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Ethylene plays an essential role in the ripening of peach, a climacteric stone fruit. However, several studies have shown that other phytohormones may alter fruit organoleptic properties, nutritional value, and overall quality. Although cytokinin levels are highest during fruit set and early stages of fruit development, exogenous cytokinin application on the late stages of peach fruit development (post-lignification stage) alters the peach fruit ripening indicators and delays ripening. To better understand the molecular mechanisms by which cytokinin alters fruit ripening and fruit quality traits, we identified a conserved set of 26 peach cytokinin-regulated orthologs of the Arabidopsis cytokinin-regulated genes. All but two of these genes show expression in ripe peach fruits. The peach cytokinin-regulated genes map throughout the Prunus persica genome, located on all eight chromosome-scale pseudomolecules. However, eight of these orthologs are located on pseudomolecule 1, while five orthologs are on pseudomolecule 2. Gene Ontology enrichment analyses revealed that many of these genes are associated with metabolic processes. The region upstream of the transcription start site contained Cytokinin Response Elements (CKREs) in 77% (20/26) of these putative cytokinin-regulated genes. The cytokinin responsiveness of eight of these genes (PpeBPH1, PpeCKX4, PpeCPK28, PpeCYP18-2, PpeHSP90-7, PpeNRP2, PpeNIP1-1, and PpePCRP1) was confirmed by RT-qPCR analyses of ripe peach fruits treated exogenously with trans-zeatin for one hour. Therefore, by using a comparative genomic analysis between peach and Arabidopsis, we have identified a conserved set of cytokinin-regulated genes expressed in peach fruits that respond to exogenous application of trans-zeatin and, based upon the conserved cis-regulatory regions, are most likely regulated by the cytokinin Type-B Response Regulators.

Phosphorus deficiency is one of the major nutrient stresses affecting plant growth. Plants respond to phosphate (Pi) deficiency through multiple strategies, including the synthesis of high-affinity Pi transporters. In this study, the expression pattern of one putative wheat high-affinity phosphate transporter, TaPT2, was examined in roots and leaves under Pi-deficient conditions. TaPT2 transcript levels increased in roots of Pi-starved plants. A 579 bp fragment of the TaPT2 promoter is sufficient to drive the expression of the GUS reporter gene specifically in roots of Pi-deprived wheat. This TaPT2 promoter fragment was also able to drive expression of the GUS reporter gene in transgenic Arabidopsis thaliana, under similar growth conditions. Conserved regions and candidate regulatory motifs were detected by comparing this promoter with Pi transporter promoters from barley, rice, and Arabidopsis. Altogether, these results indicate that there are conserved cis-acting elements and trans-acting factors that enable the TaPT2 promoter to be regulated in a tissue-specific and Pi-dependent fashion in both monocots and dicots.

The plant family Rosaceae is comprised of a highly diverse group of plants, with a wide range of ornamental and agricultural uses throughout the world. Comparative genomic analyses between rosaceous species are increasingly being used to assign putative function. With the wealth of new data, there is a need to standardize nomenclature to ensure uniformity and clarity across research groups. The Rosaceae Gene Name Standardization Committee was formed to develop a naming guideline for genes in Rosaceae family members. This manuscript details the issues involved with naming genes and proposes a common nomenclature system. The Genome Database for Rosaceae (GDR) ( www.rosaceae.org ) has developed a gene database that will support user-submitted gene names and annotations in addition to the predicted genes from whole genome sequences. GDR also hosts user-curated lists of gene class symbols. To facilitate standardization of gene names and avoid misinterpretation, the committee recommends that the GDR serve as the database of record for the names of Rosaceae genes and that gene names, gene class symbols, and gene annotation be registered in GDR prior to publication in peer reviewed journals.

Mealiness, a chilling injury symptom, is one of the most important quality limiting factors in peaches and nectarines exported from Chile. The development of mealiness was analyzed over 3 years to quantify the expression of this chilling injury (CI) symptom in different growth seasons. For such a purpose, ‘O’Henry’ peaches, considered a CI susceptible cultivar, were harvested and stored at 0 °C (non-CI inducing conditions) and 4 °C (CI inducing conditions) for 15, 21 and 30 days. Quantitative measurements of juice content in the fruits, an indicator of mealiness, showed that there was a significant variation in the expression of the disorder over the years, being higher in 2 years of evaluations. As expected, there was a reduction in juice content, or a higher incidence of mealiness, with longer cold-storage especially at 4 °C. There was no detectable correlation between juice content and quality attributes and physiological parameters, including skin color, flesh firmness, soluble solids content, respiration and ethylene production rates, suggesting factors other than those analyzed in this study, are involved in this disorder.

Background Through the diversity of cytokinin regulated processes, this phytohormone has a profound impact on plant growth and development. Cytokinin signaling is involved in the control of apical and lateral meristem activity, branching pattern of the shoot, and leaf senescence. These processes influence several traits, including the stem diameter, shoot architecture, and perennial life cycle, which define the development of woody plants. To facilitate research about the role of cytokinin in regulation of woody plant development, we have identified genes associated with cytokinin signaling and homeostasis pathways from two hardwood tree species. Results Taking advantage of the sequenced black cottonwood (Populus trichocarpa) and peach (Prunus persica) genomes, we have compiled a comprehensive list of genes involved in these pathways. We identified genes belonging to the six families of cytokinin oxidases (CKXs), isopentenyl transferases (IPTs), LONELY GUY genes (LOGs), two-component receptors, histidine containing phosphotransmitters (HPts), and response regulators (RRs). All together 85 Populus and 45 Prunus genes were identified, and compared to their Arabidopsis orthologs through phylogenetic analyses. Conclusions In general, when compared to Arabidopsis, differences in gene family structure were often seen in only one of the two tree species. However, one class of genes associated with cytokinin signal transduction, the CKI1-like family of two-component histidine kinases, was larger in both Populus and Prunus than in Arabidopsis.

et al., The woodland strawberry, Fragaria vesca (2n = 2x = 14), is a versatile experimental plant system. This diminutive herbaceous perennial has a small genome (240 Mb), is amenable to genetic transformation and shares substantial sequence identity with the cultivated strawberry (Fragaria × ananassa) and other economically important rosaceous plants. Here we report the draft F. vesca genome, which was sequenced to ×39 coverage using second-generation technology, assembled de novo and then anchored to the genetic linkage map into seven pseudochromosomes. This diploid strawberry sequence lacks the large genome duplications seen in other rosids. Gene prediction modeling identified 34,809 genes, with most being supported by transcriptome mapping. Genes critical to valuable horticultural traits including flavor, nutritional value and flowering time were identified. Macrosyntenic relationships between Fragaria and Prunus predict a hypothetical ancestral Rosaceae genome that had nine chromosomes. New phylogenetic analysis of 154 protein-coding genes suggests that assignment of Populus to Malvidae, rather than Fabidae, is warranted., This work was supported by Roche and 454 Sequencing; the Virginia Bioinformatics Institute; the University of Florida Institute of Food and Agricultural Sciences (IFAS) Dean for Research; the University of Florida Strawberry Breeding Program; The Province of Trento, Italy (to R.V.); Driscoll's Strawberry Associates; United States Department of Agriculture/Cooperative State Research, Education and Extension Service (USDA/CSREES) Hatch Project VA-135816 (to B.F.); Rutgers Busch Biomedical Funding (to T.P.M.); East Malling Trust (EMT) and Biotechnology and Biological Sciences Research Council (BBSRC) (to D.J.S. and E.L.G.); the Oregon State Agricultural Research Foundation #ARF4435 (to T.C.M.); the Oregon State Computational and Genome Biology Initiative (to T.C.M.); Oregon State University start-up fund (to P.J.); the Center for Genomics and Bioinformatics, supported in part by the METACyt Initiative of Indiana University (to K.M.); US National Institutes of Health (grant HG00783; to M.B.); USDA-CSREES National Research Initiative (NRI) Plant Genome Grant 2008-35300-04411 and New Hampshire Agricultural Experiment Station Project NH00535 (to T.M.D.); and USDA/ARS CRIS #1275-21000-180-01R (to J.P.S.).

Background Cold acclimation is the process by which plants adapt to the low, non freezing temperatures that naturally occur during late autumn or early winter. This process enables the plants to resist the freezing temperatures of winter. Temperatures similar to those associated with cold acclimation are also used by the fruit industry to delay fruit ripening in peaches. However, peaches that are subjected to long periods of cold storage may develop chilling injury symptoms (woolliness and internal breakdown). In order to better understand the relationship between cold acclimation and chilling injury in peaches, we isolated and functionally characterized cold-regulated promoters from cold-inducible genes identified by digitally analyzing a large EST dataset. Results Digital expression analyses of EST datasets, revealed 164 cold-induced peach genes, several of which show similarities to genes associated with cold acclimation and cold stress responses. The promoters of three of these cold-inducible genes (Ppbec1, Ppxero2 and Pptha1) were fused to the GUS reporter gene and characterized for cold-inducibility using both transient transformation assays in peach fruits (in fruta) and stable transformation in Arabidopsis thaliana. These assays demonstrate that the promoter Pptha1 is not cold-inducible, whereas the Ppbec1 and Ppxero2 promoter constructs are cold-inducible. Conclusion This work demonstrates that during cold storage, peach fruits differentially express genes that are associated with cold acclimation. Functional characterization of these promoters in transient transformation assays in fruta as well as stable transformation in Arabidopsis, demonstrate that the isolated Ppbec1 and Ppxero2 promoters are cold-inducible promoters, whereas the isolated Pptha1 promoter is not cold-inducible. Additionally, the cold-inducible activity of the Ppbec1 and Ppxero2 promoters suggest that there is a conserved heterologous cold-inducible regulation of these promoters in peach and Arabidopsis. These results reveal that digital expression analyses may be used in non-model species to identify candidate genes whose promoters are differentially expressed in response to exogenous stimuli.

Background The isolation of green fluorescent protein (GFP) and the development of spectral variants over the past decade have begun to reveal the dynamic nature of protein trafficking and organelle motility. In planta analyses of this dynamic process have typically been limited to only two organelles or proteins at a time in only a few cell types. Results We generated a transgenic Arabidopsis plant that contains four spectrally different fluorescent proteins. Nuclei, plastids, mitochondria and plasma membranes were genetically tagged with cyan, red, yellow and green fluorescent proteins, respectively. In addition, methods to track nuclei, mitochondria and chloroplasts and quantify the interaction between these organelles at a submicron resolution were developed. These analyzes revealed that N-ethylmaleimide disrupts nuclear-mitochondrial but not nuclear-plastids interactions in root epidermal cells of live Arabidopsis seedlings. Conclusion We developed a tool and associated methods for analyzing the complex dynamic of organelle-organelle interactions in real time in planta. Homozygous transgenic Arabidopsis (Kaleidocell) is available through Arabidopsis Biological Resource Center.

Thapsigargin, a specific inhibitor of most animal intracellular SERCA-type Ca 2+ pumps present in thesarcoplasmic/endoplasmic reticulum, was originally isolated from the roots of the Mediterranean plant Thapsia gargancia L . Here, we demonstrate that this root-derived compound is capable of altering rootgravitropism in Arabidopsis thaliana . Thapsigargin concentrations as low as 0.1 µM alter root gravitropismwhereas under similar conditions cyclopiazonic acid does not. Furthermore, a fluorescently conjugatedthapsigargin (BODIPY FL thapsigargin) suggests that target sites for thapsigargin are located inintracellular organelles in the root distal elongation zone and the root cap, regions known to regulate rootgravitropism. Key terms: Arabidopsis thaliana , Ca 2+ -ATPases, calcium, gravitropism, thapsigargin, root. Corresponding author: Lee Meisel, Plant Biotechnology Center, Faculty of Ecology and Natural Resources, UniversidadAndres Bello, Av. Republica 217, Santiago, Chile, Tel: (56-2) 661-8449, Fax: (56-2) 661-5832, E-mail: lmeisel@unab.clReceived: October 3, 2005. In revised form: January 2. 2006. Accepted: January 9, 2006.INTRODUCTION

The synthesis of noncellulosic polysaccharides and glycoproteins in the plant cell Golgi apparatus requires UDP-galactose as a substrate. We have cloned and characterized a nucleotide sugar transporter from Arabidopsis thaliana (L.) Heynh. named AtUTr2. Expression in tobacco and Saccharomyces cerevisiae and subsequent biochemical characterization indicate that AtUTr2 transports UDP-galactose, but not UDP-glucose, UDP-N-acetyl glucosamine, UDP-xylose, UDP-glucuronic acid, GDP-fucose or GDP-mannose. Experiments expressing an AtUTr2-GFP fusion protein in onion epidermal cells suggest that AtUTr2 is located in the Golgi apparatus. Finally, northern analysis indicates that the AtUTr2 transcript was more abundant in roots and calli although it was also present in other Arabidopsis organs but at lower levels. Therefore, AtUTr2 is a nucleotide sugar transporter capable of transporting UDP-galactose that may play an important role in the synthesis of galactose-containing glycoconjugates in Arabidopsis.

http://www.scielo.cl/scielo.php?script=sci_arttext&pid=S0716-97602005000100010&lng=es&nrm=iso Prunus persica has been proposed as a genomic model for deciduous trees and the Rosaceae family. Optimized protocols for RNA isolation are necessary to further advance studies in this model species such that functional genomics analyses may be performed. Here we present an optimized protocol to rapidly and efficiently purify high quality total RNA from peach fruits (Prunus persica). Isolating high-quality RNA from fruit tissue is often difficult due to large quantities of polysaccharides and polyphenolic compounds that accumulate in this tissue and co-purify with the RNA. Here we demonstrate that a modified version of the method used to isolate RNA from pine trees and the woody plant Cinnamomun tenuipilum is ideal for isolating high quality RNA from the fruits of Prunus persica. This RNA may be used for many functional genomic based experiments such as RT-PCR and the construction of large-insert cDNA libraries.

We performed a genealogical analysis of the ionotropic glutamate receptor (iGluR) gene family, which includes the animal iGluRs and the newly isolated glutamate receptor-like genes (GLR) of plants discovered in Arabidopsis. Distance measures firmly placed the plant GLR genes within the iGluR clade as opposed to other ion channel clades and indicated that iGluRs may be a primitive signaling mechanism that predated the divergence of animals and plants. Moreover, phylogenetic analyses using both parsimony and neighbor joining indicated that the divergence of animal iGluRs and plant GLR genes predated the divergence of iGluR subtypes (NMDA vs. AMPA/KA) in animals. By estimating the congruence of the various glutamate receptor gene regions, we showed that the different functional domains, including the two ligand-binding domains and the transmembrane regions, have coevolved, suggesting that they assembled together before plants and animals diverged. Based on residue conservation and divergence as well as positions of residues with respect to functional domains of iGluR proteins, we attempted to examine structure-function relationships. This analysis defined M3 as the most highly conserved transmembrane domain and identified potential functionally important conserved residues whose function can be examined in future studies.

An important question in developmental biology concerns the mechanisms by which a few cells coordinate division and differentiation to yield the complex structures and organs found in multicellular organisms. During vegetative growth in plants, cells in the apical meristem must coordinate division and differentiation to yield the fully mature leaf organ. Alterations in these processes may result in an abnormal leaf. In this paper we present the isolation and characterization of an EMS-generated, cold-temperature-sensitive mutation in Arabidopsis thaliana, designated lem7 (leaf morphogenesis). lem7 is a semidominant mutation that maps to a novel locus on chromosome 2. When grown at 16 degrees C, lem7 reversibly arrests leaf development at the shoot apex. In contrast, lem7 grown at 30 degrees C appears phenotypically normal. Our data also suggest that the Lem7 locus may not be involved solely in leaf organogenesis, but may also play a role in floral development and the maintenance of patterns and structures after cellular differentiation. At an intermediate temperature of 23 degrees C, leaves on the lem7 plant emerged phenotypically normal but began to show drastic changes at about 13 days postgermination. These changes include a reduced bilateral symmetry, a rough leaf lamina, a reduced number of trichomes, and an altered vascular network. Leaves that developed at the permissive temperature (30 degrees C) and shifted to the nonpermissive temperature (16 degrees C) form tumor-like outgrowths. Histological analysis of these tumor-like outgrowths and leaves grown at the intermediate temperature reveal abnormally large mesophyll cells, a disorganized mesophyll layer, and collapsed epidermal cells. We propose that the reversible inhibition of leaf development in lem7 under nonpermissive temperatures may serve as a useful tool for identifying genes involved in Arabidopsis leaf organogenesis.

http://www.scielo.cl/scielo.php?script=sci_arttext&pid=S0716-97602010000100012&lng=es&nrm=iso The basic body plan of a plant is established early in embryogenesis when cells differentiate, giving rise to the apical and basal regions of the embryo. Using chlorophyll fluorescence as a marker for chloroplasts, we have detected specific patterns of chloroplast-containing cells at specific stages of embryogenesis. Non-randomly distributed chloroplast-containing cells are seen as early as the globular stage of embryogenesis in Arabidopsis. In the heart stage of embryogenesis, chloroplast containing cells are detected in epidermal cells as well as a central region of the heart stage embryo, forming a triangular septum of chloroplast-containing cells that divides the embryo into three equal sectors. Torpedo stage embryos have chloroplast-containing epidermal cells and a central band of chloroplast-containing cells in the cortex layer, just below the shoot apical meristem. In the walking-stick stage of embryogenesis, chloroplasts are present in the epidermal, cortex and endodermal cells. The chloroplasts appear reduced or absent from the provascular and columella cells of walking-stick stage embryos. These results suggest that there is a tight regulation of plastid differentiation during embryogenesis that generates specific patterns of chloroplast-containing cells in specific cell layers at specific stages of embryogenesis.