Search Results (199)

PIWI, from the German word Pilzwiderstandsfähig, meaning “fungus-resistant”, refers to grapevine cultivars bred for resistance to fungal pathogens such as Erysiphe necator (the causal agent of powdery mildew) and Plasmopara viticola (the causal agent of downy mildew), two major diseases in viticulture. These varieties are typically developed through traditional breeding, often crossbreeding European Vitis vinifera with American or Asian species that carry natural disease resistance. This study investigates the transcriptional profiles of exocarp tissues in mature berries from four PIWI grapevine varieties compared to their elite parental counterparts using RNA-seq analysis. We performed RNA-seq on four PIWI varieties (two red and two white) and their noble parents to identify differential gene expression patterns. Comprehensive analyses, including Differential Gene Expression (DEGs), Gene Set Enrichment Analysis (GSEA), Weighted Gene Co-expression Network Analysis (WGCNA), and tau analysis, revealed distinct gene clusters and individual genes characterizing the transcriptional landscape of PIWI varieties. Differentially expressed genes indicated significant changes in pathways related to organic acid metabolism and membrane transport, potentially contributing to enhanced resilience. WGCNA and k-means clustering highlighted co-expression modules linked to PIWI genotypes and their unique tolerance profiles. Tau analysis identified genes uniquely expressed in specific genotypes, with several already known for their defense roles. These findings offer insights into the molecular mechanisms underlying grapevine resistance and suggest promising avenues for breeding strategies to enhance disease resistance and overall grape quality in viticulture. Full article

Fungi infection, especially derived from Plasmopara viticola, causes severe grapevine economic losses worldwide. Despite the availability of chemical treatments, looking for eco-friendly ways to control Vitis vinifera infection is gaining much more attention. When a plant is infected, multiple disease-control molecular mechanisms are activated. PRRs (Pattern Recognition Receptors) and particularly RLKs (receptor-like kinases) take part in the first barrier of the immune system, and, as a consequence, the kinase signaling cascade is activated, resulting in an immune response. In this context, discovering new lectin-RLK (LecRLK) membrane-bounded proteins has emerged as a promising strategy. The genome-wide localization of potential LecRLKs involved in disease defense was reported in two grapevine varieties of great economic impact: Chardonnay and Pinot Noir. A total of 23 potential amino acid sequences were identified, exhibiting high-sequence homology and evolution related to tandem events. Based on the domain architecture, a carbohydrate specificity ligand assay was conducted with docking, revealing two sequences as candidates for specific Vitis vinifera–Plasmopara viticola host–pathogen interaction. This study confers a starting point for designing new effective antifungal treatments directed at LecRLK targets in Vitis vinifera. Full article

This study aimed to assess the effect of using selected herbs as companion crops in soybean cultivation on the yield and overall health of soybeans. A three-year field experiment (2021–2023) was conducted using a randomized block design with three replications, where the primary experimental variable was the sowing method. The innovative cropping system involved cultivating soybeans alongside different companion herbs, such as alyssum (Lobularia maritima L.), fennel (Foeniculum vulgare Mill.), borage (Borago officinalis L.), French marigold (Tagetes patula L.), calendula (Calendula officinalis L.), and a herbal mixture referred to as ‘MIX’. The study showed that cultivation of soybean with fennel improved the quantitative and qualitative characteristics of the yield, with a significant increase in seed yield (on average by 0.27 t ha⁻¹) as well as protein (7.67%) and oil yield (8.57%) compared to the pure soybean crop. The following fungal diseases were identified during the three-year study period (2021–2023): Cercospora leaf blight, Ascochyta blight, Fusarium wilt, and downy mildew. Cultivation of soybean with herbs as companion crops was implemented to improve the health of soybean to a varied extent. Borage, marigold, and calendula companion crops reduced infection of soybean by the fungi C. kikuchii and F. oxysporum. Cultivation with fennel and marigold was also beneficial for soybean health. On the other hand, cultivation with sweet alyssum and a mixture of herbs increased the occurrence of the fungus A. sojaecola. Cultivation of soybean in association with herbs is legitimate and requires further research given the priorities facing 21st-century agriculture. Full article

Cucumber (Cucumis sativus L.) is a vital economic vegetable crop, and the TONNEAU1 Recruiting Motif (TRM) gene plays a key role in cucumber organ growth. However, the pan-genomic characteristics of the TRM gene family and their expression patterns under different stresses have not been reported in cucumber. In this study, we identified 29 CsTRMs from the pan-genomes of 13 cucumber accessions, with CsTRM29 existing only in PI183967. Most CsTRM proteins exhibited differences in sequence length, except five CsTRMs having consistent protein sequence lengths among the 13 accessions. All CsTRM proteins showed amino acid variations. An analysis of CsTRM gene expression patterns revealed that six CsTRM genes strongly changed in short-fruited lines compared with long-fruited lines. And four CsTRM genes strongly responded to salt and heat stress, while CsTRM14 showed responses to salt stress, powdery mildew, gray mold, and downy mildew. Some CsTRM genes were induced or suppressed at different treatment timepoints, suggesting that cucumber TRM genes may play different roles in responses to different stresses, with expression patterns varying with stress changes. Remarkably, the expression of CsTRM21 showed considerable change between long and short fruits and in responses to abiotic stresses (salt stress and heat stress), as well as biotic stresses (powdery mildew and gray mold), suggesting a dual role of CsTRM21 in both fruit shape determination and stress resistance. Collectively, this study provided a base for the further functional identification of CsTRM genes in cucumber plant growth and stress resistance. Full article

Thanks to several Vitis vinifera backcrosses with an initial V. vinifera L. × V. rotundifolia (previously Muscadinia rotundifolia) interspecific cross, the MrRUN1/MrRPV1 locus (resistance to downy and powdery mildews) was introgressed in genotypes phenotypically close to V. vinifera varieties. To check the consequences of introgressing parts of the V. rotundifolia genome on gene expression during fruit development, we conducted a comparative RNA-seq study on single berries from different V. vinifera cultivars and V. vinifera × V. rotundifolia hybrids, including ‘G5’ and two derivative microvine lines, ‘MV102’ (resistant) and ‘MV32’ (susceptible) segregating for the MrRUN1/RPV1 locus. RNA-Seq profiles were analyzed on a comprehensive set of single berries from the end of the herbaceous plateau to the ripe stage. Pair-end reads were aligned both on V. vinifera PN40024.V4 reference genome, V. rotundifolia cv ‘Trayshed’ and cv ‘Carlos’, and to the few resistance genes from the original V. rotundifolia cv ‘52’ parent available at NCBI. Weighted Gene Co-expression Network Analysis (WGCNA) led to classifying the differentially expressed genes into 15 modules either preferentially correlated with resistance or berry phenology and composition. Resistance positively correlated transcripts predominantly mapped on the 4–5 Mb distal region of V. rotundifolia chromosome 12 beginning with the MrRUN1/MrRPV1 locus, while the negatively correlated ones mapped on the orthologous V. vinifera region, showing this large extremity of LG12 remained recalcitrant to internal recombination during the successive backcrosses. Some constitutively expressed V. rotundifolia genes were also observed at lower densities outside this region. Genes overexpressed in developing berries from resistant accessions, either introgressed from V. rotundifolia or triggered by these in the vinifera genome, spanned various functional groups, encompassing calcium signal transduction, hormone signaling, transcription factors, plant–pathogen-associated interactions, disease resistance proteins, ROS and phenylpropanoid biosynthesis. This transcriptomic insight provides a foundation for understanding the disease resistance inherent in these hybrid cultivars and suggests a constitutive expression of NIR NBS LRR triggering calcium signaling. Moreover, these results illustrate the magnitude of transcriptomic changes caused by the introgressed V. rotundifolia background in backcrossed hybrids, on a large number of functions largely exceeding the ones constitutively expressed in single resistant gene transformants. Full article

Plant breeders utilize marker-assisted selection (MAS) to identify favorable or unfavorable alleles in seedlings early. In this task, they need methods that provide maximum information with minimal input of time and economic resources. Grape breeding aimed at producing cultivars resistant to pathogens employs several resistance loci (Rpv, Ren, and Run) that are ideal for implementing MAS. In this work, a sustainable MAS protocol was developed based on non-purified DNA (crude), multiplex PCR of SSR markers, and capillary electrophoresis, and its application on grapevine seedlings to follow some main resistance loci was described. The optimized protocol was utilized on 8440 samples and showed high efficiency, reasonable throughput (2–3.2 min sample), easy handling, flexibility, and tolerable costs (reduced by at least 3.5 times compared to a standard protocol). The Rpv, Ren, and Run allelic data analysis did not show limitations to loci combination and pyramiding, but segregation distortions were frequent and displayed both low (undesired) and high rates of inheritance. The protocol and results presented are useful tools for grape breeders and beyond, and they can address sustainable changes in MAS. Several progenies generated have valuable pyramided resistance and will be the subject of new studies and implementation in the breeding program. Full article

It is of great significance to develop early prediction technology for controlling downy mildew and promoting cucumber production. In this study, a cucumber downy mildew prediction method was proposed by fusing quantitative disease information and environmental data. Firstly, the number of cucumber downy mildew spores during the experiment was collected by a portable spore catcher, and the proportion of cucumber downy mildew leaf area to all cucumber leaf area was recorded, which was used as the incidence degree of cucumber plants. The environmental data in the greenhouse were monitored and recorded by the weather station in the greenhouse. Environmental data outside the greenhouse were monitored and recorded by a weather station in front of the greenhouse. Then, the influencing factors of cucumber downy mildew were analyzed based on the Pearson correlation coefficient method. The influencing factors of the cucumber downy mildew early warning model in greenhouse were identified. Finally, the CNN-LSTM (Convolutional Neural Network-Long Short-Term Memory) algorithm was used to establish the cucumber downy mildew incidence prediction model. The results showed that the Mean Absolute Error (MAE), Mean Square Error (MSE), Root Mean Square Error (RMSE), and determination coefficient (R²) of the CNN-LSTM network model were 0.069, 0.0098, 0.0991, and 0.9127, respectively. The maximum error between the predicted value and the true value for all test sets was 16.9398%. The minimum error between the predicted value and the true value for all test sets was 0.3413%. The average error between the predicted and true values for all test sets was 6.6478%. The Bland–Altman method was used to analyze the predicted and true values of the test set, and 95.65% of the test set data numbers were within the 95% consistency interval. This work can serve as a foundation for the creation of early prediction models of greenhouse crop airborne diseases. Full article

To obtain effective biocontrol strains for downy mildew of grape, 38 endophytic bacteria were isolated from fruits, seeds, and old stems of six grape varieties. Using spot inoculation mixtures of sporangial suspensions of Plasmopara viticola and biocontrol bacterial suspension, this screen yielded three strains (G1, G5, and G9) with good antagonistic effects against P. viticola. The growth inhibition rate was 100%, which was comparable to the effect of the positive control Bacillus subtilis strain CN181. The enzyme activity and the metabolites of strain G1 were examined on casein hydrolysate medium, sodium carboxymethyl cellulose agar plates, and chrome azurol sulfonate (CAS) agar plates. The antifungal protein component was identified by liquid chromatography–mass spectrometry (LC–MS). The results showed that strain G1 was more effective against Plasmopara viticola after two field trials, and the inhibition rates of strain G1 on the seventh day of the two field trials were 47.5% and 36.9%, respectively. Strain G1 was identified as Bacillus amyloliquefaciens based on morphological examination and 16S rDNA sequence analysis. It produced proteases, cellulases, and siderophores. Crude protein of the strain mainly included the putative segregation protein SpoVG, which inhibited P. viticola. Full article

Black rot (Guignardia bidwellii) and downy mildew (Plasmopara viticola) are two major grapevine diseases against which the development of efficient biocontrol solutions is required in a context of sustainable viticulture. This study aimed at evaluating and comparing the efficacy and modes of action of bacterial culture supernatants from Bacillus velezensis Buz14 and B. ginsengihumi S38. Both biocontrol agents (BCA) were previously demonstrated as highly effective against Botrytis cinerea in grapevines. In semi-controlled conditions, both supernatants provided significant protection against black rot and downy mildew. They exhibited antibiosis against the pathogens by significantly decreasing G. bidwellii mycelial growth, but also the release and motility of P. viticola zoospores. They also significantly induced grapevine defences, as stilbene production. The LB medium, used for the bacterial cultures, also showed partial effects against both pathogens and induced plant defences. This is discussed in terms of choice of experimental controls when studying the biological activity of BCA supernatants. Thus, we identified two bacterial culture supernatants as new potential biocontrol products exhibiting multi-spectrum antagonist activity against different grapevine key pathogens and having a dual mode of action. Full article

This study focused on downy mildew in hop caused by the pathogen Pseudoperonospora humuli. A systematic literature review was conducted using bibliometric analysis to explore trends in publishing, prominent research themes, and where research is being conducted on hop downy mildew. The databases Scopus, Web of Science, and ScienceDirect were used to identify publications spanning from 1928 to 2023. The analysis yielded 54 publications, with the most cited studies primarily focusing on disease management and host resistance. Additionally, these studies explored the genetic and pathogenic relationship between P. cubensis and P. humuli. A word co-occurrence map revealed that the main themes addressed in the publications included “hop”, “disease”, “downy”, “humuli”, “mildew”, and “Pseudoperonospora”. Notably, there was a particular emphasis on subtopics such as disease management, the disease reaction of hop cultivars, and the influence of weather factors on hop downy mildew. Notably, there was limited knowledge about the disease in regions with tropical climates. This study provides valuable information that can support and guide future research endeavors concerning downy mildew in hop cultivation. Full article

Roses (genus Rosa), renowned for their economic significance and aesthetic appeal, face multifaceted challenges in cultivation due to biotic and abiotic stressors. To address these challenges, this study explores the role of osmolytes, particularly polyamines, proline and glycine betaine, as well as antioxidant capacities and condensed tannins, in enhancing stress tolerance in roses. Despite the genetic diversity inherent in roses, the metabolic aspect of stress tolerance has been underexplored in breeding programs. This paper investigates the intraspecific variability among 22 rose cultivars, focusing on osmolyte content (proline and glycine betaine), individual polyamines (putrescine, spermine and spermidine), as well as antioxidant activities, measuring radical scavenging capacity against 2,2′-azinobis(3-ethylbenzothiozoline-6-sulfonic acid (ABTS^•+) and NO^• radicals. Employing a targeted metabolomic approach, we quantified the levels of individual polyamines in both the petals and leaves of rose cultivars. This was achieved through high-performance liquid chromatography coupled with fluorescent detection following a derivatization pretreatment process. Within the evaluated cultivars, “Unique Aroma”, “Andre Rieu”, “Aroma 3”, “Frayla Marija” and “Trendy Fashion” stood out for their significantly elevated levels of total foliar polyamines. The predominant polyamine detected at both petal and leaf levels was putrescine, with concentrations ranging from 335.81 (“Zora Frayla”) to 2063.81 nmol g⁻¹ DW (“Unique Aroma”) at the leaf level. Following putrescine, foliar spermidine levels varied from 245.08 (“Olivera Frayla”) to 1527.16 nmol g⁻¹ DW (“Andre Rieu”). Regarding antioxidant capacity, the leaf extracts of rose cultivars “Zora Frayla” and “Natalija Frayla” were prominent by showing 68.08 and 59.24 mmol Trolox equivalents (TE) g⁻¹ DW, respectively. The results highlight the intricate biochemical variability across rose cultivars and show that osmolytes, such as glycine betaine, proline and polyamines, and other biochemical markers can be used as reliable criteria for the selection of rose cultivars that are more resilient to biotic stress factors, especially powdery and downy mildew. Bridging fundamental research with practical applications, this study aims to contribute to the development of stress-tolerant rose cultivars adaptable to dynamic environmental conditions. Full article

This paper focuses on the creation of an in vitro collection of grapevine hybrids from the breeding program of the Kazakh Scientific Research Institute of Fruit Growing and Viticulture and investigates the presence of Plasmopara viticola resistance mediated by Rpv3 and Rpv12 loci. We looked at the optimization of in vitro establishment using either shoots taken directly from field-grown plants or from budwood cuttings forced indoors. We further screened for the presence of endophyte contamination in the initiated explants and optimized the multiplication stage. Finally, the presence of the resistance loci against P. viticola was studied. The shoots initiated from the field-sourced explants were the more effective method of providing plant sources for in vitro initiation once all plant accessions met the goal of in vitro establishment. The concentration of phytohormones and the acidity of the culture medium have a great effect on the multiplication rate and the quality of in vitro stock cultures. Out of 17 grapevine accessions, 16 showed the presence of single or combined resistance loci against P. viticola. The grapevine accessions identified as carrying Rpv3 and Rpv12 alleles represent important genetic resources for disease resistance breeding programs. These accessions may further contribute to the creation of new elite cultivars of economic interest. Full article

Sorghum (Sorghum bicolor L.) ranks fifth as the most crucial cereal crop globally, yet its seed morphology remains relatively unexplored. This study investigated seed morphology in sorghum based on 115 mini-core and 130 Senegalese germplasms. Eight seed morphology traits encompassing size, shape, and color parameters were assessed. Statistical analyses explored potential associations between these traits and resistance to three major sorghum diseases: anthracnose, head smut, and downy mildew. Furthermore, genome-wide association studies (GWAS) were conducted using phenotypic data from over 24,000 seeds and over 290,000 publicly available single nucleotide polymorphisms (SNPs) through the Genome Association and Prediction Integrated Tool (GAPIT) R package. Significant SNPs associated with various seed morphology traits were identified and mapped onto the reference sorghum genome to identify novel candidate defense genes. Full article

Downy mildew is a severe disease that leads to significant losses in grape yields worldwide. It is caused by the oomycete Plasmopara viticola. The study of the distribution of this agent and the search for endophytic organisms that inhibit the growth of P. viticola are essential objectives to facilitate the transition to sustainable and high-yield agriculture, while respecting the environment. In this study, high-throughput sequencing of the ITS (ITS1f/ITS2 region) and 16S (V4 region) amplicons was employed to analyze 80 samples of leaves and stems from different grapevine species and cultivars grown in the Russian Far East (Vitis amurensis Rupr., Vitis coignetiae Pulliat, and several grapevine cultivars). The analysis revealed the presence of P. viticola in 53.75% of the grape samples. The pathogen P. viticola was not detected in V. amurensis samples collected near Vladivostok and Russky Island. Among the P. viticola-affected samples, only two (out of the eighty analyzed grape samples) from the Makarevich vineyard in Primorsky Krai exhibited disease symptoms, while the majority appeared visually healthy. We also found six distinct P. viticola ASVs in our metagenomic data. Based on phylogenetic analysis, we hypothesize that the P. viticola population in the Russian Far East may have originated from the invasive P. viticola clade aestivalis, which has spread around the world from North America. To identify putative microbial antagonists of P. viticola, a differential analysis of high-throughput sequencing data was conducted using the DESeq2 method to compare healthy and P. viticola-affected samples. The in silico analysis revealed an increased representation of certain taxa in healthy samples compared to P. viticola-affected ones: fungi—Kabatina sp., Aureobasidium sp., and Vishniacozyma sp.; bacteria—Hymenobacter spp., Sphingomonas spp., Massilia spp., Methylobacterium-Methylorubrum spp., and Chryseobacterium spp. This in-silico-obtained information on the potential microbial antagonists of P. viticola serves as a theoretical basis for the development of biocontrol agents for grapevine downy mildew. Full article