Image-Based Methods to Score Fungal Pathogen Symptom Progression and Severity in Excised Arabidopsis Leaves

Pavicic, Mirko; Overmyer, Kirk; Rehman, Attiq Ur; Jones, Piet; Jacobson, Daniel; Himanen, Kristiina

doi:10.3390/plants10010158

Cited by 20 publications

(34 citation statements)

References 34 publications

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“…f The content of chlorotic pixels of wild-type (WT), empty vector (EV), mutant lines ( d6pkl2-1 , d6pkl2-3 ), and VmD6PKL2 -overexpressing transgenic lines (#2, #5, #7) infected with Fof -1 at 7 dpi. The analysis was conducted with reference to Pavicic et al 56 . g Disease symptoms of mutant lines ( d6pkl2-1 , d6pkl2-3 ) and WT, EV, and VmD6PKL2 -overexpressing transgenic lines (#2, #5, #7) infected with Fof -1 at 7 dpi.…”

Section: Resultsmentioning

confidence: 99%

D6 protein kinase in root xylem benefiting resistance to Fusarium reveals infection and defense mechanisms in tung trees

Zhang

Yin

et al. 2021

Hortic Res

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Fusarium oxysporum, a global soil-borne pathogen, causes severe disease in various cultivated plants. The mechanism underlying infection and resistance remains largely elusive. Vernicia fordii, known as the tung tree, suffers from disease caused by F. oxysporum f. sp. fordiis (Fof-1), while its sister species V. montana displays high resistance to Fof-1. To investigate the process of infection and resistance ability, we demonstrated that Fof-1 can penetrate the epidermis of root hairs and then centripetally invade the cortex and phloem in both species. Furthermore, Fof-1 spread upwards through the root xylem in susceptible V. fordii trees, whereas it failed to infect the root xylem in resistant V. montana trees. We found that D6 PROTEIN KINASE LIKE 2 (VmD6PKL2) was specifically expressed in the lateral root xylem and was induced after Fof-1 infection in resistant trees. Transgenic analysis in Arabidopsis and tomato revealed that VmD6PKL2 significantly enhanced resistance in both species, whereas the d6pkl2 mutant displayed reduced resistance against Fof-1. Additionally, VmD6PKL2 was identified to interact directly with synaptotagmin (VmSYT3), which is specifically expressed in the root xylem and mediates the negative regulation responding to Fof-1. Our data suggested that VmD6PKL2 could act as a resistance gene against Fof-1 through suppression of VmSYT3-mediated negative regulation in the lateral root xylem of the resistant species. These findings provide novel insight into Fusarium wilt resistance in plants.

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Section: Resultsmentioning

confidence: 99%

D6 protein kinase in root xylem benefiting resistance to Fusarium reveals infection and defense mechanisms in tung trees

Zhang

Yin

et al. 2021

Hortic Res

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“…While non-stressed plants maintain a consistent F v / F m value, various studies have shown that plants experiencing biotic or abiotic stresses have decreased F v / F m values ( Berger et al., 2006 ; Matous et al., 2006 ; Baker, 2008 ; Rolfe and Scholes, 2010 ; Wang et al., 2018 ), and changes in this parameter occur before visible disease symptoms occur ( Rolfe and Scholes, 2010 ). Furthermore, healthy tissues were reported to yield F v / F m values around 0.84 for numerous plant species ( Maxwell and Johnson, 2000 ; Rousseau et al., 2013 ; Pavicic et al., 2021 ). Thus, using F v / F m decrease as an indicator of plant stress, ( Rousseau et al., 2013 ) developed a thresholding approach to segment diseased areas of bean leaflets infected by a common bacterial blight.…”

Section: Methodsmentioning

confidence: 99%

“…Several challenges exist for disease annotation in CFI at the earlier stages, such as (a) detection by the eye of the disease spots in noisy monochromatic images; (b) extremely tiny size of disease lesions; (c) a large number of scattered lesions to annotate. So far, to the best of our knowledge, only one annotated dataset of fluorescent images of diseased Arabidopsis thaliana plants is currently available ( Pavicic et al., 2021 ). However, the automated annotation of Botrytis cinerea fungal disease was performed for disease severity exceeding 8%.…”

Section: Introductionmentioning

confidence: 99%

Plant disease symptom segmentation in chlorophyll fluorescence imaging with a synthetic dataset

2022

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Despite the wide use of computer vision methods in plant health monitoring, little attention is paid to segmenting the diseased leaf area at its early stages. It can be explained by the lack of datasets of plant images with annotated disease lesions. We propose a novel methodology to generate fluorescent images of diseased plants with an automated lesion annotation. We demonstrate that a U-Net model aiming to segment disease lesions on fluorescent images of plant leaves can be efficiently trained purely by a synthetically generated dataset. The trained model showed 0.793% recall and 0.723% average precision against an empirical fluorescent test dataset. Creating and using such synthetic data can be a powerful technique to facilitate the application of deep learning methods in precision crop protection. Moreover, our method of generating synthetic fluorescent images is a way to improve the generalization ability of deep learning models.

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“…Image-based phenotyping of disease processes in time series can help to study both climate-dependent and genotype-dependent disease progression and severity ( Pavicic et al , 2021 ). Automated phenotyping with the help of UAVs or robotics can increase the number of measuring times compared with manual handling by traditional scoring based on visual inspection.…”

Section: Plant Health and Crop Management In Nordic Conditionsmentioning

confidence: 99%

Functional phenomics for improved climate resilience in Nordic agriculture

Roitsch

Himanen

Chawade

et al. 2022

Journal of Experimental Botany

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The five Nordic countries span the most northern region for field cultivation in the world. This presents challenges per se with short growing seasons, long days and a need for frost tolerance. Climate change has additionally increased risks for micro-droughts and water logging as well as pathogens and pests expanding northwards. Thus, Nordic agriculture demands crops that are adapted to the special Nordic growth conditions and future climate scenarios. A focus on crop varieties and traits important to Nordic agriculture, including the unique resource of nutritious wild crops, can meet these needs. In fact, with a future longer growing season due to climate change the region could contribute proportionally more to the global agricultural production. This also applies to other northern regions, including the Arctic. To address current growth conditions, mitigate impacts of climate change and meet market demands, the adaptive capacity of crops that both perform well in northern latitudes and are more climate resilient has to be increased, and better crop management systems be built. This requires functional phenomics approaches that integrate versatile high-throughput phenotyping, physiology and bioinformatics. This review stresses key target traits, the opportunities of latitudinal studies and infrastructure needs for phenotyping to support Nordic agriculture.

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Image-Based Methods to Score Fungal Pathogen Symptom Progression and Severity in Excised Arabidopsis Leaves

Cited by 20 publications

References 34 publications

D6 protein kinase in root xylem benefiting resistance to Fusarium reveals infection and defense mechanisms in tung trees

D6 protein kinase in root xylem benefiting resistance to Fusarium reveals infection and defense mechanisms in tung trees

Plant disease symptom segmentation in chlorophyll fluorescence imaging with a synthetic dataset

Functional phenomics for improved climate resilience in Nordic agriculture

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