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Abstract: Specific polyphenol compound concentrations and gene expression patterns were determined by both microarray and qRT-PCR analyses in the epicarp of red-skinned grape berries (Vitis vinifera L. cv ‘Raboso Piave’) dehydrated, after harvest, at slow (S) and rapid (R) rates of up to 10 and 30% weight loss (WL). Increases in flavonols (quercetin) and trans-resveratrol concentrations were observed in the skins of all dehydrated samples, whereas flavan-3-ols concentrations showed a decreasing trend, which was more pronounced in S samples. The decrease in flavan-3-ol concentrations was paralleled by a reduction in procyanidin B1 and, particularly B2. Computational analysis of microarray data revealed that several key genes of the flavonoid pathways were unaffected or down-regulated during berry dehydration, with the exception of flavonol synthase, which was induced as well as one MybB transcription factor. Chalcone synthase (CHS), flavanone 3-hydroxylase (F3H), leucoanthocyanidin dioxygenase (LDOX) and MybA were markedly down-regulated, particularly in relation to 30% WL, whereas UDP-glucose:flavonoid 3-O-glucosyltransferase (UFGT) was unaffected in all the samples considered. Specific genes involved in the lignin biosynthetic pathway, including laccase, were induced in the most dehydrated samples. Considering the accumulation pattern and gene expression profiles, stilbenes and flavonols may represent useful biomarkers to monitor postharvest dehydration. [Copyright &y& Elsevier]

Background: Field observations and a few physiological studies have demonstrated that peach embryogenesis and fruit development are tightly coupled. In fact, attempts to stimulate parthenocarpic fruit development by means of external tools have failed. Moreover, physiological disturbances during early embryo development lead to seed abortion and fruitlet abscission. Later in embryo development, the interactions between seed and fruit development become less strict. As there is limited genetic and molecular information about seed-pericarp crosstalk and development in peach, a massive gene approach based on the use of the μPEACH 1.0 array platform and quantitative real time RT-PCR (qRT-PCR) was used to study this process. Results: A comparative analysis of the transcription profiles conducted in seed and mesocarp (cv Fantasia) throughout different developmental stages (S1, S2, S3 and S4) evidenced that 455 genes are differentially expressed in seed and fruit. Among differentially expressed genes some were validated as markers in two subsequent years and in three different genotypes. Seed markers were a LTP1 (lipid transfer protein), a PR (pathogenesis-related) protein, a prunin and LEA (Late Embryogenesis Abundant) protein, for S1, S2, S3 and S4, respectively. Mesocarp markers were a RD22-like protein, a serin-carboxypeptidase, a senescence related protein and an Aux/IAA, for S1, S2, S3 and S4, respectively. The microarray data, analyzed by using the HORMONOMETER platform, allowed the identification of hormoneresponsive genes, some of them putatively involved in seed-pericarp crosstalk. Results indicated that auxin, cytokinins, and gibberellins are good candidates, acting either directly (auxin) or indirectly as signals during early development, when the cross-talk is more active and vital for fruit set, whereas abscisic acid and ethylene may be involved later on. Conclusions: In this research, genes were identified marking different phases of seed and mesocarp development. The selected genes behaved as good seed markers, while for mesocarp their reliability appeared to be dependent upon developmental and ripening traits. Regarding the cross-talk between seed and pericarp, possible candidate signals were identified among hormones. Further investigations relying upon the availability of whole genome platforms will allow the enrichment of a marker genes repertoire and the elucidation of players other than hormones that are involved in seed-pericarp cross-talk (i.e. hormone peptides and microRNAs). [ABSTRACT FROM AUTHOR]

A large-scale transcriptome analysis was conducted using an oligo-based microarray (14,562 probes) on skins of wine grape (Vitis vinifera L.) berries dehydrated at different rates (slow, S and rapid, R) after harvest up to 10 and 30% of weight loss (WL). At 10% WL, a total of 84 and 68 probes were differentially expressed following S and R dehydration, respectively. At 30% WL, 309 and 262 differentially expressed probes were detected in S and R samples, respectively, indicating that grape berries are still reactive at advanced stages of postharvest dehydration. Bioinformatic analysis revealed that about 70% of the differentially expressed probes could be annotated and putative functions were assigned. Functional characterization highlighted that, independently of the rate and intensity of dehydration, differential expression occurred in particular for genes associated with general metabolism, regulatory processes, and responses to biotic and abiotic stimuli. A total of 16 (induced) and 10 (repressed) probes, common to all four dehydrated samples, were associated with hormone (ethylene) metabolism, transcription factors, carbohydrate and secondary (polyphenols) metabolism, transport and stress responses. Together with the total number of differentially expressed probes, enhancing the dehydration level from 10 to 30% WL also affected the distribution of genes within functional categories: this behaviour was observed in particular for R samples. A higher level of water stress in grapes appears to be associated with modification to the expression of genes mainly involved in hormone and sugar metabolism, and defence mechanisms. Besides the intensity of dehydration, a significant effect on gene expression was also associated with rate of water loss: an increase in the percentage incidence of differentially expressed probes was present for categories involved in defence and environmental stress when comparing R and S samples. The microarray data, validated by RT-PCR analyses, represent robust evidence for the marked effects of postharvest water loss on metabolic processes in fruit tissues. [Copyright &y& Elsevier]

Peach (Prunus persica L. Batsch) was chosen as a model to shed light on the physiological role of jasmonates (JAs) during fruit ripening. To this aim, the effects of methyl jasmonate (MJ, 0.40 mM) and propyl dihydrojasmonate (PDJ, 0.22 mM), applied in planta at different fruit developmental stages, on the time-course of ethylene production and fruit quality traits were evaluated. MJ-induced changes in fruit transcriptome at harvest and the expression profiling of relevant JA-responsive genes were analysed in control and JA-treated fruit. Exogenously applied JAs affected the onset of ripening depending upon the fruit developmental stage, with PDJ being more active than MJ. Both compounds enhanced the transcription of allene oxide synthase (PpAOS1), the first specific enzyme in the biosynthesis of jasmonic acid, and altered the pattern of jasmonic acid accumulation. Microarray transcriptome profiling showed that MJ down-regulated some ripening-related genes, such as 1-aminocyclopropane-1-carboxylic acid oxidase (PpACO1) and polygalacturonase (PG), and the transcriptional modulator IAA7. MJ also altered the expression of cell wall-related genes, namely pectate lyase (PL) and expansins (EXPs), and up-regulated several stress-related genes, including some of those involved in JA biosynthesis. Time-course expression profiles of PpACO1, PL, PG, PpExp1, and the transcription factor LIM confirmed the array results. Thus, in peach fruit, exogenous JAs led to a ripening delay due to an interference with ripening- and stress/defence-related genes, as reflected in the transcriptome of treated fruit at harvest. [ABSTRACT FROM PUBLISHER]

Abstract: The transition from pre-climacteric to climacteric phase is a critical step during fruit development. A holistic approach to study this transition has been undertaken using the first available peach microarray (μPEACH1.0) containing about 4800 oligonucleotide probes corresponding to a set of unigenes most of them expressed during the last stages of fruit development. Microarray hybridizations indicated that among the genes present in the microarray slide, 267 and 109 genes are up- and down-regulated, respectively. Genes have been classified according to the TAIR Gene Ontology into three main categories based on cellular localization, molecular function and biological process. Considering the cellular localization, the most significant up- and down-regulated gene products belong to cell wall and chloroplast compartments. Within the molecular function and biological process categories, a dramatic up-regulation has been detected for genes encoding transcription factors and enzymes involved in ethylene biosynthesis and action. A new member of ETR peach family (Pp-ETR2) has been characterized: this gene shows high similarity to Arabidopsis EIN4, tomato Le-ETR4, and strawberry Fa-ETR2. Transition from S3 to S4 is paralleled by changes in expression of 19 genes encoding transcription factors (TFs) belonging to several families including MADS-box, AUX/IAA, bZIP, bHLH, HD, and Myb. Differential expression of genes involved in specific quality traits has also been observed: besides confirming previous data on cell wall-related gene expression, a new pectin-methyl esterase and two new expansins have been identified. Several genes encoding enzymes acting in the isoprenoid biosynthetic pathway appeared to be strongly induced at S3/S4 transition. Among those involved in carotenoid biosynthesis we found also a β-carotene hydroxylase, responsible for the formation of β-cryptoxanthin, the most abundant carotenoid of ripe yellow peaches. [Copyright &y& Elsevier]

We report the isolation of a new peach gene, Pp-MLP1, that shows significant similarity to a family of fruit- and flower-specific genes, designated as major latex protein (MLP) homologues. Transcript of Pp-MLP1 highly accumulated in cells of fruit pedicel, similar to lacticifers, adjacent to the abscission zone (non-abscission zone) and, to a lesser extent, in epicotyls, stems and roots, while no accumulation was detected in leaves. In contrast to the MLP homologues isolated so far, the Pp-MLP1 transcript was detected during fruit cells expansion, though its expression appeared unrelated to fruit ripening. Propylene treatment caused a decrease in mRNA accumulation of Pp-MLP1 in all tested tissues. The function of Pp-MLP1, as with all previously described MLP homologues, is unknown. MLPs are associated with fruit and flower development in addition to plant pathogenesis responses. Expression in tissues associated with abscission would be consistent with a role in implementing this aspect of floral development or possibly protective responses to plant pathogens which may infect post-abscission wounds. In addition, the high similarity between proteins encoding by Pp-MLP1 and Csf2, an MLP gene associated with the early development of cucumber fruit, could suggest an alternative developmental role such as cell and tissue expansion. [Copyright &y& Elsevier]

The characterization and expression of PP-ACO1 and PP-ACO2, two members of the peach 1-aminocyclopropane-1-carboxylate (ACC) oxidase (ACO) gene family, are reported. PP-ACO1 is organized in 4 exons interrupted by 3 introns, whereas PP-ACO2 has only 2 of the 3 introns present in PP-ACO1. Comparison of the deduced amino acid sequences of PP-ACO1 and PP-ACO2 reveals a 77.7% identity. PP-ACO1 and PP-ACO2 show highest degree of similarity with petunia (PH-ACO3; 84.1%) and apple (85.4%) ACO genes, respectively. PP-ACO1 is expressed in flowers, fruitlet abscission zones, mesocarp and in young fully expanded leaves. PP-ACO1 transcript accumulation strongly increases during fruitlet abscission, in ripe mesocarp and senescing leaves, and is enhanced by propylene. PP-ACO2 mRNA accumulation is detected in fruits only during early development and is unaffected by propylene treatment. Both ACO genes are expressed in epicotyl and roots of growing seedlings, although a stronger accumulation of PP-ACO2 mRNA is observed. [ABSTRACT FROM AUTHOR]

In grapevines, as in other plants, sucrose and its constituents glucose and fructose are fundamentally important and carry out a multitude of roles. The aims of this review are three-fold. First, to provide a summary of the metabolism and transport of sucrose in grapevines, together with new insights and interpretations. Second, to stress the importance of considering the compartmentation of metabolism. Third, to outline the key role of acid invertase in osmoregulation associated with sucrose metabolism and transport in plants. [ABSTRACT FROM AUTHOR]

Studies the increase in cell size and the activities of cell wall lytic enzymes during fruit growth supported by the mesocarp cell enlargement in peach of the freestone cultivar Redhaven. Light and electron microscopy of tissue samples from the inner mesocarp; Double sigmoid pattern of fruit growth; Absence of visible cell alterations during cell enlargement.

During peach (Prunus persica [L.] Batsch) fruit development and ripening the cell wall undergoes several structural and biochemical changes driven by several hydrolases. Among these, the endo-β-1,4-D-glucanase (EGase, EC 3.2.1.4), or cellulase, may play a crucial role. Involvement of EGase throughout development and ripening of the fruit of cv. Redhaven was assessed by monitoring enzyme activity, specific polypeptide accumulation and gene transcription. During the four stages of growth EGase activity was high during S1 and in the early S2, declined during S3, and increased with the onset of ripening (S4). Two isoforms with isolectric points of 6.5 and 9.5 were identified. The pI 6.5 EGase was the only form present during the early stages of growth. whereas the pI 9.5 EGase was most abundant during ripening. The same isoforms were present in leaf and fruit abscission zones. The antibody raised against the pI 9.5 EGase, purified from leaf abscission zones, cross-reacted with a protein of 54 kDa. A cDNA clone of 753 bp encoding peach EGase was obtained by RT-PCR. EGase transcripts, detectable only after amplification of total RNA by RT-PCR, were observed during S1, and at the preclimacteric and climacteric stages. However, the strongest hybridisation occurred at ripening, in correspondence with the maximal enzyme activity and polypeptide accumulation, which took place before the ethylene climacteric and in the early stage of flesh softening. Propylene treatments reduced EGase activity during the early stage of fruit growth but dramatically enhanced enzyme activity and the related transcript accumulation at ripening, and accelerated the loss of firmness. In fruit treated with 2,5-norbornadiene the softening process was strongly inhibited and the rise in EGase transcripts and activity did not take place. The results point to the EGases being involved in early fruit growth and the initial phases of softening. The presence of two isoforms and the dual effect of propylene on enzyme activity suggest that different EGase genes operate during the early and late developmental stages in peach fruit. [ABSTRACT FROM AUTHOR]

In deciduous fruit trees, entrance into dormancy occurs in later summer/fall, concomitantly with the shortening of day length and decrease in temperature. Dormancy can be divided into endodormancy, ecodormancy and paradormancy. In Prunus species flower buds, entrance into the dormant stage occurs when the apical meristem is partially differentiated; during dormancy, flower verticils continue their growth and differentiation. Each species and/or cultivar requires exposure to low winter temperature followed by warm temperatures, quantified as chilling and heat requirements, to remove the physiological blocks that inhibit budburst. A comprehensive meta-analysis of transcriptomic studies on flower buds of sweet cherry, apricot and peach was conducted, by investigating the gene expression profiles during bud endo- to ecodormancy transition in genotypes differing in chilling requirements. Conserved and distinctive expression patterns were observed, allowing the identification of gene specifically associated with endodormancy or ecodormancy. In addition to the MADS-box transcription factor family, hormone-related genes, chromatin modifiers, macro- and micro-gametogenesis related genes and environmental integrators, were identified as novel biomarker candidates for flower bud development during winter in stone fruits. In parallel, flower bud differentiation processes were associated to dormancy progression and termination and to environmental factors triggering dormancy phase-specific gene expression. [ABSTRACT FROM AUTHOR]

Summary: In temperate zones, fruit trees regulate their annual growth cycle to seasonal environmental changes. During the cold season, growth is limited by both environmental and genetic factors. After the exposure to low temperature and fulfillment of chilling requirements, mild temperatures promote the growth and flowering. However, an insufficient chilling exposure may lead to nonuniform blooming, with a negative impact on fruit set.To gain insights into flower development in the fruit tree buds, peach is an interesting model, the flower and vegetative bud being distinct organs. To understand how flower bud development is regulated, we integrated cytological observations and epigenetic and chromatin genome‐wide data with transcriptional changes to identify the main regulatory factors involved in flower development during chilling accumulation.We demonstrated that growth cessation does not occur in peach flower buds during chilling accumulation, but that there are changes in transcript abundance of key genes of hormone metabolism and flower bud development, distribution of histone modifications (H3K4me3 and H3K27me3) and DNA methylation.Altogether, our findings indicate that during the cold season the flower bud is in a nondormant state and that the chilling experience allows flower differentiation to be completed. [ABSTRACT FROM AUTHOR]

Abstract: Stony hard (SH) peaches are characterized, at ripening, by the maintenance of flesh firmness and the lack of ethylene production due to a reduced expression of Pp-ACS1. In a trial comparing melting flesh (MF, cv. ‘Summer Rich’) and SH (‘IFF331’ selection) fruit at two different postharvest temperatures (10 and 20°C), unexpected behaviour was observed in SH peaches that displayed an increase in ethylene production and a decrease in flesh firmness when stored at 10°C, a temperature regime basically ineffective in delaying ripening in MF fruit. This appeared to be the result of an induction of Pp-ACS1 transcription, making this genotype of particular interest for studying temperature stress physiology and ethylene-related ripening processes in peaches. Comparative expression analyses of genes involved in cell wall metabolism pointed out the presence of a negative (Pp-EG4), positive (Pp-endoPG) or no (one member of the PL family) relationship with ethylene at ripening. Results clearly showed that the last stage of firmness decrease (melting) only occurs in fruit producing ethylene and is associated with Pp-endoPG transcript accumulation. The expression of genes involved in ethylene biosynthesis and signalling pathways was evaluated using QRT-PCR. Pp-ACO1 appeared to be induced in SH kept at 10°C but not at 20°C. Transient increases in Pp-CTR1 and Pp-EIN2like gene expression have only been detected at the early stages of ripening in samples producing ethylene, indicating that a causal relationship might exist between ethylene and elements of its transduction pathway during peach fruit ripening. [Copyright &y& Elsevier]

• The time course of ethylene biosynthesis and perception was investigated in ripening peach fruit ( Prunus persica) following treatments with the polyamines putrescine (Pu) and spermidine (Sd), and with aminoethoxyvinylglycine (AVG). • Fruit treatments were performed in planta. Ethylene production was measured by gas chromatography, and polyamine content by high-performance liquid chromatography; expression analyses were performed by Northern blot or real-time polymerase chain reaction. • Differential increases in the endogenous polyamine pool in the epicarp and mesocarp were induced by treatments; in both cases, ethylene production, fruit softening and abscission were greatly inhibited. The rise in 1-aminocyclopropane-1-carboxylate oxidase ( PpACO1) mRNA was counteracted and delayed in polyamine-treated fruit, whereas transcript abundance of ethylene receptors PpETR1 (ethylene receptor 1) and PpERS1 (ethylene sensor 1) was enhanced at harvest. Transcript abundance of arginine decarboxylase (ADC) and S-adenosylmethionine decarboxylase (SAMDC) was transiently reduced in both the epicarp and mesocarp. AVG, here taken as a positive control, exerted highly comparable effects to those of Pu and Sd. • Thus, in peach fruit, increasing the endogenous polyamine pool in the epicarp or in the mesocarp strongly interfered, both at a biochemical and at a biomolecular level, with the temporal evolution of the ripening syndrome. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Two peach genes homologous to the Arabidopsis ethylene receptor genes ETR1 and ERS1, named Pp‐ETR1 and Pp‐ERS1 respectively, have been isolated and characterized. Pp‐ETR1 and Pp‐ERS1 are conserved in terms of exon numbers and intron positions, although the first and fifth introns of Pp‐ETR1 have an unusual length. In addition, two putative polyadenylation sites, that may cause an incomplete splicing at the 3′ terminus, are present in the fifth intron. A motif of 28 nt, which shows high homology with ethylene responsive elements found in promoters of genes up‐regulated by ethylene, is present in the promoter region of Pp‐ERS1. Expression analysis, carried out by quantitative RT‐PCR, was performed during fruit development and ripening, and leaf and fruitlet abscission. The level of Pp‐ETR1 transcripts remained unchanged in all the tissues and developmental stages examined, whereas Pp‐ERS1 mRNA abundance increased in ripening mesocarp, in leaf and fruitlet activated abscission zones, and following propylene application. 1‐methylcyclopropene (1‐MCP), an inhibitor of ethylene action, did not affect Pp‐ETR1 transcription, while it down‐regulated Pp‐ERS1. A rise in ethylene evolution, accompanied by an increase of Pp‐ERS1 transcript accumulation occurred within 24 h from the end of 1‐MCP treatment. These results indicate that Pp‐ERS1 might play a role in abscission and ripening. [ABSTRACT FROM PUBLISHER]

In light of ongoing climate changes in wine-growing regions, the selection of drought-tolerant rootstocks is becoming a crucial factor for developing a sustainable viticulture. In this study, M, a new rootstock genotype that shows tolerance to drought, was compared from a genomic and transcriptomic point of view with the less drought-tolerant genotype 101.14. The root and leaf transcriptome of both 101.14 and the M4 rootstock genotype was analysed, following exposure to progressive drought conditions. Multifactorial analyses indicated that stress treatment represents the main factor driving differential gene expression in roots, whereas in leaves the genotype is the prominent factor. Upon stress, M4 roots and leaves showed a higher induction of resveratrol and flavonoid biosynthetic genes, respectively. The higher expression of VvSTS genes in M, confirmed by the accumulation of higher levels of resveratrol in M4 roots compared with 101.1, was coupled to an up-regulation of several VvWRKY transcription factors. Interestingly, VvSTS promoter analyses performed on both the resequenced genomes highlighted a significantly higher number of W-BOX elements in the tolerant genotype. It is proposed that the elevated synthesis of resveratrol in M4 roots upon water stress could enhance the plant's ability to cope with the oxidative stress usually associated with water deficit. [ABSTRACT FROM AUTHOR]

The KNOTTED-like transcription factors (KNOX) contribute to plant organ development. The expression patterns of peach KNOX genes showed that the class 1 members act precociously (S1–S2 stages) and differentially during drupe growth. Specifically, the transcription of KNOPE1 and 6 decreased from early (cell division) to late (cell expansion) S1 sub-stages, whilst that of STMlike1 , 2, KNOPE2 , 2.1 ceased at early S1. The KNOPE1 role in mesocarp was further addressed by studying the mRNA localization in the pulp cells and vascular net at early and late S1. The message signal was first diffuse in parenchymatous cells and then confined to hypodermal cell layers, showing that the gene down-tuning accompanied cell expansion. As for bundles, the mRNA mainly featured in the procambium/phloem of collateral open types and subsequently in the phloem side of complex structures (converging bundles, ducts). The KNOPE1 overexpression in Arabidopsis caused fruit shortening, decrease of mesocarp cell size, diminution of vascular lignification together with the repression of the major gibberellin synthesis genes AtGA20ox1 and AtGA3ox1 . Negative correlation between the expression of KNOPE1 and PpGA3ox1 was observed in four cultivars at S1, suggesting that the KNOPE1 repression of PpGA3ox1 may regulate mesocarp differentiation by acting on gibberellin homeostasis. [ABSTRACT FROM AUTHOR]

Differences in gene expression were studied after Plum pox virus ( PPV, sharka disease) infection in peach GF305 leaves with and without sharka symptoms using RNA-Seq. For each sample, more than 80% of 100-nucleotide paired-end ( PE) Illumina reads were aligned on the peach reference genome. In the symptomatic sample, a significant proportion of reads were mapped to PPV reference genomes (1.04% compared with 0.00002% in non-symptomatic leaves), allowing for the ultra-deep assembly of the complete genome of the PPV isolate used (9775 nucleotides, missing only 11 nucleotides at the 5′ genome end). In addition, significant alternative splicing events were detected in 359 genes and 12 990 single nucleotide polymorphisms ( SNPs) were identified, 425 of which could be annotated. Gene ontology annotation revealed that the high-ranking mRNA target genes associated with the expression of sharka symptoms are mainly related to the response to biotic stimuli, to lipid and carbohydrate metabolism and to the negative regulation of catalytic activity. A greater number of differentially expressed genes were observed in the early asymptomatic phase of PPV infection in comparison with the symptomatic phase. These early infection events were associated with the induction of genes related to pathogen resistance, such as jasmonic acid, chitinases, cytokinin glucosyl transferases and Lys- M proteins. Once the virus had accumulated, the overexpression of Dicer protein 2a genes suggested a gene silencing plant response that was suppressed by the virus HCPro and P1 proteins. These results illustrate the dynamic nature of the peach- PPV interaction at the transcriptome level and confirm that sharka symptom expression is a complex process that can be understood on the basis of changes in plant gene expression. [ABSTRACT FROM AUTHOR]

Highlights: [•] Transcript profiles in peach mesocarp markedly change following wounding. [•] Melting and slow melting varieties differ in their responses to wounding. [•] Polyphenol and flavonoid content and the expression of related genes are selectively affected. [•] Mechanical stress activates regulatory and signaling mechanisms. [•] Different hormone categories appear to be involved in the responses to wounding. [Copyright &y& Elsevier]

Background Alternative splicing (AS) significantly enhances transcriptome complexity. It is differentially regulated in a wide variety of cell types and plays a role in several cellular processes. Here we describe a detailed survey of alternative splicing in grape based on 124 SOLiD RNAseq analyses from different tissues, stress conditions and genotypes. Results We used the RNAseq data to update the existing grape gene prediction with 2,258 new coding genes and 3,336 putative long non-coding RNAs. Several gene structures have been improved and alternative splicing was described for about 30% of the genes. A link between AS and miRNAs was shown in 139 genes where we found that AS affects the miRNA target site. A quantitative analysis of the isoforms indicated that most of the spliced genes have one major isoform and tend to simultaneously co-express a low number of isoforms, typically two, with intron retention being the most frequent alternative splicing event. Conclusions As described in Arabidopsis, also grape displays a marked AS tissue-specificity, while stress conditions produce splicing changes to a minor extent. Surprisingly, some distinctive splicing features were also observed between genotypes. This was further supported by the observation that the panel of Serine/Arginine-rich splicing factors show a few, but very marked differences between genotypes. The finding that a part the splicing machinery can change in closely related organisms can lead to some interesting hypotheses for evolutionary adaptation, that could be particularly relevant in the response to sudden and strong selective pressures. [ABSTRACT FROM AUTHOR]

Highlights: [•] A quality traits re-equilibration of Raboso Piave musts was obtained by applying DMR. [•] DMR strongly affected genes involved in malate catabolism and flavonoids biosynthesis. [•] Less astringency of DMR musts is due to a reduction of tannin precursors. [•] The increase of quercitin maintains a brighter color in the wine. [Copyright &y& Elsevier]

Peach ( Prunus persica var. laevis Gray) was chosen to unravel the molecular basis underlying the ability of spermidine (Sd) to influence fruit development and ripening. Field applications of 1 m M Sd on peach fruit at an early developmental stage, 41 days after full bloom (dAFB), i.e. at late stage S1, led to a slowing down of fruit ripening. At commercial harvest (125 dAFB, S4II) Sd-treated fruits showed a reduced ethylene production and flesh softening. The endogenous concentration of free and insoluble conjugated polyamines (PAs) increased (0.3-2.6-fold) 1 day after treatment (short-term response) butsoon it declined to control levels; starting from S3/S4, when soluble conjugated forms increased (up to five-fold relative to controls at ripening), PA levels became more abundant in treated fruits, (long-term response). Real-time reverse transcription-polymerase chain reaction analyses revealed that peaks in transcript levels of fruit developmental marker genes were shifted ahead in accord with a developmental slowing down. At ripening (S4I-S4II) the upregulation of the ethylene biosynthetic genes ACO1 and ACS1 was dramatically counteracted by Sd and this led to a strong downregulation of genes responsible for fruit softening, such as PG and PMEI. Auxin-related gene expression was also altered both in the short term ( TRPB) and in the long term ( GH3, TIR1 and PIN1), indicating that auxin plays different roles during development and ripening processes. Messenger RNA amounts of other hormone-related ripening-regulated genes, such as NCED and GA2-OX, were strongly downregulated at maturity. Results suggest that Sd interferes with fruit development/ripening by interacting with multiple hormonal pathways. [ABSTRACT FROM AUTHOR]

Background: Auxins act as repressors of ripening inception in grape (véraison), while ethylene and abscisic acid (ABA) play a positive role as inducers of the syndrome. Despite the increasing amount of information made available on this topic, the complex network of interactions among these hormones remains elusive. In order to shed light on these aspects, a holistic approach was adopted to evaluate, at the transcriptomic level, the crosstalk between hormones in grape berries, whose ripening progression was delayed by applying naphtalenacetic acid (NAA) one week before véraison. Results: The NAA treatment caused significant changes in the transcription rate of about 1,500 genes, indicating that auxin delayed grape berry ripening also at the transcriptional level, along with the recovery of a steady state of its intracellular concentration. Hormone indices analysis carried out with the HORMONOMETER tool suggests that biologically active concentrations of auxins were achieved throughout a homeostatic recovery. This occurred within 7 days after the treatment, during which the physiological response was mainly unspecific and due to a likely pharmacological effect of NAA. This hypothesis is strongly supported by the up-regulation of genes involved in auxin conjugation (GH3-like) and action (IAA4- and IAA31-like). A strong antagonistic effect between auxin and ethylene was also observed, along with a substantial 'synergism' between auxins and ABA, although to a lesser extent. Conclusions: This study suggests that, in presence of altered levels of auxins, the crosstalk between hormones involves diverse mechanisms, acting at both the hormone response and biosynthesis levels, creating a complex response network. [ABSTRACT FROM AUTHOR]

transcriptome analysis was applied on two peach ( Prunus persica L.) cultivars with different sensitivity to low temperature regimes to identify genes that might be involved in tolerance to extended low temperature storage. Peach fruit from 'Morettini No2' to 'Royal Glory', cultivars sensitive and tolerant to chilling injury (CI), respectively, were harvested at commercial maturity stage and allowed to ripen at room temperature (shelf-life, 25°C) or subjected to 4 and 6 weeks of cold storage (0°C, 95% R.H.) followed by ripening at room temperature. The use of μPEACH 1.0 microarray platform identified a number of genes that were differentially expressed in 'Morettini No2' and 'Royal Glory' fruit after the extended storage period. Based on their possible involvement in physiological processes related to cold storage and on their differential expression pattern, two heat shock proteins, a β-D-xylosidase, an expansin, a dehydrin and a pathogenesis-related (PR) protein were further selected for detailed analysis via RNA blot analysis. It is suggested that β- d-xylosidase and PR-4B precursor genes could be related to the different tolerance to CI observed in the two peach cultivars since generally higher expression levels were observed in cv. 'Royal Glory', the tolerant one. These two genes could play a role in peach tolerance to chilling injury. [ABSTRACT FROM AUTHOR]

Abstract: Aspergillus carbonarius is responsible for the majority of mycotoxin contaminations in grapes and its derivatives. Most of A. carbonarius strains are ochratoxin A (OTA) producers, even though at very different levels. This broad variability was used to identify genes whose expression is linked with the ability of producing OTA. A cDNA-AFLP differential display screening was performed in two strains of A. carbonarius, antagonists for the ability of producing OTA, allowing the identification of 119 differentially expressed sequences putatively involved in the regulation of OTA biosynthesis. A likely connection was pointed out between the biosynthesis of the toxin, vegetative growth and sexual/asexual developmental progression, along with common signalling pathways involving G protein and Ca2+/calmodulin dependent phosphorylation and dephoshorylation cascades. [Copyright &y& Elsevier]

A large-scale transcriptome analysis has been conducted using μPEACH1.0 microarray on nectarine (Prunus persica L. Batsch) fruit treated with 1-methylcyclopropene (1-MCP). 1-MCP maintained flesh firmness but did not block ethylene biosynthesis. Compared with samples at harvest, only nine genes appeared to be differentially expressed when fruit were sampled immediately after treatment, while a total of 90 targets were up- or down-regulated in untreated fruit. The effect of 1-MCP was confirmed by a direct comparison of transcript profiles in treated and untreated fruit after 24 h of incubation with 106 targets differentially expressed. About 30% of these targets correspond to genes involved in primary metabolism and response processes related to ethylene, auxin, and other hormones. In treated fruit, altered transcript accumulation was detected for some genes with a role in ripening-related events such as softening, colour development, and sugar metabolism. A rapid decrease in flesh firmness and an increase in ethylene production were observed in treated fruit maintained for 48 h in air at 20 °C after the end of the incubation period. Microarray comparison of this sample with untreated fruit 24 h after harvest revealed that about 45% of the genes affected by 1-MCP at the end of the incubation period changed their expression during the following 48 h in air. Among these genes, an ethylene receptor (ETR2) and three ethylene-responsive factors (ERF) were present, together with other transcription factors and ethylene-dependent genes involved in quality parameter changes. [ABSTRACT FROM PUBLISHER]

Abstract: In this paper, ethylene production, ACC quantification, and the determination of ACC-oxidase (ACO) activity and the transcript levels PdACS1, PdACO1, and PdACO2, have been evaluated in different parts of developing flowers (sepals, petals, stamens, and pistils) and fruits (epicarp, mesocarp, and seed) of damson plum (Prunus domestica L. subsp. Syriaca), which is a drupe. The fertilized pistil was the only floral organ to register net ethylene production. PdACS1 mRNA was detected exclusively in the stamen. Regarding PdACO1 and PdACO2 transcription, at pre-anthesis, anthesis, and post-anthesis, it was found that: (a) both genes were expressed in all studied floral organs, but accumulation of PdACO1 transcripts was consistently higher; (b) anthesis provoked a sharp accumulation of PdACO1 in sepals, petals, and stamens, while in the pistil no changes occurred; (c) an increase of PdACO2 transcription occurred in sepals concomitantly with anthesis; (d) pollination appeared to activate the transcription of PdACO1 in the pistil. The whole fruit of this plum produced ethylene only at the beginning of S1 and in S4 (climacteric), while the seed produced it at the end of the S1 and throughout S2, when a great richness in ACC and high ACO activity occurred. PdACS1 expression was detectable in the whole fruit at the beginning of development and in the epicarp and mesocarp during ripening. No expression of PdACS1 has been detected in isolated seeds. Even though the transcript for PdACO2 was temporal and spatially absent in fruit development, mRNA levels of PdACO1 notably changed. In the seed, the higher transcriptional activity of PdACO1 appeared at the end of phase S1. The greatest amounts of ACC were registered in the ripening mesocarp and epicarp. Whereas PdACO1 mRNA was detected in the mesocarp at the middle of S1, during the breaker stage (S3), and at the end of the climacteric phase (S4), in epicarp the expression occurred only in S4 stage. These results clearly demonstrate that the seed actively participates in ethylene production during the first phase of damson plum development. [Copyright &y& Elsevier]

To investigate the transcriptional regulation of two 1-aminocyclopropane-1-carboxylate (ACC) oxidase (ACO) genes of peach, chimeric fusions between β-glucuronidase (GUS) reporter gene, and Pp-ACO1 and Pp-ACO2 promoters have been constructed and introduced in tomato (cv Microtom). Pp-ACO1 promoter is able to induce in transgenic tomato plants the same pattern of expression observed in peach. In fact, Pp-ACO1–GUS activity was localized in leaf blade, ovary, leaf and fruit abscission zones and pericarp, and it is up-regulated by propylene and wounding. A gradient of transcript accumulation has been observed in ripening fruit tissues: in tomato it decreased moving from the inner to the outer pericarp, while in peach the opposite occurred. This different behavior could be related to the fruit type (berry vs. drupe). In order to identify cis-acting element involved in ethylene induction of Pp-ACO1, portions of its promoter fused with the GUS gene have been constructed and used in peach fruit transient activity assay. The deletion analysis has shown that a region located between −716 and −346 bp, containing an ethylene-responsive element (ERE), is responsible for the higher stimulation by the gas. In addition, two auxin-responsive elements (AUXre), probably responsible for the auxin suppression of the propylene induction of Pp-ACO1 gene expression, are present upstream from EREs. Pp-ACO2 promoter is able to drive the expression in vascular bundles of immature and ripe fruit, senescent leaf blade, and in fruit and leaf abscission zones. In peach, Pp-ACO2 mRNA is detected only in immature fruit, epicotyl and root of seedling. This discrepancy might be imputed to a lesser stability and translation of Pp-ACO2 mRNA in comparison to that of chimeric one. [Copyright &y& Elsevier]

Two cDNA clones (named Pp-LTP1 and Pp-LTP2) corresponding to different lipid transfer protein (LTP) genes have been isolated from peach (Prunus persica L. Batsch) epicarp and ovary, respectively. Sequence analysis revealed that the two fragments share 54% identity at nucleotide level and show common features of plant LTP genes, such as conserved cysteine residues and lipid-binding motifs. Phylogenetic analysis grouped Pp-LTP1 and Pp-LTP2 in two distinct clusters, the former with most of LTP genes sequenced in the Rosaceae family, the latter only with one almond LTP. Genomic Southern data indicated that a small LTP gene family is present in peach. Pp-LTP1 and Pp-LTP2 have been used as gene-specific probes to describe expression in flowers and fruits throughout development. In petals, sepals and stamen only Pp-LTP1 was expressed whereas transcripts of Pp-LTP2 strongly accumulated in non-pollinated and pollinated ovary with a decreasing trend in the period of four weeks after pollination. In fruits, a dramatic accumulation of Pp-LTP1 mRNA was detected in epicarp at all stages of fruit development and, with the exception of the early growth stage, no Pp-LTP1 transcripts have been detected in mesocarp. When Pp-LTP2 was used as a probe in the same fruit tissues, a faint hybridisation signal was observed only in epicarp of fruitlets collected at an early growth stage. Infection with Monilia induced only a slight increase of Pp-LTP1 transcript in epicarp of pre-climacteric and climacteric fruits. These results support the hypothesis of multiple roles played by LTPs and, considering that LTPs have been recognised as the major allergen of peach, indicate that Pp-LTP1 could be related to the allergenicity of peach. [Copyright &y& Elsevier]

Superficial scald is a post-harvest chilling storage injury leading to browning of the surface of the susceptible cv Granny Smith apples. Wounding of skins has been reported to play a preventive role on scald development however its underlying molecular factors are unknown. We have artificially wounded the epidermal and sub-epidermal layers of apple skins consistently obtaining the prevention of superficial scald in the surroundings of the wounds during two independent vintages. Time course RNA-Seq analyses of the transcriptional changes in wounded versus unwounded skins revealed that two transcriptional waves occurred. An early wave included genes up-regulated by wounding already after 6 h, highlighting a specific transcriptional rearrangement of genes connected to the biosynthesis and signalling of JA, ethylene and ABA. A later transcriptional wave, occurring after three months of cold storage, included genes up-regulated exclusively in unwounded skins and was prevented from its occurrence in wounded skins. A significant portion of these genes was related to decay of tissues and to the senescence hormones ABA, JA and ethylene. Such changes suggest a wound-inducible reversed hormonal balance during post-harvest storage which may explain the local inhibition of scald in wounded tissues, an aspect that will need further studies for its mechanistic explanation. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]