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An annotated image dataset of downy mildew symptoms on Merlot grape variety.

ABSTRACT: This article introduces a dataset of high-resolution colour images of grapevines. It contains 99 images acquired in the vineyard from a cruising tractor. Each image includes the full foliage of a grapevine plant. These images display a diverse range of symptoms caused by the grapevine downy mildew (Plasmopara viticola), a major fungal disease. The dataset also includes various confounding factors, i.e. anomalies that are not related to the disease. These anomalies are the natural and common phenomena affecting vineyards such as results of mechanical wounds, necroses, chemical burns or yellowing and discolorations due to nutritional or hydric deficiencies. Images were acquired in-situ on "Le Domaine de la Grande Ferrade" a public experimental facility of INRAE, in the area of Bordeaux. Acquisitions took place at early fruiting stages (BBCH 75-79) corresponding to the main sanitary pressure during growth. The acquisition device, embedded on a vine tractor, is composed of an industrial colour camera synchronised with powerful flashes. The purpose of this device is to produce a "day for night" effect that mitigates the variation of sunlight. It enables to homogenise images acquired during different weathers and time of the day and to ensure that the foreground (containing foliage) displays appropriate brightness, with minimum shadows while the background is darker. The images of the dataset were annotated manually by photo-interpretation with a careful review of expertise regarding phytopathology and physiological disorders. The annotation process consists in associating pixels with a class that defines its membership to a type of organ and its physiological state. Pixels from healthy, symptomatic or abnormal grapevine tissues were labelled into seven classes: "Limbus", "Leaf edges", "Berries", "Stems", "Foliar mildew", "Berries mildew" and "Anomalies". The annotation is achieved with the GIMP2 software as mask images where the value attributed to each pixel corresponds to one of the seven considered classes.

SUBMITTER: Abdelghafour F

PROVIDER: S-EPMC8258852 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:BACKGROUND: Downy mildew (DM), caused by pathogen Plasmopara viticola (PV) is the single most damaging disease of grapes (Vitis L.) worldwide. However, the mechanisms of the disease development in grapes are poorly understood. A method for estimating gene expression levels using Solexa sequencing of Type I restriction-endonuclease-generated cDNA fragments was used for deep sequencing the transcriptomes resulting from PV infected leaves of Vitis amurensis Rupr. cv. Zuoshan-1. Our goal is to identify genes that are involved in resistance to grape DM disease. RESULTS: Approximately 8.5 million (M) 21-nt cDNA tags were sequenced in the cDNA library derived from PV pathogen-infected leaves, and about 7.5 M were sequenced from the cDNA library constructed from the control leaves. When annotated, a total of 15,249 putative genes were identified from the Solexa sequencing tags for the infection (INF) library and 14,549 for the control (CON) library. Comparative analysis between these two cDNA libraries showed about 0.9% of the unique tags increased by at least five-fold, and about 0.6% of the unique tags decreased more than five-fold in infected leaves, while 98.5% of the unique tags showed less than five-fold difference between the two samples. The expression levels of 12 differentially expressed genes were confirmed by Real-time RT-PCR and the trends observed agreed well with the Solexa expression profiles, although the degree of change was lower in amplitude. After pathway enrichment analysis, a set of significantly enriched pathways were identified for the differentially expressed genes (DEGs), which associated with ribosome structure, photosynthesis, amino acid and sugar metabolism. CONCLUSIONS: This study presented a series of candidate genes and pathways that may contribute to DM resistance in grapes, and illustrated that the Solexa-based tag-sequencing approach was a powerful tool for gene expression comparison between control and treated samples.

Project description:UNLABELLED:Downy mildew of sunflower is caused by Plasmopara halstedii (Farlow) Berlese & de Toni. Plasmopara halstedii is an obligate biotrophic oomycete pathogen that attacks annual Helianthus species and cultivated sunflower, Helianthus annuus. Depending on the sunflower developmental stage at which infection occurs, the characteristic symptoms range from young seedling death, plant dwarfing, leaf bleaching and sporulation to the production of infertile flowers. Downy mildew attacks can have a great economic impact on sunflower crops, and several Pl resistance genes are present in cultivars to protect them against the disease. Nevertheless, some of these resistances have been overcome by the occurrence of novel isolates of the pathogen showing increased virulence. A better characterization of P.?halstedii infection and dissemination mechanisms, and the identification of the molecular basis of the interaction with sunflower, is a prerequisite to efficiently fight this pathogen. This review summarizes what is currently known about P.?halstedii, provides new insights into its infection cycle on resistant and susceptible sunflower lines using scanning electron and light microscopy imaging, and sheds light on the pathogenicity factors of P.?halstedii obtained from recent molecular data. TAXONOMY:Kingdom Stramenopila; Phylum Oomycota; Class Oomycetes; Order Peronosporales; Family Peronosporaceae; Genus Plasmopara; Species Plasmopara halstedii. DISEASE SYMPTOMS:Sunflower seedling damping off, dwarfing of the plant, bleaching of leaves, starting from veins, and visible white sporulation, initially on the lower side of cotyledons and leaves. Plasmopara halstedii infection may severely impact sunflower seed yield. INFECTION PROCESS:In spring, germination of overwintered sexual oospores leads to sunflower root infection. Intercellular hyphae are responsible for systemic plant colonization and the induction of disease symptoms. Under humid and fresh conditions, dissemination structures are produced by the pathogen on all plant organs to release asexual zoosporangia. These zoosporangia play an important role in pathogen dissemination, as they release motile zoospores that are responsible for leaf infections on neighbouring plants. DISEASE CONTROL:Disease control is obtained by both chemical seed treatment (mefenoxam) and the deployment of dominant major resistance genes, denoted Pl. However, the pathogen has developed fungicide resistance and has overcome some plant resistance genes. Research for more sustainable strategies based on the identification of the molecular basis of the interaction are in progress. USEFUL WEBSITES:http://www.heliagene.org/HP, http://lipm-helianthus.toulouse.inra.fr/dokuwiki/doku.php?id=start, https://www.heliagene.org/PlasmoparaSpecies (soon available).

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An annotated image dataset of downy mildew symptoms on Merlot grape variety.

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