P. Tonutti

The high-quality draft genome of peach (Prunus persica) identifies unique patterns of genetic diversity, domestication and genome evolution

Rosaceae is the most important fruit-producing clade, and its key commercially relevant genera (Fragaria, Rosa, Rubus and Prunus) show broadly diverse growth habits, fruit types and compact diploid genomes. Peach, a diploid Prunus species, is one of the best genetically characterized deciduous trees. Here we describe the high-quality genome sequence of peach obtained from a completely homozygous genotype. We obtained a complete chromosome-scale assembly using Sanger whole-genome shotgun methods. We predicted 27,852 protein-coding genes, as well as noncoding RNAs. We investigated the path of peach domestication through whole-genome resequencing of 14 Prunus accessions. The analyses suggest major genetic bottlenecks that have substantially shaped peach genome diversity. Furthermore, comparative analyses showed that peach has not undergone recent whole-genome duplication, and even though the ancestral triplicated blocks in peach are fragmentary compared to those in grape, all seven paleosets of paralogs from the putative paleoancestor are detectable.

Transcriptome profiling of ripening nectarine (Prunus persica L. Batsch) fruit treated with 1-MCP

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.

Computational annotation of genes differentially expressed along olive fruit development

BackgroundOlea europaea L. is a traditional tree crop of the Mediterranean basin with a worldwide economical high impact. Differently from other fruit tree species, little is known about the physiological and molecular basis of the olive fruit development and a few sequences of genes and gene products are available for olive in public databases. This study deals with the identification of large sets of differentially expressed genes in developing olive fruits and the subsequent computational annotation by means of different software.ResultsmRNA from fruits of the cv. Leccino sampled at three different stages [i.e., initial fruit set (stage 1), completed pit hardening (stage 2) and veraison (stage 3)] was used for the identification of differentially expressed genes putatively involved in main processes along fruit development. Four subtractive hybridization libraries were constructed: forward and reverse between stage 1 and 2 (libraries A and B), and 2 and 3 (libraries C and D). All sequenced clones (1,132 in total) were analyzed through BlastX against non-redundant NCBI databases and about 60% of them showed similarity to known proteins. A total of 89 out of 642 differentially expressed unique sequences was further investigated by Real-Time PCR, showing a validation of the SSH results as high as 69%. Library-specific cDNA repertories were annotated according to the three main vocabularies of the gene ontology (GO): cellular component, biological process and molecular function. BlastX analysis, GO terms mapping and annotation analysis were performed using the Blast2GO software, a research tool designed with the main purpose of enabling GO based data mining on sequence sets for which no GO annotation is yet available. Bioinformatic analysis pointed out a significantly different distribution of the annotated sequences for each GO category, when comparing the three fruit developmental stages. The olive fruit-specific transcriptome dataset was used to query all known KEGG (Kyoto Encyclopaedia of Genes and Genomes) metabolic pathways for characterizing and positioning retrieved EST records. The integration of the olive sequence datasets within the MapMan platform for microarray analysis allowed the identification of specific biosynthetic pathways useful for the definition of key functional categories in time course analyses for gene groups.ConclusionThe bioinformatic annotation of all gene sequences was useful to shed light on metabolic pathways and transcriptional aspects related to carbohydrates, fatty acids, secondary metabolites, transcription factors and hormones as well as response to biotic and abiotic stresses throughout olive drupe development. These results represent a first step toward both functional genomics and systems biology research for understanding the gene functions and regulatory networks in olive fruit growth and ripening.

Peach fruit ripening and quality in relation to picking time, and hypoxic and high CO2 short-term postharvest treatments

Peach fruits (Prunus persica L. Batsch, cv Springcrest) were harvested at two ripening stages (flesh firmness of 60 N, first harvest, and 45 N, second harvest) and maintained at 20°C in air (control) or for 24 and 48 h in streams of ultra low (<1%) oxygen (ULO) or high (30%) CO2 concentration and then transferred to air for up to 8 days. The decline in flesh firmness was strongly reduced by ULO and CO2 treatments in fruits of both harvests, although the effect was stronger in fruits picked earlier in which ethylene biosynthesis remained at the basal level. In fruits of the second harvest, endo β-1,4-glucanase (EGase) activity was lower in ULO- and CO2-treated fruits than in control fruits at the end of the 24 h treatment and the following two days in air. Acetaldehyde (AA) gradually accumulated in control fruit and the highest concentrations were detected during late ripening. Both treatments induced a strong accumulation of AA but, with the exception of the 24 and 48 h CO2 treatments performed on fruits of the second harvest, a decrease in AA content was observed when the fruits were transferred to air. A slight increase in ethanol (EtOH) was found throughout the ripening process in control fruits; ULO and CO2 strongly stimulated EtOH production. When fruits were transferred to air, EtOH concentration declined rapidly. Alcohol dehydrogenase (ADH) activity significantly increased in control fruit only in the late stages of ripening. Greater ADH activity was found throughout the experimental period in fruits of the first harvest treated for 24 h in ULO and CO2, whereas, at day 8, control and treated fruits of the second harvest showed similar ADH activity values. Hypoxic and, to a lesser extent, CO2-enriched atmospheres stimulated Adh gene expression.

Fruit firmness and ethylene biosynthesis in three cultivars of peach (Prunus persica L. Batsch)

SummaryIn the three freestone peach cultivars Springcrest, Redhaven, and Fayette, ethylene evolution was studied and related to fruit softening. Loss of firmness was accompanied by an increase in ethylene biosynthesis but great variability was observed within the selected fruit populations. By plotting data on a single-fruit basis, it appeared that the climacteric was a late event occurring when the fruit had already softened to about 10 to 20 N. The highest values of whole-fruit ethylene evolution at ripening were detected in ‘Springcrest’ . During the earliest phases of softening, whole-fruit ethylene production only rose slightly, whereas a marked increase of 1-aminocyclopropane-l-carboxylicacid (ACC) content, in vivo ACC oxidase activity and ethylene evolution was observed in isolated mesocarp disks, particularly in ‘Springcrest’ and ‘Redhaven’. In the three cultivars, a gradient between epicarp and mesocarp tissue has been detected in terms of ethylene physiology, the former being characterized by a ...

Cell wall hydrolases and amylase in kiwifruit softening

Abstract The activities of amylase, β-galactosidase (β-GAL), polygalacturonase (PG), and endo-1,4-β-glucanase (EG), and ethylene evolution, were measured during ripening in kiwifruit ( Actinidia deliciosa (A.Chev.) (C.F. Liang et A.R. Ferguson var deliciosa, cv. Hayward). Fruit, harvested at firmness values (FV) of 65 N and a soluble solid (SS) content of 9%, were maintained in air at 20 °C for 40 days, until they reached the edible stage. Fruit firmness decreased throughout the experimental period and the lowest FV (about 5 N) was reached after 38 days of storage. SS content increased rapidly to about 13% within 15 days, then the rate of accumulation slowed and the SS content of 14.1% was reached after 33 days. Ethylene climacteric was a late event occurring at a FV of 10 N. The highest amylase activity was measured at harvest. During storage it declined, although a slight rise was detected at 33 days. β-GAL activity was very low at the beginning of storage and increased throughout the experimental period, while PG activity was detected only after the fruit FV was below 10 N. EG activity decreased within the first three days of storage, then increased and peaked 15 days after harvest. Later, EG activity remained low but increased again at the end of the storage period. Application of propylene (500 ppm) to fruit that had softened to 30 N in air stimulated fruit softening and EG activity, and induced the accumulation of an EG-related peptide: the other enzymes appeared not to be affected by the gas.

Biochemical and molecular aspects of fruitlet abscission

Fruitlet abscission during fruit development is due to the activation ofpre-differentiated abscission zones (AZs) located between twig andpedicel, and/or pedicel and pericarp. Major advances on biochemicaland molecular aspects are related to β-1,4-endoglucanase (EG) andpolygalacturonase (PG), two cell hydrolases involved in the cell walldisassemblement responsible for fruit shedding. AZ activation isaccompanied by an increase in activity and transcript accumulation ofone or both enzymes. Expression of PG genes specifically related toabscission has been found in tomato flower AZ. In peach, an EG genehighly expressed in leaf and fruitlet AZs has been isolated. AZactivation is preceded by an induction of ethylene biosynthesis,paralleled by a stimulation of ACO activity and transcript accumulation.Ethylene, besides a dramatic stimulation of PG and EG, up or downregulates several other abscission related genes. The specificexpression of genes encoding for ethylene receptors in the AZ wouldsupport the hypothesis that fruitlet AZ specificity may depend on theability of this region to sense ethylene.

Differential expression of two lipid transfer protein genes in reproductive organs of peach (Prunus persica L. Batsch)

Abstract 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.

Characterization of a major latex protein (MLP) gene down-regulated by ethylene during peach fruitlet abscission☆

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 alternativ ed evelopmental role such as cell and tissue expansion. # 2002 Elsevier Science Ireland Ltd. All rights reserved.

Sweet, reinforced, and fortified wines : grape biochemistry, technology and vinification

Wines from Grape Dehydration is the first of its kind in the field of grape dehydration the controlled drying process which produces a special group of wines. These types of wine are the most ancient, made in the Mediterranean basin, and are even described in Herodotus. Until few years ago, it was thought that these wines – such as Pedro Ximenez, Tokai, Passito, and Vin Santo – were the result of simple grape drying, because the grapes were left in the sun, or inside greenhouses that had no controls over temperature, relative humidity or ventilation. But Amarone wine, one of the most prized wines in the world, is the first wine in which the drying is a controlled process. This controlled process – grape dehydration – changes the grape at the biochemical level, and involves specialist vine management, postharvest technology and production processes, which are different from the typical wine-making procedure. After a history of grape dehydration, the book is then divided into two sections; scientific and technical.