Genetic Structure of a Worldwide Germplasm Collection of Prunus armeniaca L. Reveals Three Major Diffusion Routes for Varieties Coming From the Species' Center of Origin.

The characterization of the largest worldwide representative data set of apricot (Prunus armeniaca L.) germplasm was performed using molecular markers. Genetic diversity and structure of the cultivated apricot genetic resources were analyzed to decipher the history of diffusion of this species around the world. A common set of 25 microsatellite markers was used for genotyping a total of 890 apricot accessions in different collections from the center of origin to the more recent regions of apricot culture. Using a Bayesian model-based clustering approach, the apricot genotypes can be structured into five different genetic clusters (FST = 0.174), correlated with the geographical regions of origin of the accessions. Accessions from China and Central Asia were clustered together and exhibited the highest levels of diversity, confirming an origin in this region. A loss of genetic diversity was observed from the center of origin to both western and eastern zones of recent apricot culture. Altogether, our results revealed that apricot spread from China and Central Asia, defined as the center of origin, following three major diffusion routes with a decreasing gradient of genetic variation in each geographical group. The identification of specific alleles outside the center of origin confirmed the existence of different secondary apricot diversification centers. The present work provides more understanding of the worldwide history of apricot species diffusion as well as the field of conservation of the available genetic resources. Data have been used to define an apricot core collection based on molecular marker diversity which will be useful for further identification of genomic regions associated with commercially important horticultural traits through genome-wide association studies to sustain apricot breeding programs.

A collection of European sweet cherry phenology data for assessing climate change.

Professional and scientific networks built around the production of sweet cherry (Prunus avium L.) led to the collection of phenology data for a wide range of cultivars grown in experimental sites characterized by highly contrasted climatic conditions. We present a dataset of flowering and maturity dates, recorded each year for one tree when available, or the average of several trees for each cultivar, over a period of 37 years (1978-2015). Such a dataset is extremely valuable for characterizing the phenological response to climate change, and the plasticity of the different cultivars' behaviour under different environmental conditions. In addition, this dataset will support the development of predictive models for sweet cherry phenology exploitable at the continental scale, and will help anticipate breeding strategies in order to maintain and improve sweet cherry production in Europe.

Differential production of phytotoxins from Phomopsis sp. from grapevine plants showing esca symptoms.

Nine strains of the fungus Phomopsis spp. were isolated from a vineyard showing decline from the disease esca. Strains were screened for their ability to produce secondary metabolites showing chemical diversity. The culture extracts of each strain were analyzed by liquid chromatography-ultraviolet-diode array detection-mass spectrometry. Three strains were selected for the isolation and characterization of eight of the major metabolites. Structures were elucidated by spectroscopic analyses including two-dimensional NMR and mass spectrometry and by comparison to literature data. Among the isolated metabolites were the known phomopsolide B (1), sydowinin A (6), sydowinol (7), cytosporone B (8), and four new furanones named phomopsolidones A-D (2-5). The fungal strains were identified as Phomopsis sp., Phomopsis viticola Sacc and, Phomopsis viticola complex. Biological assays on Vitis vinifera leaves and callus tissue, antibacterial, and insecticidal activities were evaluated. The results revealed variability regarding secondary metabolites with species of Phomopsis sp. associated with grapevine, raising the question of cultivar-driven strain selection and phytotoxins biosynthesis in grapevine plants.

Comparative RNA-seq analysis of early-infected peach leaves by the invasive phytopathogen Xanthomonas arboricola pv. pruni.

Xanthomonas arboricola pv. pruni is a quarantine bacterial pathogen that threatens peach production by causing necrotic spots on leaves and fruits, thus with the potential of severely reducing yields. The current understanding of the host plant defense responses to the pathogen is very limited. Using whole transcriptome sequencing, differential gene expression was analyzed at two time points, 2 h and 12 h post inoculation (hpi), by comparing the inoculated samples to their respective controls. On the total of 19,781 known peach genes that were expressed in all time points and conditions, 34 and 263 were differentially expressed at 2 and 12 hpi, respectively. Of those, 82% and 40% were up-regulated, respectively; and 18% and 60% were down-regulated, respectively. The functional annotation based on gene ontology (GO) analysis highlighted that genes involved in metabolic process and response to stress were particularly represented at 2 hpi whereas at 12 hpi cellular and metabolic processes were the categories with the highest number of genes differentially expressed. Of particular interest among the differentially expressed genes identified were several pathogen-associated molecular pattern (PAMP) receptors, disease resistance genes including several RPM1-like and pathogenesis related thaumatin encoding genes. Other genes involved in photosynthesis, in cell wall reorganization, in hormone signaling pathways or encoding cytochrome were also differentially expressed. In addition, novel transcripts were identified, providing another basis for further characterization of plant defense-related genes. Overall, this study gives a first insight of the peach defense mechanisms during the very early stages of infection with a bacterial disease in the case of a compatible interaction.

A comprehensive overview of the spatial and temporal variability of apple bud dormancy release and blooming phenology in Western Europe.

In the current context of global warming, an analysis is required of spatially-extensive and long-term blooming data in fruit trees to make up for insufficient information on regional-scale blooming changes and determinisms that are key to the phenological adaptation of these species. We therefore analysed blooming dates over long periods at climate-contrasted sites in Western Europe, focusing mainly on the Golden Delicious apple that is grown worldwide. On average, blooming advances were more pronounced in northern continental (10 days) than in western oceanic (6-7 days) regions, while the shortest advance was found on the Mediterranean coastline. Temporal trends toward blooming phase shortenings were also observed in continental regions. These regional differences in temporal variability across Western Europe resulted in a decrease in spatial variability, i.e. shorter time intervals between blooming dates in contrasted regions (8-10-day decrease for full bloom between Mediterranean and continental regions). Fitted sequential models were used to reproduce phenological changes. Marked trends toward shorter simulated durations of forcing period (bud growth from dormancy release to blooming) and high positive correlations between these durations and observed blooming dates support the notion that blooming advances and shortenings are mainly due to faster satisfaction of the heating requirement. However, trends toward later dormancy releases were also noted in oceanic and Mediterranean regions. This could tend toward blooming delays and explain the shorter advances in these regions despite similar or greater warming. The regional differences in simulated chilling and forcing periods were consistent with the regional differences in temperature increases.

Effect of long-term vineyard monoculture on rhizosphere populations of pseudomonads carrying the antimicrobial biosynthetic genes phlD and/or hcnAB.

The impact of repeated culture of perennial plants (i.e. in long-term monoculture) on the ecology of plant-beneficial bacteria is unknown. Here, the influence of extremely long-term monocultures of grapevine (up to 1603 years) on rhizosphere populations of fluorescent pseudomonads carrying the biosynthetic genes phlD for 2,4-diacetylphloroglucinol and/or hcnAB for hydrogen cyanide was determined. Soils from long-term and adjacent short-term monoculture vineyards (or brushland) in four regions of Switzerland were baited with grapevine or tobacco plantlets, and rhizosphere pseudomonads were studied by most probable number (MPN)-PCR. Higher numbers and percentages of phlD(+) and of hcnAB(+) rhizosphere pseudomonads were detected on using soil from long-term vineyards. On focusing on phlD, restriction fragment length polymorphism profiling of the last phlD-positive MPN wells revealed seven phlD alleles (three exclusively on tobacco, thereof two new ones). Higher numbers of phlD alleles coincided with a lower prevalence of the allele displayed by the well-studied biocontrol strain Pseudomonas fluorescens F113. The prevalence of this allele was 35% for tobacco in long-term monoculture soils vs. >60% in the other three cases. We conclude that soils from long-term grapevine monocultures represent an untapped resource for isolating novel biocontrol Pseudomonas strains when tobacco is used as bait.

Transformation of Eutypa dieback and esca disease pathogen toxins by antagonistic fungal strains reveals a second detoxification pathway not present in Vitis vinifera.

Eutypine, 4-hydroxybenzaldehyde, and 3-phenyllactic acid are some of the phytotoxins produced by the pathogens causing Eutypa dieback and esca disease, two trunk diseases of grapevine (Vitis vinifera). Known biocontrol agents such as Fusarium lateritium and Trichoderma sp. were screened for their ability to consume these toxins. Transformation time courses were performed, and an high-performance liquid chromatography-based method was developed to analyze toxin metabolism and to identify and quantify the converted products. The results show that the aldehyde function of eutypine was reduced to eutypinol, as by V. vinifera cv. Merlot, the cultivar tolerant to Eutypa dieback. We revealed a supplementary detoxification pathway, not known in Merlot, where the aldehyde function was oxidized to eutypinic acid. Moreover, some strains tested could further metabolize the transformation products. Every strain tested could transform 4-hydroxybenzaldehyde to the corresponding alcohol and acid, and these intermediates disappeared totally at the end of the time courses. When biological assays on cells of V. vinifera cv. Chasselas were carried out, the transformation products exhibited a lower toxicity than the toxins. The possibility of selecting new biocontrol agents against trunk diseases of grapevine based on microbial detoxification is discussed.