Giannina Vizzotto

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.

Three distinct mutational mechanisms acting on a single gene underpin the origin of yellow flesh in peach

Peach flesh color (white or yellow) is among the most popular commercial criteria for peach classification, and has implications for consumer acceptance and fruit nutritional quality. Despite the increasing interest in improving cultivars of both flesh types, little is known about the genetic basis for the carotenoid content diversity in peach. Here we describe the association between genotypes at a locus encoding the carotenoid cleavage dioxygenase 4 (PpCCD4), localized in pseudomolecule 1 of the Prunus persica reference genome sequence, and the flesh color for 37 peach varieties, including two somatic revertants, and three ancestral relatives of peach, providing definitive evidence that this locus is responsible for flesh color phenotype. We show that yellow peach alleles have arisen from various ancestral haplotypes by at least three independent mutational events involving nucleotide substitutions, small insertions and transposable element insertions, and that these mutations, despite being located within the transcribed portion of the gene, also result in marked differences in transcript levels, presumably as a consequence of differential transcript stability involving nonsense-mediated mRNA decay. The PpCCD4 gene provides a unique example of a gene for which humans, in their quest to diversify phenotypic appearance and qualitative characteristics of a fruit, have been able to select and exploit multiple mutations resulting from a variety of mechanisms.

Fruit thinning of peach trees

The present review deals with the importance of fruit thinning in peach.The date of treatment, the severity and the criteria underlying the practiceare discussed. Methods of fruit thinning are described, with particularemphasis on the use of chemical treatment as an alternative to handthinning. Strategies for chemical thinning are advanced.

Soil humic substances affect transport properties of tonoplast vesicles isolated from oat roots

The effect of a low molecular size (<5 KDa) humic fraction, essentially fulvic acids, on microsomal and tonoplast ion-stimulated ATPase activity was studied. After 20 min of pre-incubation with microsomal vesicles from oat roots, humic substances at organic C concentration of up to 0.5 μg cm-3 increased KCl-stimulated ATPase activity, while they inhibited enzyme activity at higher concentrations. Cl--stimulated ATPase activity of tightly sealed tonoplast-enriched vesicles was similarly affected by <5 KDa humic substances. This behaviour was not observed when gramicidin D was added to the assay medium. Proton transport by vesicles incubated up to 5 min with <5 KDa humic molecules was affected in a concentration-dependent manner, strongly resembling that observed for ATP hydrolysis, whereas it was severely reduced when the assay conditions were close to those used for measuring ATP hydrolysis (20 min pre-incubation of vesicles with humic substances). The transmembrane electrical potential was negatively affected, irrespective of the concentration of humic molecules. Furthermore, a 15-min pre-incubation strongly reduced the formation of a potential gradient. The size and concentrations of humic substances employed make an interaction with the vacuolar membrane of root cells plausible. The results show that the main target of humic molecules is the electrical membrane potential and suggest a possible way of interference of these naturally occurring substances with the biochemical mechanisms involved in plant mineral nutrition.

Neutral invertases in grapevine and comparative analysis with Arabidopsis, poplar and rice

Neutral invertases (NIs, EC 3.2.1.26) cleave sucrose to glucose and fructose. They are encoded by a small gene family of 9 members in the Arabidopsis genome, 8 in rice, 16 in poplar and 9 in Vitis vinifera (L.). The grapevine NIs were identified in the 8.4X genome assembly of the quasi-homozygous line PN40024. In addition, alleles of three NIs were sequenced in the heterozygous cultivar ‘Cabernet Sauvignon’. Analyses of sequence variation between alleles, homoeologous and paralogous copies in grapevine and their orthologues in Arabidopsis, poplar and rice are provided. In grapevine, NIs were classified into four α NIs and five β NIs and subsequently grouped into hierarchical clades using a combination of evidence including amino acid identity, exon/intron structure, rate of synonymous substitutions (Ks) and chromosomal distribution. Estimation of Ks proved the ancient origin of all NIs and the lack of expansion by gene duplication past the event of polyploidisation. We then focused on transcription analysis of five NIs for which evidence of expression was available from expressed sequence tag databases. Among these, four NIs consisted of pairs of homoeologous copies, each pair lying on a pair of chromosomes duplicated by polyploidy. Unequal expression of homoeologous genes was observed by quantitative RT-PCR in leaf, flower, seed and root tissues. Since NIs might play significant roles in fruit and wine quality, NIs expression was monitored in flesh and skin of ‘Merlot’ berries and shown in parallel with the suite of changes that accompany fruit ripening, including glucose and fructose accumulation.

Iron reduction in iron‐stressed plants of Actinidia deliciosa genotypes: Involvement of PM Fe(lll)‐Chelate reductase and H+‐ATPase activity

Abstract Micropropagated plantlets of the Actinidia rootstock D1, resistant to lime‐induced iron (Fe) deficiency, and the Actinidia deliciosa line 2084 (sel. 2084), moderately sensitive to Fe starvation, were grown in nutrient solution with or without Fe, in order to characterize the changes induced by iron starvation on physiological and biochemical behavior of this fruit tree. Iron‐stressed plants of D1 showed a higher capability to lower the pH of nutrient solution as compared with plants of sel. 2084. Also, when proton extrusion was measured in a 10 mM KCl, 1 mM CaCl2 solution, Fe‐deficient plants of Dl induced a more rapid decrease in the external pH than sel. 2084 plants. In addition, the activity of the vanadate‐sensitive H+‐ATPase of root plasma membrane (PM) enriched vesicles was about 60 % increased by Fe deficiency in D1 plants, while almost no change was observed in sel. 2084 plants. Fe(III)EDTA reduction capacity of intact roots markedly increased in condition of Fe deficiency as compared wit...

Identification and differential expression dynamics of peach small GTPases encoding genes during fruit development and ripening

The function of monomeric GTPases of the RAS superfamily in fruit development and ripening has been partially characterized. Here the identification of peach (Prunus persica) small GTPases of the RAS superfamily expressed in fruit and the characterization of their expression profiles during fruit development are described. Extensive searches on expressed sequence tag (EST) databases led to the selection of a total of 24 genes from peach encoding proteins with significant similarity to Arabidopsis small GTPases. Sequence similarity analyses and identification of conserved motifs, diagnostic of specific RAS families and subfamilies, enabled bona fide assignment of fourteen PpRAB, seven PpARF/ARL/SAR, two PpROP and one PpRAN GTPases. Transcriptional expression profiles of peach monomeric GTPases, analysed by real-time quantitative reverse transcription-PCR, were obtained for mesocarp samples, collected in two consecutive years. Reproducible patterns of expression could be identified for five peach RAB-encoding genes (PpRABA1-1, PpRABA2, PpRABD2-1, PpRABD2-2, and PpRABC2), two ARFs (PpARFA1-1 and PpARLB1), and two ROPs (PpROP3 and PpROP4). Interestingly, the transient transcriptional up-regulation of PpARF genes and of PpRAB genes of the A and D clades, putatively controlling the exocytic delivery of cell wall components and modifying enzymes, appeared to coincide with peaks of growth speed and sugar accumulation and with the final phases of ripening. To our knowledge, this is the first description of the co-ordinated differential expression of a set of genes encoding small GTPases of the ARF and RAB families which takes place during key moments of fruit development and maturation.

Iron deficiency responses in roots of kiwi

Abstract Many dicotyledonous species respond to iron (Fe) deficiency by morphological and physiological changes at root level, which are usually defined as Strategy I. Particularly, these latter modifications include a higher acidification of the external medium and the induction of a high root Fe reductase activity. The aim of this work was to investigate the response of kiwi (Actinidia deliciosa cv. Hayward) plants, which often exhibit Fe chlorosis in the field, to Fe deficiency. Actinidia kept for two weeks in nutrient solution without Fe showed visual deficiency symptoms (leaf chlorosis). Moreover, upon prolonged micronutrient shortage shoot, and to a lesser extent, root dry weight accumulation was greatly impaired. Roots of Fe‐deficient Actinidia showed an increased capacity of net proton extrusion and higher ferric ethylenediaminetetraacetate [Fe(III)EDTA] reductase activity as compared to plants grown in the presence of 10 μM Fe(III)EDTA. Localization of the increased acidification and reductase ca...

Sucrose transport and phloem unloading in peach fruit: potential role of two transporters localized in different cell types

Several complex physiological processes, which include long-distance translocation in the phloem and unloading in sink tissues, govern the partitioning of sugars in economically important organs, such as peach fruit. In this study, we took advantage of a symplastic tracer, carboxyfluorescein (CF), providing evidence for an apoplastic sucrose transfer in the early (SI) and middle (SIII) phases of peach fruit development. Moreover, using a combination of in situ hybridization and laser microdissection-assisted expression analysis, three putative sucrose transporters encoding genes (PpSUT1, PpSUT2, PpSUT4) were transcriptionally analyzed to relate their expression with sucrose storage in this organ. Our study revealed that PpSUT2 and PpSUT4 are the genes predominantly expressed in fruit flesh, and the detailed analysis of their expression pattern in the different cell types enabled us to suggest a specialized role in sucrose distribution. Both PpSUTs transporters could be involved in the retrieval of sucrose lost from the symplastic continuum of the phloem and, when expressed in parenchyma cells, they could be active in the import of sucrose into sink tissues, via symport from the apoplast. An alternative hypothesis has been proposed and discussed for PpSUT4 because of its putative tonoplastic localization. Taken together, our results provide new insights into the molecular mechanisms underpinning sucrose unloading and accumulation in peach fruit.

Translating time-course gene expression profiles into semi-algebraic hybrid automata via dimensionality reduction

Biotechnological innovations which sample gene expressions allow to measure the gene expression levels of a biological system with varying degree of accuracy, cost and speed. By repeating the measurement steps at different sampling rates, one can both infer relations among the genes and define a dynamic model of the underlying biological system. When a very large number of genes and measurements are involved, they raise several difficult algorithmic questions, as accurate model-building, checking and inference tasks. Semi-algebraic hybrid automata were proposed as a modeling formalism for biological systems (see, e.g., [17,6]), and demonstrated their abilities to handle complex biochemical pathways. This paper proposes an automatic procedure to build semi-algebraic hybrid automata from gene-expression profiles. In order to reduce the size of the resulting automata and to minimize their analysis computational complexity, our approach exploits various dimensionality reduction techniques. The paper concludes with several experimental results about peach fruit.