The peach HECATE3-like gene FLESHY plays a double role during fruit development

A gibberellin-assisted study of the transcriptional and hormonal changes occurring at floral transition in peach buds (Prunus persica L. Batsch)

BACKGROUND

Flower load in peach is an important determinant of final fruit quality and is subjected to cost-effective agronomical practices, such as the thinning, to finely balance the sink-source relationships within the tree and drive the optimal amount of assimilates to the fruits. Floral transition in peach buds occurs as a result of the integration of specific environmental signals, such as light and temperature, into the endogenous pathways that induce the meristem to pass from vegetative to reproductive growth. The cross talk and integration of the different players, such as the genes and the hormones, are still partially unknown. In the present research, transcriptomics and hormone profiling were applied on bud samples at different developmental stages. A gibberellin treatment was used as a tool to identify the different phases of floral transition and characterize the bud sensitivity to gibberellins in terms of inhibition of floral transition.

RESULTS

Treatments with gibberellins showed different efficacies and pointed out a timeframe of maximum inhibition of floral transition in peach buds. Contextually, APETALA1 gene expression was shown to be a reliable marker of gibberellin efficacy in controlling this process. RNA-Seq transcriptomic analyses allowed to identify specific genes dealing with ROS, cell cycle, T6P, floral induction control and other processes, which are correlated with the bud sensitivity to gibberellins and possibly involved in bud development during its transition to the reproductive stage. Transcriptomic data integrated with the quantification of the main bioactive hormones in the bud allowed to identify the main hormonal regulators of floral transition in peach, with a pivotal role played by endogenous gibberellins and cytokinins.

CONCLUSIONS

The peach bud undergoes different levels of receptivity to gibberellin inhibition. The stage with maximum responsiveness corresponded to a transcriptional and hormonal crossroad, involving both flowering inhibitors and inductors. Endogenous gibberellin levels increased only at the latest developmental stage, when floral transition was already partially achieved, and the bud was less sensitive to exogenous treatments. A physiological model summarizes the main findings and suggests new research ideas to improve our knowledge about floral transition in peach.

Differential gene expression associated with flower development of mango (Mangifera indica L.) varieties with different shelf-life

Mango (Mangifera indica L.) is one of the most important commercial fruit crop grown in many parts of the world. Major challenges affecting mango trade are short shelf-life, high susceptibility to chilling injury, post-harvest diseases and consumer demand for improved fruit quality. The objective of the present study was to reveal the key regulators present in bud and flower tissues during flower development stage, associated with fruit development and affect the shelf-life of the mango fruit. RNA-sequencing of contrasting genotypes having short and long shelf-life, was carried out. Comparative differential expression pathway studies of long shelf-life (Totapuri) and short shelf-life (Bombay Green) mango genotypes revealed a total of 177 highly differentially expressed genes. Out of 177 total genes, 101 genes from endoplasmic reticulum pathway and very few from gibberellins (3) and jasmonic acid (1) pathway were identified. Genes from endoplasmic reticulum pathway like hsp 90, SRC2, DFRA, CHS, BG3 and ASPG1 mainly up regulated in Bombay Green. Uniprotein B9R8D3 also shows up regulation in Bombay Green. Ethylene insensitive pathway gene EIL1 up regulated in Bombay Green. Gene CAD1 from phenylpropanoid pathway mainly up regulated in Bombay Green. A total of 4 SSRs and 227 SNPs were mined from these pathways specific to the shelf-life. Molecular studies of endoplasmic reticulum, phenylpropanoid, ethylene, polygalacturonase and hormone pathways at the time of bud and flower formation revealed key regulators that determine the shelf-life of mango fruit.

CsIVP Modulates Low Nitrogen and High-Temperature Resistance in Cucumber

Crop plants experience various abiotic stresses that reduce yield and quality. Although several adaptative physiological and defense responses to single stress have been identified, the behavior and mechanisms of plant response to multiple stresses remain underexamined. Herein, we determined that the leaf and vascular changes in Cucumis sativus Irregular Vasculature Patterning (CsIVP)-RNAi cucumber plants can enhance resistance to nitrogen deficiency and high-temperature stress. CsIVP negatively regulated high nitrate affinity transporters (NRT2.1, NRT2.5) and reallocation transporters (NRT1.7, NRT1.9, NRT1.12) under low nitrogen stress. Furthermore, CsIVP-RNAi plants have high survival rate with low heat injury level under high-temperature condition. Several key high-temperature regulators, including Hsfs, Hsps, DREB2C, MBF1b and WRKY33 have significant expression in CsIVP-RNAi plants. CsIVP negatively mediated high-temperature responses by physically interacting with CsDREB2C. Altogether, these results indicated that CsIVP integrates innate programming of plant development, nutrient transport and high-temperature resistance, providing a potentially valuable target for breeding nutrient-efficient and heat-resistant crops.

An efficient chromatin immunoprecipitation (ChIP) protocol for studying histone modifications in peach reproductive tissues

BACKGROUND

Perennial fruit trees display a growth behaviour characterized by annual cycling between growth and dormancy, with complex physiological features. Rosaceae fruit trees represent excellent models for studying not only the fruit growth/patterning but also the progression of the reproductive cycle depending upon the impact of climate conditions. Additionally, current developments in high-throughput technologies have impacted Rosaceae tree research while investigating genome structure and function as well as (epi)genetic mechanisms involved in important developmental and environmental response processes during fruit tree growth. Among epigenetic mechanisms, chromatin remodelling mediated by histone modifications and other chromatin-related processes play a crucial role in gene modulation, controlling gene expression. Chromatin immunoprecipitation is an effective technique to investigate chromatin dynamics in plants. This technique is generally applied for studies on chromatin states and enrichment of post-transcriptional modifications (PTMs) in histone proteins.

RESULTS

Peach is considered a model organism among climacteric fruits in the Rosaceae family for studies on bud formation, dormancy, and organ differentiation. In our work, we have primarily established specific protocols for chromatin extraction and immunoprecipitation in reproductive tissues of peach (Prunus persica). Subsequently, we focused our investigations on the role of two chromatin marks, namely the trimethylation of histone H3 at lysine in position 4 (H3K4me3) and trimethylation of histone H3 at lysine 27 (H3K27me3) in modulating specific gene expression. Bud dormancy and fruit growth were investigated in a nectarine genotype called Fantasia as our model system.

CONCLUSIONS

We present general strategies to optimize ChIP protocols for buds and mesocarp tissues of peach and analyze the correlation between gene expression and chromatin mark enrichment/depletion. The procedures proposed may be useful to evaluate any involvement of histone modifications in the regulation of gene expression during bud dormancy progression and core ripening in fruits.

Classical Food Quality Attributes and the Metabolic Profile of Cambuci, a Native Brazilian Atlantic Rainforest Fruit

The cambuci is a native Brazilian fruit from the Atlantic Forest biome. A soft and astringent pulp, a green color, and a sweet aroma are its main characteristics. Classical food quality attributes (fresh fruit mass, fruit height, diameters, total soluble solid, titratable acidity, and ratio) and the metabolic profile from ten accessions from three different locations were analyzed herein by analytical methods (refractometry and neutralization titration) and nuclear magnetic resonance spectroscopy. Concerning sugar content, sucrose was the predominant compound, with glucose and fructose alternating in second, depending on the accession. Citric acid was the most relevant acid, followed by shikimic and quinic acids in quite variable amounts. These three main acids vary in amounts for each accession. Ascorbic acid content emerges as an important quality attribute and makes this fruit nutritionally attractive, due to values comparable to those contained in citric fruits. The main amino acids identified in cambuci were glutamic acid individually or in comprising the tripeptide glutathione (glutamic acid, cysteine, glycine). The quality diversity of the evaluated accessions suggests the potentiality of cambuci use in future breeding programs.

Regulation of Fruit Growth in a Peach Slow Ripening Phenotype

Consumers' choices are mainly based on fruit external characteristics such as the final size, weight, and shape. The majority of edible fruit are by tree fruit species, among which peach is the genomic and genetic reference for Prunus. In this research, we used a peach with a slow ripening (SR) phenotype, identified in the Fantasia (FAN) nectarine, associated with misregulation of genes involved in mesocarp identity and showing a reduction of final fruit size. By investigating the ploidy level, we observed a progressive increase in endoreduplication in mesocarp, which occurred in the late phases of FAN fruit development, but not in SR fruit. During fruit growth, we also detected that genes involved in endoreduplication were differentially modulated in FAN compared to SR. The differential transcriptional outputs were consistent with different chromatin states at loci of endoreduplication genes. The impaired expression of genes controlling cell cycle and endocycle as well as those claimed to play a role in fruit tissue identity result in the small final size of SR fruit.

Shotgun proteomics of peach fruit reveals major metabolic pathways associated to ripening

BACKGROUND

Fruit ripening in Prunus persica melting varieties involves several physiological changes that have a direct impact on the fruit organoleptic quality and storage potential. By studying the proteomic differences between the mesocarp of mature and ripe fruit, it would be possible to highlight critical molecular processes involved in the fruit ripening.

RESULTS

To accomplish this goal, the proteome from mature and ripe fruit was assessed from the variety O'Henry through shotgun proteomics using 1D-gel (PAGE-SDS) as fractionation method followed by LC/MS-MS analysis. Data from the 131,435 spectra could be matched to 2740 proteins, using the peach genome reference v1. After data pre-treatment, 1663 proteins could be used for comparison with datasets assessed using transcriptomic approaches and for quantitative protein accumulation analysis. Close to 26% of the genes that code for the proteins assessed displayed higher expression at ripe fruit compared to other fruit developmental stages, based on published transcriptomic data. Differential accumulation analysis between mature and ripe fruit revealed that 15% of the proteins identified were modulated by the ripening process, with glycogen and isocitrate metabolism, and protein localization overrepresented in mature fruit, as well as cell wall modification in ripe fruit. Potential biomarkers for the ripening process, due to their differential accumulation and gene expression pattern, included a pectin methylesterase inhibitor, a gibbellerin 2-beta-dioxygenase, an omega-6 fatty acid desaturase, a homeobox-leucine zipper protein and an ACC oxidase. Transcription factors enriched in NAC and Myb protein domains would target preferentially the genes encoding proteins more abundant in mature and ripe fruit, respectively.

CONCLUSIONS

Shotgun proteomics is an unbiased approach to get deeper into the proteome allowing to detect differences in protein abundance between samples. This technique provided a resolution so that individual gene products could be identified. Many proteins likely involved in cell wall and sugar metabolism, aroma and color, change their abundance during the transition from mature to ripe fruit.

Metabolism of Stone Fruits: Reciprocal Contribution Between Primary Metabolism and Cell Wall

Cell wall turnover and modification in its composition are key factors during stone fruit development and patterning. Changes in cell wall disassembly and reassembly are essential for fruit growth and ripening. Modifications in cell wall composition, resulting in the formation of secondary cell walls, are necessary for producing the most distinctive trait of drupes: the lignified endocarp. The contribution of primary metabolism to cell wall synthesis has been investigated in detail, while the knowledge on the contribution of the cell wall to primary metabolites and related processes is still fragmented. In this review, starting from peculiarities of cell wall of drupes cells (in mesocarp and endocarp layers), we discuss the structure and composition of cell wall, processes related to its modification and contribution to the synthesis of primary metabolites. In particular, our attention has been focused on the ascorbate synthesis cell wall-related and on the potential role of cyanogenic compounds in the deposition of the secondary cell wall.

Metabolite Fruit Profile Is Altered in Response to Source-Sink Imbalance and Can Be Used as an Early Predictor of Fruit Quality in Nectarine

Peaches and nectarines [Prunus persica (L.) Batsch] are among the most exported fresh fruit from Chile to the Northern Hemisphere. Fruit acceptance by final consumers is defined by quality parameters such as the size, weight, taste, aroma, color, and juiciness of the fruit. In peaches and nectarines, the balance between soluble sugars present in the mesocarp and the predominant organic acids determines the taste. Biomass production and metabolite accumulation by fruits occur during the different developmental stages and depend on photosynthesis and carbon export by source leaves. Carbon supply to fruit can be potentiated through the field practice of thinning (removal of flowers and young fruit), leading to a change in the source-sink balance favoring fruit development. Thinning leads to fruit with increased size, but it is not known how this practice could influence fruit quality in terms of individual metabolite composition. In this work, we analyzed soluble metabolite profiles of nectarine fruit cv "Magique" at different developmental stages and from trees subjected to different thinning treatments. Mesocarp metabolites were analyzed throughout fruit development until harvest during two consecutive harvest seasons. Major polar compounds such as soluble sugars, amino acids, organic acids, and some secondary metabolites were measured by quantitative ¹H-NMR profiling in the first season and GC-MS profiling in the second season. In addition, harvest and ripening quality parameters such as fruit weight, firmness, and acidity were determined. Our results indicated that thinning (i.e., source-sink imbalance) mainly affects fruit metabolic composition at early developmental stages. Metabolomic data revealed that sugar, organic acid, and phenylpropanoid pathway intermediates at early stages of development can be used to segregate fruits impacted by the change in source-sink balance. In conclusion, we suggest that the metabolite profile at early stages of development could be a metabolic predictor of final fruit quality in nectarines.

Plant metabolism as studied by NMR spectroscopy

The study of plant metabolism impacts a broad range of domains such as plant cultural practices, plant breeding, human or animal nutrition, phytochemistry and green biotechnologies. Plant metabolites are extremely diverse in terms of structure or compound families as well as concentrations. This review attempts to illustrate how NMR spectroscopy, with its broad variety of experimental approaches, has contributed widely to the study of plant primary or specialized metabolism in very diverse ways. The review presents recent developments of one-dimensional and multi-dimensional NMR methods to study various aspects of plant metabolism. Through recent examples, it highlights how NMR has proved to be an invaluable tool for the global characterization of sample composition within metabolomic studies, and shows some examples of use for targeted phytochemistry, with a special focus on compound identification and quantitation. In such cases, NMR approaches are often used to provide snapshots of the plant sample composition. The review also covers dynamic aspects of metabolism, with a description of NMR techniques to measure metabolic fluxes - in most cases after stable isotope labelling. It is mainly intended for NMR specialists who would be interested to learn more about the potential of their favourite technique in plant sciences and about specific details of NMR approaches in this field. Therefore, as a practical guide, a paragraph on the specific precautions that should be taken for sample preparation is also included. In addition, since the quality of NMR metabolic studies is highly dependent on approaches to data processing and data sharing, a specific part is dedicated to these aspects. The review concludes with perspectives on the emerging methods that could change significantly the role of NMR in the field of plant metabolism by boosting its sensitivity. The review is illustrated throughout with examples of studies selected to represent diverse applications of liquid-state or HR-MAS NMR.

Fine-tuning of the flavonoid and monolignol pathways during apple early fruit development

A coordinated regulation of different branches of the flavonoid pathway was highlighted that may contribute to elucidate the role of this important class of compounds during the early stages of apple fruit development. Apple (Malus × domestica Borkh.) is an economically important fruit appreciated for its organoleptic characteristics and its benefits for human health. The first stages after fruit set represent a very important and still poorly characterized developmental process. To enable the profiling of genes involved in apple early fruit development, we combined the suppression subtractive hybridization (SSH) protocol to next-generation sequencing. We identified and characterized genes induced and repressed during fruit development in the apple cultivar 'Golden Delicious'. Our results showed an opposite regulation of genes coding for enzymes belonging to flavonoid and monolignol pathways, with a strong induction of the former and a simultaneous repression of the latter. Two isoforms of phenylalanine ammonia-lyase and 4-coumarate:CoA ligase, key enzymes located at the branching point between flavonoid and monolignol pathways, showed opposite expression patterns during the period in analysis, suggesting a possible regulation mechanism. A targeted metabolomic analysis supported the SSH results and revealed an accumulation of the monomers catechin and epicatechin as well as several forms of procyanidin oligomers in apple fruitlets starting early after anthesis, together with a decreased production of other classes of flavonoids such as some flavonols and the dihydrochalcone phlorizin. Moreover, gene expression and metabolites accumulation of 'Golden Delicious' were compared to a wild apple genotype of Manchurian crabapple (Malus mandshurica (Maxim.) Kom.). Significant differences in both gene expression and metabolites accumulation were found between the two genotypes.

Rosaceae Fruit Development, Ripening and Post-harvest: An Epigenetic Perspective

Rosaceae is a family with an extraordinary spectrum of fruit types, including fleshy peach, apple, and strawberry that provide unique contributions to a healthy diet for consumers, and represent an excellent model for studying fruit patterning and development. In recent years, many efforts have been made to unravel regulatory mechanism underlying the hormonal, transcriptomic, proteomic and metabolomic changes occurring during Rosaceae fruit development. More recently, several studies on fleshy (tomato) and dry (Arabidopsis) fruit model have contributed to a better understanding of epigenetic mechanisms underlying important heritable crop traits, such as ripening and stress response. In this context and summing up the results obtained so far, this review aims to collect the available information on epigenetic mechanisms that may provide an additional level in gene transcription regulation, thus influencing and driving the entire Rosaceae fruit developmental process. The whole body of information suggests that Rosaceae fruit could become also a model for studying the epigenetic basis of economically important phenotypes, allowing for their more efficient exploitation in plant breeding.

Genome-Wide Identification, Expression Patterns, and Functional Analysis of UDP Glycosyltransferase Family in Peach (Prunus persica L. Batsch)

Peach (Prunus persica L. Batsch) is a commercial grown fruit trees, important because of its essential nutrients and flavor promoting secondary metabolites. The glycosylation processes mediated by UDP-glycosyltransferases (UGTs) play an important role in regulating secondary metabolites availability. Identification and characterization of peach UGTs is therefore a research priority. A total of 168 peach UGT genes that distributed unevenly across chromosomes were identified based on their conserved PSPG motifs. Phylogenetic analysis of these genes with plant UGTs clustered them into 16 groups (A-P). Comparison of the patterns of intron-extron and their positions within genes revealed one highly conserved intron insertion event in peach UGTs. Tissue specificity, temporal expression patterns in peach fruit during development and ripening, and in response to abiotic stress UV-B irradiation was investigated using RNA-seq strategy. The relationship between UGTs transcript levels and concentrations of glycosylated volatiles was examined to select candidates for functional analysis. Heterologous expressing these candidate genes in Escherichia coli identified UGTs that were involved in the in vitro volatile glycosylation. Our results provide an important source for the identification of functional UGT genes to potential manipulate secondary biosynthesis in peach.