Verde I.,Fruit Tree Research Center |
Bassil N.,National Clonal Germplasm Repository |
Scalabrin S.,Instituto Of Genomica Applicata |
Gilmore B.,National Clonal Germplasm Repository |
And 18 more authors.
PLoS ONE | Year: 2012
Although a large number of single nucleotide polymorphism (SNP) markers covering the entire genome are needed to enable molecular breeding efforts such as genome wide association studies, fine mapping, genomic selection and marker-assisted selection in peach [Prunus persica (L.) Batsch] and related Prunus species, only a limited number of genetic markers, including simple sequence repeats (SSRs), have been available to date. To address this need, an international consortium (The International Peach SNP Consortium; IPSC) has pursued a coordinated effort to perform genome-scale SNP discovery in peach using next generation sequencing platforms to develop and characterize a high-throughput Illumina Infinium® SNP genotyping array platform. We performed whole genome re-sequencing of 56 peach breeding accessions using the Illumina and Roche/454 sequencing technologies. Polymorphism detection algorithms identified a total of 1,022,354 SNPs. Validation with the Illumina GoldenGate® assay was performed on a subset of the predicted SNPs, verifying ~75% of genic (exonic and intronic) SNPs, whereas only about a third of intergenic SNPs were verified. Conservative filtering was applied to arrive at a set of 8,144 SNPs that were included on the IPSC peach SNP array v1, distributed over all eight peach chromosomes with an average spacing of 26.7 kb between SNPs. Use of this platform to screen a total of 709 accessions of peach in two separate evaluation panels identified a total of 6,869 (84.3%) polymorphic SNPs. The almost 7,000 SNPs verified as polymorphic through extensive empirical evaluation represent an excellent source of markers for future studies in genetic relatedness, genetic mapping, and dissecting the genetic architecture of complex agricultural traits. The IPSC peach SNP array v1 is commercially available and we expect that it will be used worldwide for genetic studies in peach and related stone fruit and nut species.
Kusaba S.,Japan National Agriculture and Food Research Organization |
Matsuoka K.,Japan National Agriculture and Food Research Organization |
Abe K.,Fruit Tree Research Center |
Ajito H.,Fruit Tree Research Center |
And 4 more authors.
Soil Science and Plant Nutrition | Year: 2015
Abstract: We investigated changes in the radiocesium concentration in a blueberry (Vaccinium virgatum Aiton) orchard in Fukushima prefecture to clarify the radiocesium contamination for 3 years after the Tokyo Electric Power Company’s Fukushima Daiichi nuclear power plant accident occurred in mid-March 2011. In the aboveground part of blueberry bushes, the concentrations of radiocesium in branches that were directly affected by radioactive fallout were the highest among the samples investigated, and the concentrations in fruits were the lowest. The concentration of radiocesium decreased exponentially in the fruits and leaves over 3 years. The radiocesium concentrations in soils were higher in the surface layer. The amount of radiocesium in organic matter on the soil surface under the canopy greatly decreased from 2011 to 2012. The transfer factor of the radiocesium from soil to blueberry fruits decreased annually. These results suggest that radiocesium adhered directly to the aboveground organs of blueberry bushes in March 2011, and it is possible that the accumulation of radiocesium in fruits is mainly due to radiocesium transfer from the branches and trunk to fruits for several years after the nuclear power plant accident. © 2014, Japanese Society of Soil Science and Plant Nutrition.
Sciubba F.,University of Rome La Sapienza |
Di Cocco M.E.,University of Rome La Sapienza |
Gianferri R.,University of Rome La Sapienza |
Capuani G.,University of Rome La Sapienza |
And 4 more authors.
Journal of Agricultural and Food Chemistry | Year: 2015
Apple scab, caused by the fungus Venturia inaequalis, is the most serious disease of the apple worldwide. Two cultivars (Malus domestica), having different degrees of resistance against fungi attacks, were analyzed by 1H and 13C nuclear magnetic resonance (NMR) spectroscopy. Aqueous and organic extracts of both apple flesh and skin were studied, and over 30 metabolites, classified as organic acids, amino acids, carbohydrates, phenolic compounds, lipids, sterols, and other metabolites, were quantified by means of one-dimensional (1D) and two-dimensional (2D) NMR experiments. The metabolic profiles of the two apple cultivars were compared, and the differences were correlated with the different degrees of resistance to apple scab by means of univariate analysis. Levels of metabolites with known antifungal activity were observed not only to be higher in the Almagold cultivar but also to show different correlation patterns in comparison to Golden Delicious, implying a difference in the metabolic network involved in their biosynthesis. © 2015 American Chemical Society.
Sgamma T.,University of Warwick |
Sgamma T.,University of Tuscia |
Cirilli M.,University of Tuscia |
Caboni E.,Fruit Tree Research Center |
And 3 more authors.
Acta Horticulturae | Year: 2016
The juvenile to adult switch is the most important post-embryonic transition. In woody plants the juvenile phase can last many years with a great economic impact. In Arabidopsis, the small RNAs miR156 and miR172 play a crucial but opposite role in the regulation of this process. miR156 maintains juvenility, negatively regulating SPLs genes, while miR172 promotes adult transition, targeting the floral repressors AP2-like transcription factors. In this work, peach (Prunus persica L. Batch) orthologs of Arabidopsis epigenetic and genetic factors involved in the juvenility to adult phase transition were studied. In peach, higher levels of ppa-miR156 were detected in seedlings, in vitro and extra vitro plants than in adult plants. Also, PpSPLs were more expressed in adult plants, confirming a possible role for the miR156-SPL pathway in promoting juvenile-like characteristics. ppa-miR172 expression level was low in seedlings and in vitro plants but an increase was observed in the adult donor plant, corresponding to lower expression of PpAP2-like genes. In Arabidopsis, flower induction is also promoted by activation of the FLOWERING LOCUS T (FT) gene. In peach leaf tissue, low levels of PpFT-like expression in rejuvenated plants and seedlings were detected. We propose that, in peach, conserved key genes present in herbaceous plants and woody species are involved in juvenile to adult and adult to juvenile-like phase transitions.
PubMed | University of Rome La Sapienza, Fruit Tree Research Center and Edmund Machinery Foundation
Type: Comparative Study | Journal: Journal of agricultural and food chemistry | Year: 2015
Apple scab, caused by the fungus Venturia inaequalis, is the most serious disease of the apple worldwide. Two cultivars (Malus domestica), having different degrees of resistance against fungi attacks, were analyzed by (1)H and (13)C nuclear magnetic resonance (NMR) spectroscopy. Aqueous and organic extracts of both apple flesh and skin were studied, and over 30 metabolites, classified as organic acids, amino acids, carbohydrates, phenolic compounds, lipids, sterols, and other metabolites, were quantified by means of one-dimensional (1D) and two-dimensional (2D) NMR experiments. The metabolic profiles of the two apple cultivars were compared, and the differences were correlated with the different degrees of resistance to apple scab by means of univariate analysis. Levels of metabolites with known antifungal activity were observed not only to be higher in the Almagold cultivar but also to show different correlation patterns in comparison to Golden Delicious, implying a difference in the metabolic network involved in their biosynthesis.
PubMed | The Sainsbury Laboratory, University of Basel, Fruit Tree Research Center, Japan National Institute for Basic Biology and RWTH Aachen
Type: Journal Article | Journal: Proceedings of the National Academy of Sciences of the United States of America | Year: 2016
Sensing of potential pathogenic bacteria is of critical importance for immunity. In plants, this involves plasma membrane-resident pattern recognition receptors, one of which is the FLAGELLIN SENSING 2 (FLS2) receptor kinase. Ligand-activated FLS2 receptors are internalized into endosomes. However, the extent to which these spatiotemporal dynamics are generally present among pattern recognition receptors (PRRs) and their regulation remain elusive. Using live-cell imaging, we show that at least three other receptor kinases associated with plant immunity, PEP RECEPTOR 1/2 (PEPR1/2) and EF-TU RECEPTOR (EFR), internalize in a ligand-specific manner. In all cases, endocytosis requires the coreceptor BRI1-ASSOCIATED KINASE 1 (BAK1), and thus depends on receptor activation status. We also show the internalization of liganded FLS2, suggesting the transport of signaling competent receptors. Trafficking of activated PRRs requires clathrin and converges onto the same endosomal vesicles that are also shared with the hormone receptor BRASSINOSTERIOD INSENSITIVE 1 (BRI1). Importantly, clathrin-dependent endocytosis participates in plant defense against bacterial infection involving FLS2-mediated stomatal closure and callose deposition, but is uncoupled from activation of the flagellin-induced oxidative burst and MAP kinase signaling. In conclusion, immunity mediated by pattern recognition receptors depends on clathrin, a critical component for the endocytosis of signaling competent receptors into a common endosomal pathway.
Hoshi H.,Fruit Tree Research Center |
Takabe M.,Horticultural Experiment Station of Yamagata Integrated Agricultural Research Center |
Nakamuta K.,Chiba University
Journal of Chemical Ecology | Year: 2016
Mating disruption of the carpenter moth, Cossus insularis (Staudinger) (Lepidoptera: Cossidae), with a synthetic version of its sex pheromone, a mixture of (E)-3-tetradecenyl acetate and (Z)-3-tetradecenyl acetate, was tested for three successive years in apple (Malus domestica Borkh.) orchards. Pheromone trap catches, percentage mating of tethered females and females enclosed with males in a mating cage, and tree damage were measured in both the pheromone-treated and untreated control orchards. The attraction of male moths to pheromone traps at heights of 1.5, 3, and 5 m was strongly disrupted when the pheromone dispensers were placed at 1.5 m height. Mating of tethered females placed at 1 m was completely inhibited, and the mating of tethered females at a height of 3 m was significantly reduced by the treatment in comparison to matings in an untreated control orchard. Similarly, mating of pairs of moths enclosed in mating cages was significantly reduced by the synthetic pheromone treatment in comparison to controls. The percentage of damaged trees in the pheromone-treated orchard also decreased significantly over the course of the experiment. These results suggest that mating disruption with the synthetic sex pheromone appears promising for reducing damage caused by C. insularis in apple orchards in Japan, and a commercial mating disruption product has been developed and registered. © 2016 Springer Science+Business Media New York
Sato M.,Fruit Tree Research Center |
Takata D.,University of Tokyo |
Tanoi K.,University of Tokyo |
Ohtsuki T.,Tohoku University |
Muramatsu Y.,Gakushuin University
Soil Science and Plant Nutrition | Year: 2015
Abstract: Following the accident at the Tokyo Electric Power Company, Fukushima Daiichi Nuclear Power Plant (FDNPP), radiocesium (134Cs + 137Cs) concentrations in deciduous mature fruits were determined in orchards in the northern area of Fukushima Prefecture. At the time of the nuclear accident, most deciduous fruit trees were in the dormant stage prior to bud burst. To evaluate the relationship between radiocesium deposition in the soil and fruit contamination, radiocesium concentrations were measured from the 5-cm topsoil and from six fruit species across 17 orchards in 2011. The vertical distribution of radiocesium in the topsoil (0–30 cm in depth) and its spatial distribution in the 5-cm topsoil underlying the tree canopy of a peach, Prunus persica (L.) Batsh, orchard (“Akatsuki” cultivar) were also investigated. Significant correlations between the radiocesium concentration in the mature fruit and that in the 5-cm topsoil layer were observed for the 17 orchards as well as for the trees of the peach orchard. However, 93% of the 137Cs found in the 30-cm soil core was retained within the top 3 cm of the soil in the peach orchard. Considering the profile of the root of this deciduous fruit tree, we assumed a negligible level of radiocesium uptake via the roots. However, the possibility of inward migration via the bark was undeniable, because some radiocesium adhered to the tree canopy before bud burst while depositing on the soil surface. Additionally, transfer factors for peach and grape, hybrid of Vitis labrusca L. and Vitis vinifera L., from young, uncontaminated trees cultivated with contaminated soil were lower than those previously reported. © 2014, Japanese Society of Soil Science and Plant Nutrition.
Yoshihara T.,Japan Central Research Institute of Electric Power Industry |
Hashida S.-N.,Japan Central Research Institute of Electric Power Industry |
Abe K.,Fruit Tree Research Center |
Ajito H.,Fruit Tree Research Center
Journal of Environmental Radioactivity | Year: 2014
Radiocesium (134Cs+137Cs) concentrations, primarily derived from the Fukushima accident in March 2011, were measured in litterfalls and green leaves of Japanese flowering cherry trees (Prunus x yedoensis cv. Somei-Yoshino). The sampling was performed mainly during the defoliation season in 2011 and 2012 using traps to collect litterfalls before contact with the ground. The average radiocesium concentration in litterfalls in 2012 fell to one-third of that in 2011 (0.43 and 1.2kBqkg-DW-1, respectively). Interestingly, the concentrations in litterfalls collected in late autumn in both 2011 and 2012 (0.68 and 0.19kBqkg-DW-1, respectively) were significantly lower than those in litterfalls collected in the early autumn (1.7 and 1.1kBqkg-DW-1, respectively). In addition, the reductions in radiocesium concentrations in the litterfall were nearly synchronous with those in potassium concentrations (p≤0.05). On the contrary, radiocesium concentrations in green leaves were also correlated with potassium concentrations; however, the slopes of the regression lines between the radiocesium and potassium concentrations were very similar in the 2011 litterfalls and the 2012 litterfalls, while the slopes were significantly different between these litterfalls and the green leaves. Consequently, the correlation between potassium and radiocesium was clear but independently observable in each of the litterfalls and the green leaves. It is possible that the reduction in radiocesium concentration occurred as a part of physiological demand, a translocation of potassium from the leaves to the body/twigs. © 2013 The Authors.
Ceccarelli D.,Fruit Tree Research Center |
Simeone A.M.,Fruit Tree Research Center |
Nota P.,Fruit Tree Research Center |
Piazza M.G.,Fruit Tree Research Center |
And 2 more authors.
Plant Biosystems | Year: 2016
Interest in phenolic compounds of fruit is growing due to their positive effects on reducing the risk of cardiovascular and carcinogen diseases. The role of the flesh colour, of the tissue (exocarp or mesocarp) and of the cultivar on the content of phenolic compounds (hydroxycinnamic acids, flavan-3-ols, flavonols) was evaluated in peach, Prunus persica (L.) Batsch, with a HPLC-DAD analysis, on 10 varieties deriving from the Italian breeding programmes, never previously characterized by this approach. The flavan-3-ols (catechin, epicatechin and procyanidin B1) were the most abundant class of phenolic compounds in peach cultivars analysed. Among hydroxycinnamic acids, neochlorogenic and chlorogenic acids were also identified and measured in the peach cultivars analysed. Quercetin-3-O-rutinoside was the only flavonol found in the exocarp of all the cultivars evaluated, but in the mesocarp of only some cultivars. Content of phenolic compounds was confirmed to be strongly dependent on the cultivar and, in general, the content was significantly higher in exocarp than in mesocarp. An overall significant difference in phenolic compounds as associated with flesh colour was not observed. © 2016 Società Botanica Italiana