Brown Rot Strikes Prunus Fruit: An Ancient Fight Almost Always Lost

Prunin: An Emerging Anticancer Flavonoid

Despite the substantial advances in cancer therapies, developing safe and effective treatment methodologies is critical. Natural (plant-derived compounds), such as flavonoids, might be crucial in developing a safe treatment methodology without toxicity toward healthy tissues. Prunin is a flavonoid with the potential to be used in biomedical applications. Prunin has yet to undergo thorough scientific research, and its precise molecular mechanisms of action remain largely unexplored. This review summarizes the therapeutic potential of prunin for the first time, focusing on its underlying mechanisms as an anticancer compound. Prunin has gained significant attention due to its antioxidant, anti-inflammatory, and anticancer effects. This review aims to unlock how prunin functions at the molecular level to exert its anticancer effects, primarily modulating key cellular pathways. Furthermore, we have discussed the prunin's potential as an adjunctive therapy with conventional treatments, highlighting its ability to strengthen treatment responses while decreasing drug resistance. Moreover, the discussion probes into innovative delivery methods, particularly nanoformulations, that might address prunin's bioavailability, solubility, and stability limitations and optimize its therapeutic application. By providing a comprehensive analysis of prunin's properties, this review aims to stimulate further exploration of using prunin as an anticancer agent, thereby progressing the development of targeted, selective, safe, and effective therapeutic methods.

Control of Peach Brown Rot Disease Produced by Monilinia fructicola and Monilinia laxa Using Benzylidene-Cycloalkanones

Fruit rots caused by filamentous fungi such as Monilinia fructicola and Monilinia laxa have a strong impact on crop yield and fruit commercialization, especially as they affect a wide variety of stone fruits. The antifungal efficacy of benzylidene-cycloalkanones has been previously described in in vitro assays against M. fructicola; so, this study aims to evaluate the in vivo inhibitory potential of these hybrids on fruits that have been inoculated with M. fructicola, and use molecular docking to visualize the main interactions of these molecules in the active site of the enzyme succinate dehydrogenase (SDH). The results indicate that compound C achieves the highest inhibition of both Monilinia species (15.7-31.4 µg/mL), spore germination in vitro (<10 µg/mL), and has promising results in vivo, without causing phytotoxicity in fruits. The results from molecular docking suggest that hydroxyl groups play a crucial role in enhancing the binding of compound C to SDH and contribute to the formation of hydrogen bonds with amino acid residues on the enzyme active site.

Identification of bioactive compounds of Bacillus velezensis HNA3 that contribute to its dual effects as plant growth promoter and biocontrol against post-harvested fungi

IMPORTANCE

The current study is an extension to our previous work on the plant growth-promoting rhizobacteria (PGPR) Bacillus velezensis HNA3 strain, which comes to confirm and reveals the huge stock of active secondary metabolites produced by HNA3. HNA3-emitted volatile organic compounds (VOCs) have demonstrated the capacity to impede the growth of phytopathogens affecting some fruits and vegetables, even in the absence of direct contact. Additionally, these volatiles enhanced soybean seed germination by breaking seed dormancy and inducing root system development. Furthermore, they promoted seedling growth, giving it prominence in soybean cultivation. The relevance of active volatiles derives from the fact that they can be developed as natural-safe biocontrol agents and plant promoters. This research validates the remarkable bioactivities exhibited by the Bacillus velezensis HNA3 and their potential applications in agriculture as an inoculant, encompassing biocontrol, plant growth promotion, and seed germination activities, thereby offering a safer alternative to hazardous chemicals.

Genome-wide association analysis of Monilinia fructicola lesion in a collection of Spanish peach landraces

Brown rot, caused by the Monilinia spp., is the disease that causes the greatest losses in stone fruit worldwide. Currently, M. fructicola has become the dominant species in the main peach production area in Spain. The fruit cuticle is the first barrier of protection against external aggressions and may have a key role in the susceptibility to brown rot. However, information on the role of skin fruit on the resistance to brown rot in peach is scarce. Previous genetic analyses in peach have demonstrated that brown rot resistance is a complex and quantitative trait in which different fruit parts and resistance mechanisms are involved. To search for genomic areas involved in the control of the cultivar susceptibility to brown rot and to elucidate the role of fruit skin against this infection, we have studied, for two consecutive seasons (2019 and 2020), the fruit susceptibility to M. fructicola, together with fruit cuticle thickness (CT) and density (CD), in a collection of 80 Spanish and 5 foreign peach cultivars from the National Peach Collection at CITA (Zaragoza, Spain). Brown rot incidence, lesion diameter, and severity index were calculated after 5 days of inoculation on non-wounded fruit. The peach collection has also been genotyped using the new peach SNP chip (9 + 9K). Genotypic and phenotypic data have been used to perform a genome-wide association analysis (GWAS). Phenotyping has shown a wide variability on the brown rot susceptibility within the Spanish germplasm as well as on CD and CT. The GWAS results have identified several significant SNPs associated with disease severity index (DSI), CD, and CT, five of which were considered as reliable SNP-trait associations. A wide protein network analysis, using 127 genes within the regions of the reliable SNPs and previously identified candidate genes (169) associated with Monilinia spp. resistance, highlighted several genes involved in classical hypersensitive response (HR), genes related to wax layers as ceramidases and lignin precursors catalyzers, and a possible role of autophagy during brown rot infection. This work adds relevant information on the complexity resistance mechanisms to brown rot infection in peach fruits and the genetics behind them.

Evaluating Food Additives Based on Organic and Inorganic Salts as Antifungal Agents against Monilinia fructigena and Maintaining Postharvest Quality of Apple Fruit

A set of commonly used food additives was evaluated for their antifungal activity against the brown rot disease of fruits caused by the fungal pathogen Monilinia fructigena, which is one of the most economically important agents, causing important damage to pome fruits, such as pears and apples. The radial mycelial growth of the fungal pathogen was assessed in PDA amended with different concentrations (0.5, 2, 2.5, and 5%) of each additive. The results underlined that most of the additives displayed a significant inhibition of mycelial growth, with the extent of inhibition varying depending on the specific additive and concentration used. Five food additives showed high inhibition rates (above 88%), of which sodium bicarbonate, sodium carbonate, copper sulphate, and sodium hydroxide were the most effective, whereas ammonium carbonate, magnesium chlorite, and citric acid were the least effective. Interestingly, the coatings containing sodium bicarbonate, copper sulphate, and ammonium bicarbonate significantly reduced the incidence of brown rot disease in apples, but other additives were not effective, such as ammonium carbonate and magnesium sulphate. The anhydrous sodium sulphate used at a concentration of 2%, was found to be one of the least effective additives, with a reduction rate of 20%. Subsequently, food additives showing good growth inhibition rates and reduction in disease severity were then tested in semi-commercial trials at temperatures of 4 °C and 22 °C. The results indicated that these additives demonstrate effectiveness in controlling M. fructigena at specific concentrations, and lower temperatures (4 °C) can improve the efficiency of the control measures. In addition, the selected food additives exhibited significant antimicrobial activity against M. fructigena, suggesting their application as a promising alternative for managing brown rot disease in apple fruits.

Stone fruit phenolic and triterpenoid compounds modulate gene expression of Monilinia spp. in culture media

Phenolic and triterpenoid compounds are essential components in stone fruit skin and flesh tissues. They are thought to possess general antimicrobial activity. However, regarding brown rot disease, investigations were only confined to a limited number of phenolics, especially chlorogenic acid. The activity of triterpenoids against Monilinia spp., as an essential part of the peach cuticular wax, has not been studied before. In this work, the anti-fungal effect of some phenolics, triterpenoids, and fruit surface compound (FSC) extracts of peach fruit at two developmental stages were investigated on Monilinia fructicola and Monilinia laxa characteristics during in vitro growth. A new procedure for assaying anti-fungal activity of triterpenoids, which are notoriously difficult to assess in vitro because of their hydrophobicity, has been developed. Measurements of colony diameter, sporulation, and germination of second-generation conidia were recorded. Furthermore, the expression of twelve genes of M. fructicola associated with germination and/or appressorium formation and virulence-related genes was studied relative to the presence of the compounds. The study revealed that certain phenolics and triterpenoids showed modest anti-fungal activity while dramatically modulating gene expression in mycelium of M. fructicola on culture medium. MfRGAE1 gene was overexpressed by chlorogenic and ferulic acids and MfCUT1 by betulinic acid, at 4- and 7- days of mycelium incubation. The stage II FSC extract, corresponding to the period when the fruit is resistant to Monilinia spp., considerably up-regulated the MfLAE1 gene. These findings effectively contribute to the knowledge of biochemical compounds effects on fungi on in vitro conditions.

Effect of peach trichome removal on post-harvest brown rot and on the fruit surface microbiome

Postharvest peaches undergo rapid soft ripening and are susceptible to fungal diseases, which often result in severe losses during storage. The peach epidermis contains trichomes that form a specific structure on the peach surface. However, the relationship between trichomes and postharvest disease and involved mechanisms has not been well studied. In this study, the removal of trichomes reduced the disease incidence of peach brown rot caused by Monilinia fructicola. Cryo-scanning electron microscope observations showed that the fungal hyphae were found attached to the surface of trichomes. The fungal and bacterial communities on the peach surface at 0 d and 6 d were obtained by amplicon sequencing technology. Fungal communities on the peach surface contained a total of 1089 amplicon sequence variants (ASVs), which were demarcated into eight fungal phyla, 25 classes, 66 orders, 137 families, and 228 genera. The bacterial communities contained 10,821 ASVs assigned to 25 phyla, 50 classes, 114 orders, 220 families, and 507 genera. Higher bacterial diversity than fungal diversity was recorded on the peach epidermis. Trichome removal changed the microbial diversity and community on the peach surface. Compared with peach epidermis samples, the peach epidermis excluded trichomes samples contained similar fungal alpha diversity but significantly lower bacterial diversity. Seventeen different fungal genera and twenty-eight different bacterial genera were identified between peach trichome and peach epidermis excluded trichomes samples. The fungal and bacterial diversity on the peach epidermis showed a decreasing trend during storage. Beta diversity analysis revealed that the microbial communities of the peach epidermis and trichomes show different change trends between 0 d and 6 d. Trichome removal decreased relative abundance of Monilinia spp. and increased relative abundance of potential yeast and bacterial biocontrol agents. This study suggested that trichomes might modulate the microbial communities on fruit surfaces, and trichome removal technology after harvest might be developed to control peach postharvest decay.

Prediction of the Potential Distributions of Prunus salicina Lindl., Monilinia fructicola, and Their Overlap in China Using MaxEnt

Prunus salicina Lindl. (P. salicina) is an essential cash crop in China, and brown rot (BR) is one of its most important diseases. In this study, we collected geographic location information on P. salicina and Monilinia fructicola (G. Winter) Honey (M. fructicola), one of the BR pathogenic species, and applied the MaxEnt model to simulate its potential suitable distribution in China. There have been discussions about the dominant environmental variables restricting its geographical distribution and their overlap. The results showed that the mean temperature of the coldest quarter, precipitation of the warmest quarter, precipitation in July, and minimum temperatures in January and November were the main climatic variables affecting the potential distribution of P. salicina, while the coldest quarter, precipitation of the driest month, precipitation of March, precipitation of October, maximum temperatures of February, October, and November, and minimum temperature of January were related to the location of M. fructicola. Southern China had suitable conditions for both P. salicina and M. fructicola. Notably, the overlap area of P. salicina and M. fructicola was primarily located southeast of 91°48' E 27°38' N to 126°47' E 41°45' N. The potential overlap area predicted by our research provided theoretical evidence for the prevention of BR during plum planting.

Brown Rot Disease in Stored Nectarines: Modeling the Combined Effects of Preharvest and Storage Conditions

Brown rot in stored stone fruits, caused by Monilinia spp., may be due to preharvest and storage factors, but the combined effect of these factors has yet to be investigated. We set up two experiments to monitor the progression of brown rot during the storage of nectarines subjected to various preharvest and storage conditions. We assessed the effects of different agricultural practices (irrigation regimen × fruit load) and harvest dates on brown rot progress during storage in 2018 and the effect of different storage temperatures in 2019. We found that the cumulative incidence of brown rot during storage increased with individual fruit mass, which was influenced by agricultural practices, and for later harvest dates. It also increased with storage temperature. We observed that during storage no secondary infections developed in nectarines not in direct contact with fruits infected with Monilinia laxa. These findings led to the identification of candidate variables describing the brown rot risk on nectarines during storage, such as individual fruit mass, meteorological conditions before fruit harvest, prevalence of brown rot at harvest, and storage temperature. We used these variables to build a mathematical model for estimating the time-to-appearance of brown rot symptoms in stored nectarines. This model fitted the experimental data well, highlighting the need to pay greater attention to the interaction between preharvest and storage conditions. This model could be used to evaluate management strategies for reducing the impact of brown rot in nectarines during storage.

Field application of Bacillus subtilis and Aureobasidium pullulans to reduce Monilinia laxa post-harvest rot on cherry

Brown rot caused by Monilinia spp. is one of the most important diseases in stone fruits worldwide. Latent infections of fruit by the pathogen often manifest once the fruit is ripe, leading to post-harvest rots. Two microbial strains (Bacillus subtilis -B91 and Aureobasidium pullulans - Y126) have shown antagonistic properties against M. laxa in previous studies. This study assessed the reduction in post-harvest rot of cherry by M. laxa when the two biocontrol (BCAs) strains were applied pre-harvest under field conditions to fruit artificially inoculated with M. laxa. The experiment was carried out for two consecutive years in cherry orchards in Kent. When applied pre-harvest, both strains (B91 and Y126) reduced the incidence of post-harvest rots by 30% - 60%. This promising result helps towards the commercialisation of the two strains, which would reduce reliance on fungicides in commercial cherry production.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s10658-022-02508-8.

Detection of Monilia Contamination in Plum and Plum Juice with NIR Spectroscopy and Electronic Tongue

Plums are one of the commercially important stone fruits that are available on the market in both fresh and processed form and the most sought-after products are prunes, cans, jams, and juices. Maturity, harvest, and post-harvest technologies fundamentally determine the relatively short shelf life of plums which is often threatened by Monilinia spp. Causing brown rot worldwide. The aim of the present research was to use advanced analytical techniques, such as hand-held near infrared spectroscopy (NIRS) and electronic tongue (e-tongue) to detect M. fructigena fungal infection on plums and quantify this fungal contamination in raw plum juices. For this purpose, plums were inoculated with fungal mycelia in different ways (control, intact, and through injury) and stored under different conditions (5 °C, and 24 °C) for eight days. The results obtained with the two instruments were analyzed with chemometric methods, such as linear discriminant analysis (LDA) and partial least squares regression (PLSR). The NIRS-based method proved successful when detectability before the appearance of visible signs of the infection was studied. E-tongue was able to detect and quantify the concentration of juice derived from plum developed with M. fructigena with RMSECV lower than 5% w/w. Overall, the two methods proved to be suitable for discriminating between the treatment groups, however, the classification accuracy was higher for samples stored at 24 °C. The research results show both NIRS and e-tongue are beneficial methods to reduce food waste by providing rapid determination of fruit quality.

Light Intensity Alters the Behavior of Monilinia spp. in vitro and the Disease Development on Stone Fruit-Pathogen Interaction

The development of brown rot caused by the necrotrophic fungi Monilinia spp. in stone fruit under field and postharvest conditions depends, among others, on environmental factors. The effect of temperature and humidity are well studied but there is little information on the role of light in disease development. Herein, we studied the effect of two lighting treatments and a control condition (darkness) on: (i) several growth parameters of two Monilinia spp. (M. laxa and M. fructicola) grown in vitro and (ii) the light effect in their capacity to rot the fruit (nectarines) when exposed to the different lighting treatments. We also assessed the effect of such abiotic factors in the development of the disease on inoculated nectarines during postharvest storage. Evaluations also included testing the effect of fruit bagging on disease development as well as on ethylene production. Under in vitro conditions, lighting treatments altered colony morphology and conidiation of M. laxa but this effect was less acute in M. fructicola. Such light-induced changes under in vitro development also altered the capacity of M. laxa and M. fructicola to infect nectarines, with M. laxa becoming less virulent. The performance of Monilinia spp. exposed to treatments was also determined in vivo by inoculating four bagged or unbagged nectarine cultivars, indicating an impaired disease progression. Incidence and lesion diameter of fruit exposed to the different lighting treatments during postharvest showed that the effect of the light was intrinsic to the nectarine cultivar but also Monilinia spp. dependent. While lighting treatments reduced M. laxa incidence, they enhanced M. fructicola development. Preharvest conditions such as fruit bagging also impaired the ethylene production of inoculated fruit, which was mainly altered by M. laxa and M. fructicola, while the bag and light effects were meaningless. Thus, we provide several indications of how lighting treatments significantly alter Monilinia spp. behavior both in vitro and during the interaction with stone fruit. This study highlights the importance of modulating the lighting environment as a potential strategy to minimize brown rot development on stone fruit and to extent the shelf-life period of fruit in postharvest, market, and consumer's house.

In Vitro Antifungal Activity and Toxicity of Dihydrocarvone-Hybrid Derivatives against Monilinia fructicola

The aim of this study was to synthesize a series of novel and known dihydrocarvone-hybrid derivatives (2-9) and to evaluate mycelial growth activity of hybrid molecules against two strains of Monilinia fructicola, as well as their toxicity. Dihydrocarvone-hybrid derivatives have been synthesized under sonication conditions and characterized by FTIR, NMR, and HRMS. Antifungal efficacy against both strains of M. fructicola was determined by half maximal effective concentration (EC50) and toxicity using the brine shrimp lethality test (BSLT). Among the synthesized compounds, 7 and 8 showed the best activity against both strains of M. fructicola with EC50 values of 148.1 and 145.9 µg/mL for strain 1 and 18.1 and 15.7 µg/mL for strain 2, respectively, compared to BC 1000® (commercial organic fungicide) but lower than Mystic® 520 SC. However, these compounds showed low toxicity values, 910 and 890 µg/mL, respectively, compared to Mystic® 520 SC, which was highly toxic. Based on the results, these hybrid compounds could be considered for the development of more active, less toxic, and environmentally friendly antifungal agents against phytopathogenic fungi.

Genome-Wide Association Study of Brown Rot (Monilinia spp.) Tolerance in Peach

Brown rot, caused by Monilinia spp., is one of the most important diseases on stone fruit worldwide. Severe yield loss can be caused by pre- and post-harvest fruit decay. Although some degree of tolerance has been reported in peach and almond, the genetic resistance in peach cultivars is still lacking. To date, only few genomic regions associated with brown rot response in fruit skin and flesh have been detected in peach. Previous studies suggested brown rot tolerance in peach being a polygenic quantitative trait. More information is needed to uncover the genetics behind brown rot tolerance in peach. To identify the genomic regions in peach associated with this trait, 26 cultivars and progeny from 9 crosses with 'Bolinha' sources of tolerance, were phenotyped across two seasons (2015 and 2016) for brown rot disease severity index in wounded and non-wounded fruits and genotyped using a newly developed 9+9K peach SNP array. Genome wide association study using single- and multi-locus methods by GAPIT version 3, mrMLM 4.0, GAPIT and G Model, revealed 14 reliable SNPs significantly associated with brown rot infection responses in peach skin (10) and flesh (4) across whole genome except for chromosome 3. Candidate gene analysis within the haplotype regions of the detected markers identified 25 predicted genes associated with pathogen infection response/resistance. Results presented here facilitate further understanding of genetics behind brown rot tolerance in peach and provide an important foundation for DNA-assisted breeding.

Cuticular waxes of nectarines during fruit development in relation to surface conductance and susceptibility to Monilinia laxa

The cuticle is composed of cutin and cuticular waxes, and it is the first protective barrier to abiotic and biotic stresses in fruit. In this study, we analysed the composition of and changes in cuticular waxes during fruit development in nectarine (Prunus persica L. Batsch) cultivars, in parallel with their conductance and their susceptibility to Monilinia laxa. The nectarine waxes were composed of triterpenoids, mostly ursolic and oleanolic acids, phytosterols, and very-long-chain aliphatics. In addition, we detected phenolic compounds that were esterified with sugars or with triterpenoids, which are newly described in cuticular waxes. We quantified 42 compounds and found that they changed markedly during fruit development, with an intense accumulation of triterpenoids during initial fruit growth followed by their decrease at the end of endocarp lignification and a final increase in very-long-chain alkanes and hydroxylated triterpenoids until maturity. The surface conductance and susceptibility to Monilinia decreased sharply at the beginning of endocarp lignification, suggesting that triterpenoid deposition could play a major role in regulating fruit permeability and susceptibility to brown rot. Our results provide new insights into the composition of cuticular waxes of nectarines and their changes during fruit development, opening new avenues of research to explore brown rot resistance factors in stone fruit.

Is the Tolerance of Commercial Peach Cultivars to Brown Rot Caused by Monilinia laxa Modulated by its Antioxidant Content?

Brown rot, caused by Monilinia spp., provokes pre- and post-harvest damage in peach (Prunus persica (L.) Batsch), which causes an economic impact in the industry. With a view to breeding for increased tolerance to this disease, a screening test based upon artificial fruit inoculation was validated on several parental lines of a peach breeding program during the two-period harvest. In addition, cultivars with different total phenolic contents were included in the two-year study. All physicochemical fruit traits recorded at harvest showed differences among all cultivars. The antioxidant compound content determined using spectrophotometry (to measure ascorbic acid and antioxidant capacity) and UPLC-MS (to measure and identify phenolic compounds) also revealed important differences among all genotypes. The rate of brown rot lesion following fruit inoculation varied widely among cultivars, and it was possible to discriminate between highly and less susceptible cultivars. Cultivars with minimal development of damage were identified as germplasm with the desirable allele combination to increase brown rot tolerance in peach breeding programs. Finally, Pearson’s correlation coefficients (r) between pairs of variables were calculated, searching for any biochemical candidate conferring tolerance. The correlation of phytopathological traits with the antioxidant composition, concerning contents of ascorbic, neochlorogenic, and chlorogenic acids and total polyphenols in fruit, is discussed.

Proteomic Studies to Understand the Mechanisms of Peach Tissue Degradation by Monilinia laxa

Monilinia laxa is a necrotrophic plant pathogen able to infect and produce substantial losses on stone fruit. Three different isolates of M. laxa were characterized according to their aggressiveness on nectarines. M. laxa 8L isolate was the most aggressive on fruit, 33L isolate displayed intermediated virulence level, and 5L was classified as a weak aggressive isolate. Nectarine colonization process by the weak isolate 5L was strongly delayed. nLC-MS/MS proteomic studies using in vitro peach cultures provided data on exoproteomes of the three isolates at equivalent stages of brown rot colonization; 3 days for 8L and 33L, and 7 days for 5L. A total of 181 proteins were identified from 8L exoproteome and 289 proteins from 33L at 3 dpi, and 206 proteins were identified in 5L exoproteome at 7 dpi. Although an elevated number of proteins lacked a predicted function, the vast majority of proteins belong to OG group "metabolism", composed of categories such as "carbohydrate transport and metabolism" in 5L, and "energy production and conversion" most represented in 8L and 33L. Among identified proteins, 157 that carried a signal peptide were further examined and classified. Carbohydrate-active enzymes and peptidases were the main groups revealing different protein alternatives with the same function among isolates. Our data suggested a subset of secreted proteins as possible markers of differential virulence in more aggressive isolates, MlPG1 MlPME3, NEP-like, or endoglucanase proteins. A core-exoproteome among isolates independently of their virulence but time-dependent was also described. This core included several well-known virulence factors involved in host-tissue factors like cutinase, pectin lyases, and acid proteases. The secretion patterns supported the assumption that M. laxa deploys an extensive repertoire of proteins to facilitate the host infection and colonization and provided information for further characterization of M. laxa pathogenesis.

Phyllosphere Fungal Communities of Plum and Antifungal Activity of Indigenous Phenazine-Producing Pseudomonas synxantha Against Monilinia laxa

European plum (Prunus domestica L.) is a significant commercial crop in Serbia in terms of total fruit production, and is traditionally processed into slivovitz brandy. The brown rot disease caused by Monilinia laxa drastically reduces plum yield almost every year. Fungal communities associated with leaves and fruits of four local Serbian plum cultivars (Požegača, Ranka, Čačanska Lepotica and Čačanska Rodna) were investigated in two phenological stages during early (May) and late (July) fruit maturation. Alpha diversity indices showed that fungal communities were heterogeneous and Beta diversity indicated that autochthonous fungal communities depended upon seasonal changes and the cultivars themselves. The phylum Ascomycota was the most abundant in all samples, with relative abundance (RA) between 46% in the Požegača cultivar (May) and 89% in the Lepotica cultivar (July). The most abundant genus for all plum cultivars in May was Aureobasidium, with RA from 19.27 to 33.69%, followed by Cryptococcus, with 4.8 to 48.80%. In July, besides Cryptococcus, different genera (Metschnikowia, Fusarium, and Hanseniaspora) were dominant on particular cultivars. Among all cultivable fungi, molecular identification of eleven M. laxa isolates from four plum cultivars was performed simultaneously. Bacterial isolates from the plum phyllosphere were tested for their potential antifungal activity against indigenous M. laxa isolates. The most potent antagonist P4/16_1, which significantly reduced mycelial growth of M. laxa, was identified as Pseudomonas synxantha. Further characterization of P4/16_1 revealed the production of volatile organic compounds and phenazine-1-carboxylic acid (PCA). Crude benzene extract of PCA exhibited 57-63% mycelial growth inhibition of M. laxa. LC/MS analysis of the crude extract confirmed the presence of phenazine derivatives amongst other compounds. Scanning electron microscopy revealed morpho-physiological changes in the hyphae of M. laxa isolates caused by the cell culture and the P. synxantha P4/16_1 crude benzene extract. This is the first report of antagonistic activity of P. synxantha against M. laxa induced by diffusible and volatile antifungal compounds, and it appears to be a promising candidate for further investigation for potential use as a biocontrol agent against brown rot-causing fungi.

New High-Quality Draft Genome of the Brown Rot Fungal Pathogen Monilinia fructicola

Brown rot is a worldwide fungal disease of stone and pome fruit that is caused by several Monilinia species. Among these, Monilinia fructicola can cause severe preharvest and postharvest losses, especially for stone fruit. Here, we present a high-quality draft genome assembly of M. fructicola Mfrc123 strain obtained using both Illumina and PacBio sequencing technologies. The genome assembly comprised 20 scaffolds, including 29 telomere sequences at both ends of 10 scaffolds, and at a single end of 9 scaffolds. The total length was 44.05 Mb, with a scaffold N50 of 2,592 kb. Annotation of the M. fructicola assembly identified a total of 12,118 genes and 13,749 proteins that were functionally annotated. This newly generated reference genome is expected to significantly contribute to comparative analysis of genome biology and evolution within Monilinia species.

Coupling epidemiological and tree growth models to control fungal diseases spread in fruit orchards

Agronomic practices can alter plant susceptibility to diseases and represent a promising alternative to the use of pesticides. Yet, they also alter crop quality and quantity so that the evaluation of their efficacy is not straightforward. Here we couple a compartmental epidemiological model for brown rot diffusion in fruit orchards with a fruit-tree growth model explicitly considering the role of agronomic practices over fruit quality. The new modelling framework permits us to evaluate, in terms of quantity and quality of the fruit production, management scenarios characterized by different levels of regulated deficit irrigation and crop load. Our results suggest that a moderate water stress in the final weeks of fruit development and a moderate fruit load provide effective control on the brown rot spreading, and eventually guarantee monetary returns similar to those that would be obtained in the absence of the disease.

Modeling the abundance of two Rhagoletis fly (Diptera: Tephritidae) pests in Washington State, U.S.A

Well-adapted and abundant insect pests can negatively affect agricultural production. We modeled the abundance of two Rhagoletis fly (Diptera: Tephritidae) pests, apple maggot fly, Rhagoletis pomonella (Walsh), and western cherry fruit fly, Rhagoletis indifferens Curran, in Washington State (WA), U.S.A. using biologically relevant environmental variables. We tested the hypothesis that abundance of the two species is influenced by different environmental variables, based on the fact that these two species evolved in different environments, have different host plants, and that R. pomonella is an introduced pest in WA while R. indifferens is native. We collected data on fly and host plant abundance at 61 randomly selected sites across WA in 2015 and 2016. We obtained land-cover, climate, and elevation data from online sources and used these data to derive relevant landscape variables and modeled fly abundance using generalized linear models. For R. pomonella, relatively high winter mean minimum temperature, low elevation, and developed land-cover were the top variables positively related to fly abundance. In contrast, for R. indifferens, the top variables related to greater fly abundance were high Hargreaves climatic moisture and annual heat-moisture deficits (indication of drier habitats), high host plant abundance, and developed land-cover. Our results identify key environmental variables driving Rhagoletis fly abundance in WA and can be used for understanding adaptation of insects to non-native and native habitats and for assisting fly quarantine and management decisions.

Exploring sources of resistance to brown rot in an interspecific almond × peach population

BACKGROUND

Monilinia spp. are responsible for brown rot, one of the most significant stone fruit diseases. Planting resistant cultivars seems a promising alternative, although most commercial cultivars are susceptible to brown rot. The aim of this study was to explore resistance to Monilinia fructicola over two seasons in a backcross one interspecific population between almond 'Texas' and peach 'Earlygold' (named T1E).

RESULTS

'Texas' almond was resistant to brown rot inoculation, whereas peach was highly susceptible. Phenotypic data from the T1E population indicated wide differences in response to M. fructicola. Additionally, several non-wounded individuals exhibited resistance to brown rot. Quantitative trait loci (QTLs) were identified in several linkage groups, but only two proximal QTLs in G4 were detected over both seasons and accounted for 11.3-16.2% of the phenotypic variation.

CONCLUSION

Analysis of the progeny allowed the identification of resistant genotypes that could serve as a source of resistance in peach breeding programs. The finding of loci associated with brown rot resistance would shed light on implementing a strategy based on marker-assisted selection (MAS) for introgression of this trait into elite peach materials. New peach cultivars resistant to brown rot may contribute to the implementation of more sustainable crop protection strategies. © 2019 Society of Chemical Industry.

De novo assembly and comparative transcriptome analysis of Monilinia fructicola, Monilinia laxa and Monilinia fructigena, the causal agents of brown rot on stone fruits

BACKGROUND

Brown rots are important fungal diseases of stone and pome fruits. They are caused by several Monilinia species but M. fructicola, M. laxa and M. fructigena are the most common all over the world. Although they have been intensively studied, the availability of genomic and transcriptomic data in public databases is still scant. We sequenced, assembled and annotated the transcriptomes of the three pathogens using mRNA from germinating conidia and actively growing mycelia of two isolates of opposite mating types per each species for comparative transcriptome analyses.

RESULTS

Illumina sequencing was used to generate about 70 million of paired-end reads per species, that were de novo assembled in 33,861 contigs for M. fructicola, 31,103 for M. laxa and 28,890 for M. fructigena. Approximately, 50% of the assembled contigs had significant hits when blasted against the NCBI non-redundant protein database and top-hits results were represented by Botrytis cinerea, Sclerotinia sclerotiorum and Sclerotinia borealis proteins. More than 90% of the obtained sequences were complete, the percentage of duplications was always less than 14% and fragmented and missing transcripts less than 5%. Orthologous transcripts were identified by tBLASTn analysis using the B. cinerea proteome as reference. Comparative transcriptome analyses revealed 65 transcripts over-expressed (FC ≥ 8 and FDR ≤ 0.05) or unique in M. fructicola, 30 in M. laxa and 31 in M. fructigena. Transcripts were involved in processes affecting fungal development, diversity and host-pathogen interactions, such as plant cell wall-degrading and detoxifying enzymes, zinc finger transcription factors, MFS transporters, cell surface proteins, key enzymes in biosynthesis and metabolism of antibiotics and toxins, and transposable elements.

CONCLUSIONS

This is the first large-scale reconstruction and annotation of the complete transcriptomes of M. fructicola, M. laxa and M. fructigena and the first comparative transcriptome analysis among the three pathogens revealing differentially expressed genes with potential important roles in metabolic and physiological processes related to fungal morphogenesis and development, diversity and pathogenesis which need further investigations. We believe that the data obtained represent a cornerstone for research aimed at improving knowledge on the population biology, physiology and plant-pathogen interactions of these important phytopathogenic fungi.

A Model for Temporal Dynamics of Brown Rot Spreading in Fruit Orchards

Brown rot, caused by Monilinia spp., is a major disease of stone fruit and, in favorable environmental conditions and in the absence of fungicide treatments, it causes important economic losses. In the present work, we propose a modification of classical susceptible, exposed, infectious and removed compartmental models to grasp the peculiarities of the progression of brown rot epidemics in stone fruit orchards in the last stage of the fruit growth (i.e., from the end of the pit hardening to harvest time). Namely, we took into account (i) the lifespan of airborne spores; (ii) the dependence of the latent period on the cuticle crack surface area, which itself varies in time with fruit growth; (iii) the impossibility of recovery in infectious fruit; and (iv) the abrupt interruption of disease development by the elimination of the host fruit at harvest time. We parametrized the model by using field data from a peach Prunus persica orchard infected by Monilinia laxa and M. fructicola in Avignon (southern France). The basic reproduction number indicates that the environmental conditions met in the field were extremely favorable to disease development and the model closely fitted the temporal evolution of the fruit abundance in the different epidemiological compartments. The model permits us to highlight crucial mechanisms undergoing brown rot build up and to evaluate the consequences of different agricultural practices on the quantity and quality of the yield. We found that winter sanitation practices (which decrease the initial infection incidence) and the control of the fruit load (which affects the host fruit density and the single fruit growth trajectory) can be effective in controlling brown rot in conjunction with or in place of fungicide treatments.

An integrated approach for increasing breeding efficiency in apple and peach in Europe

Despite the availability of whole genome sequences of apple and peach, there has been a considerable gap between genomics and breeding. To bridge the gap, the European Union funded the FruitBreedomics project (March 2011 to August 2015) involving 28 research institutes and private companies. Three complementary approaches were pursued: (i) tool and software development, (ii) deciphering genetic control of main horticultural traits taking into account allelic diversity and (iii) developing plant materials, tools and methodologies for breeders. Decisive breakthroughs were made including the making available of ready-to-go DNA diagnostic tests for Marker Assisted Breeding, development of new, dense SNP arrays in apple and peach, new phenotypic methods for some complex traits, software for gene/QTL discovery on breeding germplasm via Pedigree Based Analysis (PBA). This resulted in the discovery of highly predictive molecular markers for traits of horticultural interest via PBA and via Genome Wide Association Studies (GWAS) on several European genebank collections. FruitBreedomics also developed pre-breeding plant materials in which multiple sources of resistance were pyramided and software that can support breeders in their selection activities. Through FruitBreedomics, significant progresses were made in the field of apple and peach breeding, genetics, genomics and bioinformatics of which advantage will be made by breeders, germplasm curators and scientists. A major part of the data collected during the project has been stored in the FruitBreedomics database and has been made available to the public. This review covers the scientific discoveries made in this major endeavour, and perspective in the apple and peach breeding and genomics in Europe and beyond.

Application of a Bayesian ordinal animal model for the estimation of breeding values for the resistance to Monilinia fruticola (G.Winter) Honey in progenies of peach [Prunus persica (L.) Batsch]

Fruit brown rot caused by Monilinia spp. is the most important fungal disease of stone fruits worldwide. Several phenotyping protocols to accurately characterize and evaluate brown rot infection have been proposed; however, the outcomes from those studies have not led to consistent advances in resistance breeding programs. Breeding for disease resistance is one of the most challenging objectives for crop improvement because disease expression is tetrahedral: it is simultaneously influenced by agent, host, environment, and human management. The present study presents a strategy based on Bayesian inference to analyze a peach breeding progeny for resistance to brown rot, evaluated using a polytomous ordinal scale. A pedigree containing two sources of resistance, one from peach and the other from almond, several commercial cultivars, and two segregating populations were analyzed to estimate the narrow-sense heritability (h² ) and breeding values (EBVs) for brown rot resistance in progenies. Results show promise for genetic improvement of disease resistance and other traits characterized by strong environmental interactions.