ethylene treatments suggested that the ethylene signal transcription factors (ERF11 and ERF1A) were involved in aril cracking of T. grandis by regulation of EXP and PME. Our findings provided new insights into the aril cracking trait in T. grandis.

Applications of virus-induced gene silencing for identification of gene function in fruit

With the development of bioinformatics, it is easy to obtain information and data about thousands of genes, but the determination of the functions of these genes depends on methods for rapid and effective functional identification. Virus-induced gene silencing (VIGS) is a mature method of gene functional identification developed over the last 20 years, which has been widely used in many research fields involving many species. Fruit quality formation is a complex biological process, which is closely related to ripening. Here, we review the progress and contribution of VIGS to our understanding of fruit biology and its advantages and disadvantages in determining gene function.

OsPG1 Encodes a Polygalacturonase that Determines Cell Wall Architecture and Affects Resistance to Bacterial Blight Pathogen in Rice

BACKGROUND

Plant cell walls are the main physical barrier encountered by pathogens colonizing plant tissues. Alteration of cell wall integrity (CWI) can activate specific defenses by impairing proteins involved in cell wall biosynthesis, degradation and remodeling, or cell wall damage due to biotic or abiotic stress. Polygalacturonase (PG) depolymerize pectin by hydrolysis, thereby altering pectin composition and structures and activating cell wall defense. Although many studies of CWI have been reported, the mechanism of how PGs regulate cell wall immune response is not well understood.

RESULTS

Necrosis appeared in leaf tips at the tillering stage, finally resulting in 3-5 cm of dark brown necrotic tissue. ltn-212 showed obvious cell death and accumulation of H₂O₂ in leaf tips. The defense responses were activated in ltn-212 to resist bacterial blight pathogen of rice. Map based cloning revealed that a single base substitution (G-A) in the first intron caused incorrect splicing of OsPG1, resulting in a necrotic phenotype. OsPG1 is constitutively expressed in all organs, and the wild-type phenotype was restored in complementation individuals and knockout of wild-type lines resulted in necrosis as in ltn-212. Transmission electron microscopy showed that thicknesses of cell walls were significantly reduced and cell size and shape were significantly diminished in ltn-212.

CONCLUSION

These results demonstrate that OsPG1 encodes a PG in response to the leaf tip necrosis phenotype of ltn-212. Loss-of-function mutation of ltn-212 destroyed CWI, resulting in spontaneous cell death and an auto-activated defense response including reactive oxygen species (ROS) burst and pathogenesis-related (PR) gene expression, as well as enhanced resistance to Xanthomonas oryzae pv. oryzae (Xoo). These findings promote our understanding of the CWI mediated defense response.

Postharvest Properties of Ultra-Late Maturing Peach Cultivars and Their Attributions to Melting Flesh (M) Locus: Re-evaluation of M Locus in Association With Flesh Texture

The postharvest properties of two ultra-late maturing peach cultivars, "Tobihaku" (TH) and "Daijumitsuto" (DJ), were investigated. Fruit were harvested at commercial maturity and held at 25°C. TH exhibited the characteristics of normal melting flesh (MF) peach, including rapid fruit softening associated with appropriate level of endogenous ethylene production In contrast, DJ did not soften at all during 3 weeks experimental period even though considerable ethylene production was observed. Fruit of TH and DJ were treated with 5,000 ppm of propylene, an ethylene analog, continuously for 7 days. TH softened rapidly whereas DJ maintained high flesh firmness in spite of an increase in endogenous ethylene production, suggesting that DJ but not TH lacked the ability to be softened in response to endogenous and exogenous ethylene/propylene. DNA-seq analysis showed that tandem endo-polygalacturonase (endoPG) genes located at melting flesh (M) locus, Pp-endoPGM (PGM), and Pp-endoPGF (PGF), were deleted in DJ. The endoPG genes at M locus are known to control flesh texture of peach fruit, and it was suggested that the non-softening property of DJ is due to the lack of endoPG genes. On the other hand, TH possessed an unidentified M haplotype that is involved in determination of MF phenotype. Structural identification of the unknown M haplotype, designated as M ⁰, through comparison with previously reported M haplotypes revealed distinct differences between PGM on M ⁰ haplotype (PGM-M⁰ ) and PGM on other haplotypes (PGM-M¹ ). Peach M haplotypes were classified into four main haplotypes: M ⁰ with PGM-M⁰ ; M ¹ with both PGM-M¹ and PGF; M ² with PGM-M¹ ; and M ³ lacking both PGM and PGF. Re-evaluation of M locus in association with MF/non-melting flesh (NMF) phenotypes in more than 400 accessions by using whole genome shotgun sequencing data on database and/or by PCR genotyping demonstrated that M ⁰ haplotype was the common haplotype in MF accessions, and M ⁰ and M ¹ haplotypes were dominant over M ² and M ³ haplotypes and co-dominantly determined the MF trait. It was also assumed on the basis of structural comparison of M haplotypes among Prunus species that the ancestral haplotype of M ⁰ diverged from those of the other haplotypes before the speciation of Prunus persica.

Integrative transcriptome and proteome analyses provide new insights into different stages of Akebia trifoliata fruit cracking during ripening

BACKGROUND

Akebia trifoliata (Thunb.) Koidz may have applications as a new potential source of biofuels owing to its high seed count, seed oil content, and in-field yields. However, the pericarp of A. trifoliata cracks longitudinally during fruit ripening, which increases the incidence of pests and diseases and can lead to fruit decay and deterioration, resulting in significant losses in yield. Few studies have evaluated the mechanisms underlying A. trifoliata fruit cracking.

RESULTS

In this study, by observing the cell wall structure of the pericarp, we found that the cell wall became thinner and looser and showed substantial breakdown in the pericarp of cracking fruit compared with that in non-cracking fruit. Moreover, integrative analyses of transcriptome and proteome profiles at different stages of fruit ripening demonstrated changes in the expression of various genes and proteins after cracking. Furthermore, the mRNA levels of 20 differentially expressed genes were analyzed, and parallel reaction monitoring analysis of 20 differentially expressed proteins involved in cell wall metabolism was conducted. Among the molecular targets, pectate lyases and pectinesterase, which are involved in pentose and glucuronate interconversion, and β-galactosidase 2, which is involved in galactose metabolism, were significantly upregulated in cracking fruits than in non-cracking fruits. This suggested that they might play crucial roles in A. trifoliata fruit cracking.

CONCLUSIONS

Our findings provided new insights into potential genes influencing the fruit cracking trait in A. trifoliata and established a basis for further research on the breeding of cracking-resistant varieties to increase seed yields for biorefineries.

Fruit From Two Kiwifruit Genotypes With Contrasting Softening Rates Show Differences in the Xyloglucan and Pectin Domains of the Cell Wall

Fruit softening is controlled by hormonal and developmental cues, causing an upregulation of cell wall-associated enzymes that break down the complex sugar matrices in the cell wall. The regulation of this process is complex, with different genotypes demonstrating quite different softening patterns, even when they are closely related. Currently, little is known about the relationship between cell wall structure and the rate of fruit softening. To address this question, the softening of two Actinidia chinensis var. chinensis (kiwifruit) genotypes (a fast 'AC-F' and a slow 'AC-S' softening genotype) was examined using a range of compositional, biochemical, structural, and molecular techniques. Throughout softening, the cell wall structure of the two genotypes was fundamentally different at identical firmness stages. In the hemicellulose domain, xyloglucanase enzyme activity was higher in 'AC-F' at the firm unripe stage, a finding supported by differential expression of xyloglucan transglycosylase/hydrolase genes during softening. In the pectin domain, differences in pectin solubilization and location of methyl-esterified homogalacturonan in the cell wall between 'AC-S' and 'AC-F' were shown. Side chain analyses and molecular weight elution profiles of polyuronides and xyloglucans of cell wall extracts revealed fundamental differences between the genotypes, pointing towards a weakening of the structural integrity of cell walls in the fast softening 'AC-F' genotype even at the firm, unripe stage. As a consequence, the polysaccharides in the cell walls of 'AC-F' may be easier to access and hence more susceptible to enzymatic degradation than in 'AC-S', resulting in faster softening. Together these results suggest that the different rates of softening between 'AC-F' and 'AC-S' are not due to changes in enzyme activities alone, but that fundamental differences in the cell wall structure are likely to influence the rates of softening through differential modification and accessibility of specific cell wall polysaccharides during ripening.

Plant Cellular and Molecular Biotechnology: Following Mariotti's Steps

This review is dedicated to the memory of Prof. Domenico Mariotti, who significantly contributed to establishing the Italian research community in Agricultural Genetics and carried out the first experiments of Agrobacterium-mediated plant genetic transformation and regeneration in Italy during the 1980s. Following his scientific interests as guiding principles, this review summarizes the recent advances obtained in plant biotechnology and fundamental research aiming to: (i) Exploit in vitro plant cell and tissue cultures to induce genetic variability and to produce useful metabolites; (ii) gain new insights into the biochemical function of Agrobacterium rhizogenes rol genes and their application to metabolite production, fruit tree transformation, and reverse genetics; (iii) improve genetic transformation in legume species, most of them recalcitrant to regeneration; (iv) untangle the potential of KNOTTED1-like homeobox (KNOX) transcription factors in plant morphogenesis as key regulators of hormonal homeostasis; and (v) elucidate the molecular mechanisms of the transition from juvenility to the adult phase in Prunus tree species.