scholarly journals Phenotyping roots in darkness: disturbance-free root imaging with near infrared illumination

2018 ◽  
Vol 45 (4) ◽  
pp. 400 ◽  
Author(s):  
Rongli Shi ◽  
Astrid Junker ◽  
Christiane Seiler ◽  
Thomas Altmann
Keyword(s):  
Root System ◽  
White Light ◽  
Near Infrared ◽  
System Analysis ◽  
Dry Weight ◽  
Light Filter ◽  
Plant Performance ◽  
Plant Phenotyping ◽  
Transmitted Radiation ◽  
Maize Roots

Root systems architecture (RSA) and size properties are essential determinants of plant performance and need to be assessed in high-throughput plant phenotyping platforms. Thus, we tested a concept that involves near-infrared (NIR) imaging of roots growing along surfaces of transparent culture vessels using special long pass filters to block their exposure to visible light. Two setups were used to monitor growth of Arabidopsis, rapeseed, barley and maize roots upon exposure to white light, filter-transmitted radiation or darkness: root growth direction was analysed (1) through short-term cultivation on agar plates, and (2) using soil-filled transparent pots to monitor long-term responses. White light-triggered phototropic responses were detected for Arabidopsis in setup 1, and for rapeseed, barley and maize roots in setups 1 and 2, whereas light effects could be avoided by use of the NIR filter thus confirming its suitability to mimic darkness. NIR image-derived ‘root volume’ values correlated well with root dry weight. The root system fractions visible at the different pot sides and in different zones revealed species- and genotype-dependent variation of spatial root distribution and other RSA traits. Following this validated concept, root imaging setups may be integrated into shoot phenotyping facilities in order to enable root system analysis in the context of whole-plant performance investigations.

scholarly journals Assessing plant performance in the Enviratron

Plant Methods ◽  
2019 ◽  
Vol 15 (1) ◽  
Author(s):  
Yin Bao ◽  
Scott Zarecor ◽  
Dylan Shah ◽  
Taylor Tuel ◽  
Darwin A. Campbell ◽  
...  
Keyword(s):  
Plant Growth ◽  
Environmental Conditions ◽  
Near Infrared ◽  
Growth Parameters ◽  
Hand Movement ◽  
Pulse Amplitude ◽  
Plant Performance ◽  
Robotic Arm ◽  
Plant Phenotyping ◽  
The Impact

Abstract Background Assessing the impact of the environment on plant performance requires growing plants under controlled environmental conditions. Plant phenotypes are a product of genotype × environment (G × E), and the Enviratron at Iowa State University is a facility for testing under controlled conditions the effects of the environment on plant growth and development. Crop plants (including maize) can be grown to maturity in the Enviratron, and the performance of plants under different environmental conditions can be monitored 24 h per day, 7 days per week throughout the growth cycle. Results The Enviratron is an array of custom-designed plant growth chambers that simulate different environmental conditions coupled with precise sensor-based phenotypic measurements carried out by a robotic rover. The rover has workflow instructions to periodically visit plants growing in the different chambers where it measures various growth and physiological parameters. The rover consists of an unmanned ground vehicle, an industrial robotic arm and an array of sensors including RGB, visible and near infrared (VNIR) hyperspectral, thermal, and time-of-flight (ToF) cameras, laser profilometer and pulse-amplitude modulated (PAM) fluorometer. The sensors are autonomously positioned for detecting leaves in the plant canopy, collecting various physiological measurements based on computer vision algorithms and planning motion via “eye-in-hand” movement control of the robotic arm. In particular, the automated leaf probing function that allows the precise placement of sensor probes on leaf surfaces presents a unique advantage of the Enviratron system over other types of plant phenotyping systems. Conclusions The Enviratron offers a new level of control over plant growth parameters and optimizes positioning and timing of sensor-based phenotypic measurements. Plant phenotypes in the Enviratron are measured in situ—in that the rover takes sensors to the plants rather than moving plants to the sensors.

scholarly journals Genome-wide association analysis unveils novel QTLs for seminal root system architecture traits in Ethiopian durum wheat

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Admas Alemu ◽  
Tileye Feyissa ◽  
Marco Maccaferri ◽  
Giuseppe Sciara ◽  
Roberto Tuberosa ◽  
...  
Keyword(s):  
Durum Wheat ◽  
Root System ◽  
System Architecture ◽  
Root Length ◽  
Dry Weight ◽  
Root System Architecture ◽  
High Density ◽  
Soil Conditions ◽  
Root Dry Weight ◽  
Seminal Roots

Abstract Background Genetic improvement of root system architecture is essential to improve water and nutrient use efficiency of crops or to boost their productivity under stress or non-optimal soil conditions. One hundred ninety-two Ethiopian durum wheat accessions comprising 167 historical landraces and 25 modern cultivars were assembled for GWAS analysis to identify QTLs for root system architecture (RSA) traits and genotyped with a high-density 90 K wheat SNP array by Illumina. Results Using a non-roll, paper-based root phenotyping platform, a total of 2880 seedlings and 14,947 seminal roots were measured at the three-leaf stage to collect data for total root length (TRL), total root number (TRN), root growth angle (RGA), average root length (ARL), bulk root dry weight (RDW), individual root dry weight (IRW), bulk shoot dry weight (SDW), presence of six seminal roots per seedling (RT6) and root shoot ratio (RSR). Analysis of variance revealed highly significant differences between accessions for all RSA traits. Four major (− log10P ≥ 4) and 34 nominal (− log10P ≥ 3) QTLs were identified and grouped in 16 RSA QTL clusters across chromosomes. A higher number of significant RSA QTL were identified on chromosome 4B particularly for root vigor traits (root length, number and/or weight). Conclusions After projecting the identified QTLs on to a high-density tetraploid consensus map along with previously reported RSA QTL in both durum and bread wheat, fourteen nominal QTLs were found to be novel and could potentially be used to tailor RSA in elite lines. The major RGA QTLs on chromosome 6AL detected in the current study and reported in previous studies is a good candidate for cloning the causative underlining sequence and identifying the beneficial haplotypes able to positively affect yield under water- or nutrient-limited conditions.

scholarly journals Towards white-light generation through upconversion of low-power near-infrared photons

RSC Advances ◽  
2017 ◽  
Vol 7 (26) ◽  
pp. 16126-16130 ◽  
Author(s):  
Oleg P. Dimitriev ◽  
Julia L. Bricks ◽  
Anna L. Smirnova ◽  
Yuri L. Slominskii
Keyword(s):  
Low Power ◽  
Infrared Absorption ◽  
White Light ◽  
Near Infrared ◽  
Dye Molecules ◽  
White Light Generation ◽  
Light Generation

A broadband upconverted emission combined with a broadband infrared absorption takes place in films composed of the same infrared dye molecules.

Mechanisms underlying root system architecture adaptation to low phosphate environment

2015 ◽  
Author(s):  
Sigal Savaldi-Goldstein ◽  
Siobhan M. Brady
Keyword(s):  
Root System ◽  
System Architecture ◽  
Wild Species ◽  
Root Elongation ◽  
Steroid Hormone ◽  
Root System Architecture ◽  
Iron Accumulation ◽  
Plant Performance ◽  
P Availability ◽  
New Genes

In order to advance our understanding towards potential biotechnology improvement of plant performance, we studied root responses to limited P in two different plants, Arabidopsis and tomato. Arabidopsis is among the most studied model plants that allows rapid application of molecular and developmental experiments while tomato is an important crop, with application in agriculture. Using Arabidopsis we found that steroid hormones modulate the extent of root elongation in response to limited P, by controlling the accumulation of iron in the root. We also found that the availability of P and iron control the activity of the steroid hormone in the root. Finally, we revealed the genes involved in this nutrient-hormone interaction. Hence, the ferroxidase LPR1 that promotes iron accumulation in response to low P is repressed by the transcription factor BES1/BZR1. Low P inhibits the steroid hormone pathway by enhancing the accumulation of BKI1. High levels of BKI1 inhibit the activity of the steroid hormone receptor at the cell surface and iron accumulation increases inside the root, resulting in a slow growth. Together, the extent of root elongation depends on interactions between an internal cue (steroid hormone) and cues derived from the availability of P and iron in the environment. Using tomato, we found that the response of two cultivated tomato varieties (M82 and New Yorker) to limited P is distinct from that of the wild species, Solanumpennellii. This is implicated at both the levels of root development and whole plant physiology. Specifically, while the root system architecture of cultivated tomato is modulated by limited P availability, that of the wild type species remained unaffected. The wild species appears to be always behaving as if it is always in phosphate deprived conditions, despite sufficient levels of phosphate. Hyper-accumulation of metals appears to mediate this response. Together, this knowledge will be used to isolate new genes controlling plant adaptation to limited P environment. 

scholarly journals Horticultural Characteristics and Susceptibility of Table Beet Cultivars to Cercospora Leaf Spot in New York

2017 ◽  
Vol 27 (4) ◽  
pp. 530-538 ◽  
Author(s):  
Sarah J. Pethybridge ◽  
Niloofar Vaghefi ◽  
Julie R. Kikkert
Keyword(s):  
New York ◽  
Leaf Spot ◽  
Field Trial ◽  
Near Infrared ◽  
Value Added ◽  
Dry Weight ◽  
Disease Assessment ◽  
Canopy Reflectance ◽  
Cercospora Leaf Spot ◽  
Disease Progress

Table beet (Beta vulgaris ssp. vulgaris) production in New York is increasing for direct sale, use in value-added products, or processing. One of the most important diseases affecting table beet is cercospora leaf spot (CLS) caused by the fungus Cercospora beticola. CLS causes lesions on leaves that coalesce and leads to premature defoliation. The presence of CLS may cause buyer rejection at fresh markets. Defoliation from CLS may also result in crop loss because of the inability to harvest with top-pulling machinery. The susceptibility of popular table beet cultivars (Boldor, Detroit, Falcon, Merlin, Rhonda, Ruby Queen, and Touchstone Gold) to CLS was tested using C. beticola isolates representative of the New York population. Two trials were conducted by inoculating 6-week-old plants in the misting chamber. A small-plot replicated field trial was also conducted to examine horticultural characteristics of the cultivars. In the misting chamber trials, disease progress measured by the area under the disease progress stairs (AUDPS) was not significantly different between the red cultivars, Detroit and Ruby Queen, and was significantly higher in ‘Boldor’ than the other yellow cultivar Touchstone Gold. In the field trial, the number of CLS lesions per leaf at the final disease assessment and AUDPS were significantly lower in cultivar Ruby Queen than others and not significantly different between the yellow cultivars. The dry weight of roots was not significantly different among cultivars at first harvest (77 days after planting). At 112 days after planting, the dry weight of roots was significantly higher in cultivar Detroit than Rhonda and Boldor. Leaf blade length and the length:width ratio were cultivar-dependent, which may facilitate selection for specific fresh markets. Significant associations between canopy reflectance in the near infrared (IR) (830 nm), dry weight of foliage, and number of CLS lesions per leaf suggested that this technique may have utility for remote assessment of these variables in table beet research. Implications of these findings for the management of CLS in table beet are discussed.

scholarly journals Pemanfaatan FMA dan Tanaman Inang untuk Meningkatkan Pertumbuhan Bibit Cendana (Santalum album Linn.)

2019 ◽  
Vol 9 (3) ◽  
pp. 151-159
Author(s):  
Magdalena Sunarti Pareira ◽  
Irdika Mansur ◽  
Dewi Wulandari
Keyword(s):  
Host Plant ◽  
Root System ◽  
Quality Index ◽  
Host Plants ◽  
Root Colonization ◽  
Seed Quality ◽  
Dry Weight ◽  
Santalum Album ◽  
Capsicum Annum ◽  
Root Buds

The sandalwood tree (Santalum album Linn.) is an important tree species as well as a primadonna for the people of East Nusa Tenggara (NTT). It has high economic value for its aromatic wood and essential oil content that have a very distinctive aroma used to make various products such as handicrafts, woodcarvings, incense, and oil for the perfume and cosmetics industry. Sandalwood is a semi parasite plant that part of its life phase requires a host plant to get the nutrients and water. There are many types of host plants that have been used, among others, Casuarina equisetifolia, Acacia mangium, Terminalia microcarpa, Sesbania grandiflora, Alternanthera sp and Capsicum annum. In this research will be tested to try sandalwood planted with Cymbopogon nardus host plants, in terms of economics can provide benefits.Arbuscular mycorrhizal fungi (AMF) is a group of fungi from glomeromycota phylum that can symbiosis mutualism with root system of high level plant. The working principle of the mycorrhiza is to infect the root system of the host plant, producing intensive hyphae tissue so that the plant containing mycorrhiza will be able to increase the capacity in nutrient uptake. The utilization of host plants Alternanthera sp, Capsicum annum, and its application with AMF is the best solution to overcome the problem of developing sandalwood in TTU on the nursery. The purpose of this study was to analyze the effectiveness of AMF and utilization of the atsiri host plant to increase the growth of sandalwood seedlings in TTU. This study was designed using a complete random method (RAL) in split plot design. If the treatment has a significant effect then followed by Duncan Multiple Range Test (DMRT). Parameters observed were height (cm), number of leaf, diameter of sandalwood (mm), dry weight of root, seed quality index, ratio of root buds, and haustorium observation of Sandalwood, and also number of spore, root colonization and AMF dependency of Sandalwood.The results showed that the treatment of AMF with Capsicum annum host plant was 19.8 of high, number of leaf 18.9 on FMA treatment with host plant Capsicum annum, diameter of stem 2.24 mm on Alternanthera sp host treatments without AMF and 1.83 mm at AMF treatment with host plant Capsicum annum, dry weight of buds 2.00g on AMF treatment with Capsicum annum host plant, dry weight of roots AMF (M1) with alternanthera sp 0.70 g, root buds ratio of AMF with host plant alternanthera sp 4.05, seed quality index AMF with Alternanthera sp 4.16 and 82 % of root colonization on AMF with host plant Capsicum annum.Keywords: Santalum album Linn., AMF, host plant.

scholarly journals ROOT PHENOTYPING FROM X-RAY COMPUTED TOMOGRAPHY: SKELETON EXTRACTION

2021 ◽  
Vol XLIII-B4-2021 ◽  
pp. 417-422
Author(s):  
M. Herrero-Huerta ◽  
V. Meline ◽  
A. S. Iyer-Pascuzzi ◽  
A. M. Souza ◽  
M. R. Tuinstra ◽  
...  
Keyword(s):  
Computed Tomography ◽  
Root System ◽  
High Throughput ◽  
Skeletal Structure ◽  
Plant Phenotyping ◽  
Skeleton Extraction ◽  
X Ray ◽  
Digital Twin ◽  
Three Samples ◽  
Root Phenotyping

Abstract. Breakthrough imaging technologies are a potential solution to the plant phenotyping bottleneck in marker-assisted breeding and genetic mapping. X-Ray CT (computed tomography) technology is able to acquire the digital twin of root system architecture (RSA), however, advances in computational methods to digitally model spatial disposition of root system networks are urgently required.We extracted the root skeleton of the digital twin based on 3D data from X-ray CT, which is optimized for high-throughput and robust results. Significant root architectural traits such as number, length, growth angle, elongation rate and branching map can be easily extracted from the skeleton. The curve-skeleton extraction is computed based on a constrained Laplacian smoothing algorithm. This skeletal structure drives the registration procedure in temporal series. The experiment was carried out at the Ag Alumni Seed Phenotyping Facility (AAPF) at Purdue University in West Lafayette (IN, USA). Three samples of tomato root at 2 different times and three samples of corn root at 3 different times were scanned. The skeleton is able to accurately match the shape of the RSA based on a visual inspection.The results based on a visual inspection confirm the feasibility of the proposed methodology, providing scalability to a comprehensive analysis to high throughput root phenotyping.

scholarly journals Comparison of Root System Morphology of Cucurbit Rootstocks for Use in Watermelon Grafting

2018 ◽  
Vol 28 (5) ◽  
pp. 629-636 ◽  
Author(s):  
Matthew B. Bertucci ◽  
David H. Suchoff ◽  
Katherine M. Jennings ◽  
David W. Monks ◽  
Christopher C. Gunter ◽  
...  
Keyword(s):  
Root System ◽  
Surface Area ◽  
Root Length ◽  
Dry Weight ◽  
Root Systems ◽  
Root Surface ◽  
Root Diameter ◽  
Root Surface Area ◽  
Diameter Class ◽  
Main Effect

Grafting of watermelon (Citrullus lanatus) is an established production practice that provides resistance to soilborne diseases or tolerance to abiotic stresses. Watermelon may be grafted on several cucurbit species (interspecific grafting); however, little research exists to describe root systems of these diverse rootstocks. A greenhouse study was conducted to compare root system morphology of nine commercially available cucurbit rootstocks, representing four species: pumpkin (Cucurbita maxima), squash (Cucurbita pepo), bottle gourd (Lagenaria siceraria), and an interspecific hybrid squash (C. maxima × C. moschata). Rootstocks were grafted with a triploid watermelon scion (‘Exclamation’), and root systems were compared with nongrafted (NG) and self-grafted (SG) ‘Exclamation’. Plants were harvested destructively at 1, 2, and 3 weeks after transplant (WAT), and data were collected on scion dry weight, total root length (TRL), average root diameter, root surface area, root:shoot dry-weight ratio, root diameter class proportions, and specific root length. For all response variables, the main effect of rootstock and rootstock species was significant (P < 0.05). The main effect of harvest was significant (P < 0.05) for all response variables, with the exception of TRL proportion in diameter class 2. ‘Ferro’ rootstock produced the largest TRL and root surface area, with observed values 122% and 120% greater than the smallest root system (‘Exclamation’ SG), respectively. Among rootstock species, pumpkin produced the largest TRL and root surface area, with observed values 100% and 82% greater than those of watermelon, respectively. These results demonstrate that substantial differences exist during the initial 3 WAT in root system morphology of rootstocks and rootstock species available for watermelon grafting and that morphologic differences of root systems can be characterized using image analysis.

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