Automatic Root Length Estimation from Images Acquired In Situ without Segmentation.

Image-based root phenotyping technologies, including the minirhizotron (MR), have expanded our understanding of the in situ root responses to changing environmental conditions. The conventional manual methods used to analyze MR images are time-consuming, limiting their implementation. This study presents an adaptation of our previously developed convolutional neural network-based models to estimate the total (cumulative) root length (TRL) per MR image without requiring segmentation. Training data were derived from manual annotations in Rootfly, commonly used software for MR image analysis. We compared TRL estimation with 2 models, a regression-based model and a detection-based model that detects the annotated points along the roots. Notably, the detection-based model can assist in examining human annotations by providing a visual inspection of roots in MR images. The models were trained and tested with 4,015 images acquired using 2 MR system types (manual and automated) and from 4 crop species (corn, pepper, melon, and tomato) grown under various abiotic stresses. These datasets are made publicly available as part of this publication. The coefficients of determination (R2), between the measurements made using Rootfly and the suggested TRL estimation models were 0.929 to 0.986 for the main datasets, demonstrating that this tool is accurate and robust. Additional analyses were conducted to examine the effects of (a) the data acquisition system and thus the image quality on the models' performance, (b) automated differentiation between images with and without roots, and (c) the use of the transfer learning technique. These approaches can support precision agriculture by providing real-time root growth information.

Source-sink relations of sunflower plants as affected by a parasite modifies carbon allocations and leaf traits.

Sunflower broomrape (Orobanche cumana) is a root holoparasitic plant causing major damage to sunflower (Helianthus annuus L.). Parasite infection initiates source-sink relations between the parasite (sink) and the host (source), allocating carbohydrates, water and nutrients to the parasite. The primary aim of the current study was to explore responses of sunflower to broomrape parasitism, specifically to examine alternations in leaf area, leaf mass per area (LMA), mesophyll structure and root hydraulic conductivity. Leaf changes revealed modifications similar to described previously in shade adapted plants, causing larger and thinner leaves. These traits were accompanied with significantly higher root hydraulics. These changes were caused by carbohydrate depletion due to source-sink relationships between the host and parasite. An Imazapic herbicide (ALS inhibitor) was used for controlling broomrape attachments and by to investigate the plasticity of the traits found. Broomrape infected plants which were treated with Imazapic had leaves similar to non-infected plants, including mesophyll structure and carbon assimilation rates. These results demonstrated source-sink effects of broomrape which cause a low-light-like acclimation behavior which is reversible.

Recognition of Orobanche cumana Below-Ground Parasitism Through Physiological and Hyper Spectral Measurements in Sunflower (Helianthus annuus L.).

Broomrape (Orobanche and Phelipanche spp.) parasitism is a severe problem in many crops worldwide, including in the Mediterranean basin. Most of the damage occurs during the sub-soil developmental stage of the parasite, by the time the parasite emerges from the ground, damage to the crop has already been done. One feasible method for sensing early, below-ground parasitism is through physiological measurements, which provide preliminary indications of slight changes in plant vitality and productivity. However, a complete physiological field survey is slow, costly and requires skilled manpower. In recent decades, visible to-shortwave infrared (VIS-SWIR) hyperspectral tools have exhibited great potential for faster, cheaper, simpler and non-destructive tracking of physiological changes. The advantage of VIS-SWIR is even greater when narrow-band signatures are analyzed with an advanced statistical technique, like a partial least squares regression (PLS-R). The technique can pinpoint the most physiologically sensitive wavebands across an entire spectrum, even in the presence of high levels of noise and collinearity. The current study evaluated a method for early detection of Orobanche cumana parasitism in sunflower that combines plant physiology, hyperspectral readings and PLS-R. Seeds of susceptible and resistant O. cumana sunflower varieties were planted in infested (15 mg kg-1 seeds) and non-infested soil. The plants were examined weekly to detect any physiological or structural changes; the examinations were accompanied by hyperspectral readings. During the early stage of the parasitism, significant differences between infected and non-infected sunflower plants were found in the reflectance of near and shortwave infrared areas. Physiological measurements revealed no differences between treatments until O. cumana inflorescences emerged. However, levels of several macro- and microelements tended to decrease during the early stage of O. cumana parasitism. Analysis of leaf cross-sections revealed differences in range and in mesophyll structure as a result of different levels of nutrients in sunflower plants, manifesting the presence of O. cumana infections. The findings of an advanced PLS-R analysis emphasized the correlation between specific reflectance changes in the SWIR range and levels of various nutrients in sunflower plants. This work demonstrates potential for the early detection of O. cumana parasitism on sunflower roots using hyperspectral tools.

Ancestral QTL Alleles from Wild Emmer Wheat Enhance Root Development under Drought in Modern Wheat.

A near-isogenic line (NIL-7A-B-2), introgressed with a quantitative trait locus (QTL) on chromosome 7AS from wild emmer wheat (Triticum turgidum ssp. dicoccoides) into the background of bread wheat (T. aestivum L.) cv. BarNir, was recently developed and studied in our lab. NIL-7A-B-2 exhibited better productivity and photosynthetic capacity than its recurrent parent across a range of environments. Here we tested the hypothesis that root-system modifications play a major role in NIL-7A-B-2's agronomical superiority. Root-system architecture (dry matter and projected surface area) and shoot parameters of NIL-7A-B-2 and 'BarNir' were evaluated at 40, 62, and 82 days after planting (DAP) in a sand-tube experiment, and root tip number was assessed in a 'cigar-roll' seedling experiment, both under well-watered and water-limited (WL) treatments. At 82 DAP, under WL treatment, NIL-7A-B-2 presented greater investment in deep roots (depth 40-100 cm) than 'BarNir,' with the most pronounced effect recorded in the 60-80 cm soil depth (60 and 40% increase for root dry matter and surface area, respectively). NIL-7A-B-2 had significantly higher root-tip numbers (∼48%) per plant than 'BarNir' under both treatments. These results suggest that the introgression of 7AS QTL from wild emmer wheat induced a deeper root system under progressive water stress, which may enhance abiotic stress resistance and productivity of domesticated wheat.

Impact of treated wastewater on growth, respiration and hydraulic conductivity of citrus root systems in light and heavy soils.

Roots interact with soil properties and irrigation water quality leading to changes in root growth, structure and function. We studied these interactions in an orchard and in lysimeters with clay and sandy loam soils. Minirhizotron imaging and manual sampling showed that root growth was three times lower in the clay relative to sandy loam soil. Treated wastewater (TWW) led to a large reduction in root growth with clay (45-55%) but not with sandy loam soil (<20%). Treated wastewater increased salt uptake, membrane leakage and proline content, and decreased root viability, carbohydrate content and osmotic potentials in the fine roots, especially in clay. These results provide evidence that TWW challenges and damages the root system. The phenology and physiology of root orders were studied in lysimeters. Soil type influenced diameter, specific root area, tissue density and cortex area similarly in all root orders, while TWW influenced these only in clay soil. Respiration rates were similar in both soils, and root hydraulic conductivity was severely reduced in clay soil. Treated wastewater increased respiration rate and reduced hydraulic conductivity of all root orders in clay but only of the lower root orders in sandy loam soil. Loss of hydraulic conductivity increased with root order in clay and clay irrigated with TWW. Respiration and hydraulic properties of all root orders were significantly affected by sodium-amended TWW in sandy loam soil. These changes in root order morphology, anatomy, physiology and hydraulic properties indicate rapid and major modifications of root systems in response to differences in soil type and water quality.

Lower leaf gas-exchange and higher photorespiration of treated wastewater irrigated Citrus trees is modulated by soil type and climate.

Water quality, soil and climate can interact to limit photosynthesis and to increase photooxidative damage in sensitive plants. This research compared diffusive and non-diffusive limitations to photosynthesis as well as photorespiration of leaves of grapefruit trees in heavy clay and sandy soils having a previous history of treated wastewater (TWW) irrigation for >10 years, with different water qualities [fresh water (FW) vs TWW and sodium amended treated wastewater (TWW + Na)] in two arid climates (summer vs winter) and in orchard and lysimeter experiments. TWW irrigation increased salts (Na(+) and Cl(-) ), membrane leakage, proline and soluble sugar content, and decreased osmotic potentials in leaves of all experiments. Reduced leaf growth and higher stomatal and non-stomatal (i.e. mesophyll) limitations were found in summer and on clay soil for TWW and TWW + Na treatments in comparison to winter, sandy soil and FW irrigation, respectively. Stomatal closure, lower chlorophyll content and altered Rubisco activity are probable causes of higher limitations. On the other hand, non-photochemical quenching, an alternative energy dissipation pathway, was only influenced by water quality, independent of soil type and season. Furthermore, light and CO2 response curves were investigated for other possible causes of higher non-stomatal limitation. A higher proportion of non-cyclic electrons were directed to the O2 dependent pathway, and a higher proportion of electrons were diverted to photorespiration in summer than in winter. In conclusion, both diffusive and non-diffusive limitations contribute to the lower photosynthetic performance of leaves following TWW irrigation, and the response depends on soil type and environmental factors.

Phenotypic plasticity and water flux rates of Citrus root orders under salinity.

Knowledge about the root system structure and the uptake efficiency of root orders is critical to understand the adaptive plasticity of plants towards salt stress. Thus, this study describes the phenological and physiological plasticity of Citrus volkameriana rootstocks under severe NaCl stress on the level of root orders. Phenotypic root traits known to influence uptake processes, for example frequency of root orders, specific root area, cortical thickness, and xylem traits, did not change homogeneously throughout the root system, but changes after 6 months under 90 mM NaCl stress were root order specific. Chloride accumulation significantly increased with decreasing root order, and the Cl(-) concentration in lower root orders exceeded those in leaves. Water flux densities of first-order roots decreased to <20% under salinity and did not recover after stress release. The water flux densities of higher root orders changed marginally under salinity and increased 2- to 6-fold in second and third root orders after short-term stress release. Changes in root order frequency, morphology, and anatomy indicate rapid and major modification of C. volkameriana root systems under salt stress. Reduced water uptake under salinity was related to changes of water flux densities among root orders and to reduced root surface areas. The importance of root orders for water uptake changed under salinity from root tips towards higher root orders. The root order-specific changes reflect differences in vulnerability (indicated by the salt accumulation) and ontogenetic status, and point to functional differences among root orders under high salinity.

A root is a root is a root? Water uptake rates of Citrus root orders.

Knowledge about the physiological function of root orders is scant. In this study, a system to monitor the water flux among root orders was developed using miniaturized chambers. Different root orders of 4-year-old Citrus volkameriana trees were analysed with respect to root morphology and water flux. The eight root orders showed a broad overlap in diameter, but differences in tissue densities and specific root area (SRA) were clearly distinguishable. Thirty per cent of the root branch biomass but 50% of the surface area (SA) was possessed by the first root order, while the fifth accounted for 5% of the SA (20% biomass). The root order was identified as a determinant of water flux. First-order roots showed a significantly higher rate of water uptake than the second and third root orders, whereas the fourth and fifth root orders showed water excess. The water excess suggested the occurrence of hydraulic redistribution (HR) as a result of differences in osmotic potentials. We suggest that plants may utilize hydraulic redistribution to prevent coarse root desiccation and/or to increase nutrient acquisition. Our study showed that the novel 'miniature depletion chamber' method enabled direct measurement of water fluxes per root order and can be a major tool for future studies on root order traits.