Automated phenotyping of plant shoots using imaging methods for analysis of plant stress responses – a review

Humplík, Jan; Lazár, Dušan; Husičková, Alexandra; Spíchal, Lukáš

doi:10.1186/s13007-015-0072-8

Cited by 201 publications

(141 citation statements)

References 84 publications

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“…PlantScreen (Photon Systems Instruments), a platform for high-throughput phenotyping, was used to monitor plant growth and photosynthetic performance by measuring plant area and chlorophyll fluorescence (Humplík et al, 2015;Rungrat et al, 2016). An ANOVA with subsequent Tukey's honestly significant difference (HSD) method was utilized to test for size differences at single time points.…”

Section: High-throughput Phenotyping Using Plantscreenmentioning

confidence: 99%

The Arabidopsis DNA Methylome Is Stable under Transgenerational Drought Stress

et al. 2017

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Improving the responsiveness, acclimation, and memory of plants to abiotic stress holds substantive potential for improving agriculture. An unresolved question is the involvement of chromatin marks in the memory of agriculturally relevant stresses. Such potential has spurred numerous investigations yielding both promising and conflicting results. Consequently, it remains unclear to what extent robust stress-induced DNA methylation variation can underpin stress memory. Using a slow-onset water deprivation treatment in Arabidopsis (Arabidopsis thaliana), we investigated the malleability of the DNA methylome to drought stress within a generation and under repeated drought stress over five successive generations. While drought-associated epialleles in the methylome were detected within a generation, they did not correlate with drought-responsive gene expression. Six traits were analyzed for transgenerational stress memory, and the descendants of drought-stressed lineages showed one case of memory in the form of increased seed dormancy, and that persisted one generation removed from stress. With respect to transgenerational drought stress, there were negligible conserved differentially methylated regions in drought-exposed lineages compared with unstressed lineages. Instead, the majority of observed variation was tied to stochastic or preexisting differences in the epigenome occurring at repetitive regions of the Arabidopsis genome. Furthermore, the experience of repeated drought stress was not observed to influence transgenerational epi-allele accumulation. Our findings demonstrate that, while transgenerational memory is observed in one of six traits examined, they are not associated with causative changes in the DNA methylome, which appears relatively impervious to drought stress.

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Section: High-throughput Phenotyping Using Plantscreenmentioning

confidence: 99%

The Arabidopsis DNA Methylome Is Stable under Transgenerational Drought Stress

et al. 2017

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“…As an example, various imaging methods became common for the analysis of plant stress responses by automated phenotyping [17]. In addition, several imaging techniques have been developed to detect early signs of stress by monitoring changes in water status, photosynthetic efficiency and the accumulation of secondary metabolites or structural modifications [18][19][20][21].…”

Section: Introductionmentioning

confidence: 99%

Estimation of Water Stress in Grapevines Using Proximal and Remote Sensing Methods

et al. 2018

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Abstract:In light of climate change and its impacts on plant physiology, optimizing water usage and improving irrigation practices play a crucial role in crop management. In recent years, new optical remote sensing techniques have become widespread since they allow a non-invasive evaluation of plant water stress dynamics in a timely manner. Unmanned aerial vehicles (UAV) currently represent one of the most advanced platforms for remote sensing applications. In this study, remote and proximal sensing measurements were compared with plant physiological variables, with the aim of testing innovative services and support systems to farmers for optimizing irrigation practices and scheduling. The experiment, conducted in two vineyards located in Sardinia, Italy, consisted of two regulated deficit irrigation (RDI) treatments and two reference treatments maintained under stress and well-watered conditions. Indicators of crop water status (Crop Water Stress Index-CWSI-and linear thermal index) were calculated from UAV images and ground infrared thermal images and then related to physiological measurements. The CWSI values for moderate water deficit (RDI-1) were 0.72, 0.28 and 0.43 for 'Vermentino', 'Cabernet' and 'Cagnulari' respectively, while for severe (RDI-2) water deficit the values were 0.90, 0.34 and 0.51. The highest differences for net photosynthetic rate (Pn) and stomatal conductance (Gs) between RDI-1 and RDI-2 were observed in 'Vermentino'. The highest significant correlations were found between CWSI with Pn (R = −0.80), with Φ PSII (R = −0.49) and with Fv'/Fm' (R = −0.48) on 'Cagnulari', while a unique significant correlation between CWSI and non-photochemical quenching (NPQ) (R = 0.47) was found on 'Vermentino'. Pn, as well as the efficiency of light use by the photosystem II (PSII), declined under stress conditions and when CWSI values increased. Under the experimental water stress conditions, grapevines were able to recover their efficiency during the night, activating a photosynthetic protection mechanism such as thermal energy dissipation (NPQ) to prevent irreversible damage to the photosystem. The results presented here demonstrate that CWSI values derived from remote and proximal sensors could be valuable indicators for the assessment of the spatial variability of crop water status in Mediterranean vineyards.

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“…The rice (glycophyte) is also known as desired model plant for salinity stress investigations (Horie et al, 2012). Up to now, mostly visible RGB imaging of rice plant shoots was used for stress detection and with some early results from hyperspectral application aimed at salinity interaction in this strategic crop (Humplík et al, 2015).…”

Section: Other Applications Of Hyperspectral Image Analysis To Identimentioning

confidence: 99%

Applying hyperspectral imaging to explore natural plant diversity towards improving salt stress tolerance

Sytar

Brestič

Živčák

et al. 2017

Science of The Total Environment

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• Salinity represents an abiotic stress constraint affecting growth and productivity of plants • Better solutions is to improve the level of salt resistance using natural genetic variability within crop species • Phenomic methodology employing different non-invasive imaging systems for detecting quantitative and qualitative changes caused by salt stress at the whole plant and canopy level. Hyperspectral imaging techniques provide unique opportunities for fast and reliable evaluation of numerous characteristics associated both with various structural, biochemical and physiological traits • Salt-soil-plant interaction and sustainable coastal agriculture need powerful phenotyping tools Salinity represents an abiotic stress constraint affecting growth and productivity of plants in many regions of the world. One of the possible solutions is to improve the level of salt resistance using natural genetic variability within crop species. In the context of recent knowledge on salt stress effects and mechanisms of salt tolerance, this review present useful phenomic approach employing different non-invasive imaging systems for detection of quantitative and qualitative changes caused by salt stress at the plant and canopy level. The focus is put on hyperspectral imaging technique, which provides unique opportunities for fast and reliable estimate of numerous characteristics associated both with various structural, biochemical Science of the Total Environment 578 (2017) 90-99 ⁎ Corresponding authors at:

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Automated phenotyping of plant shoots using imaging methods for analysis of plant stress responses – a review

Cited by 201 publications

References 84 publications

The Arabidopsis DNA Methylome Is Stable under Transgenerational Drought Stress

The Arabidopsis DNA Methylome Is Stable under Transgenerational Drought Stress

Estimation of Water Stress in Grapevines Using Proximal and Remote Sensing Methods

Applying hyperspectral imaging to explore natural plant diversity towards improving salt stress tolerance

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