A5022147172- Plant nutrient uptake and metabolism
- Rice Cultivation and Yield Improvement
- Plant Molecular Biology Research
- Crop Yield and Soil Fertility
- Soil Carbon and Nitrogen Dynamics
- Legume Nitrogen Fixing Symbiosis
- Agriculture, Soil, Plant Science
- Plant Micronutrient Interactions and Effects
- Bioenergy crop production and management
- Tree Root and Stability Studies
- Genetic Mapping and Diversity in Plants and Animals
- Irrigation Practices and Water Management
- Soil and Land Suitability Analysis
- Plant Growth and Agriculture Techniques
- Wheat and Barley Genetics and Pathology
- Plant Genetic and Mutation Studies
- Smart Agriculture and AI
- Solar and Space Plasma Dynamics
- Plant Water Relations and Carbon Dynamics
- Remote Sensing in Agriculture
- Remote Sensing and LiDAR Applications
- Ion-surface interactions and analysis
- Genetics and Plant Breeding
- Plant tissue culture and regeneration
- Magnetic Properties of Alloys
Donald Danforth Plant Science Center
2021-2025
Noble Research Institute
2019-2022
University of Nottingham
2015-2022
Noble
2019-2021
University of Sheffield
1998-2017
Royal Brisbane and Women's Hospital
2009
University of California, Berkeley
1955
Abstract In plant phenotyping, it has become important to be able measure many features on large image sets in order aid genetic discovery. The size of the datasets, now often captured robotically, precludes manual inspection, hence motivation for finding a fully automated approach. Deep learning is an emerging field that promises unparalleled results data analysis problems. Building artificial neural networks, deep approaches have more hidden layers network, and greater discriminative...
Seedling root traits of wheat (Triticum aestivum L.) have been shown to be important for efficient establishment and linked mature plant such as height yield. A phenotyping pipeline, consisting a germination paper-based screen combined with image segmentation analysis software, was developed used characterize seedling in 94 doubled haploid progeny derived from cross between the winter cultivars Rialto Savannah. Field experiments were conducted measure height, grain yield, nitrogen (N) uptake...
Summary O pen S im R oot is an open‐source, functional–structural plant model and mathematical description of root growth function. We describe its functionality to broaden the benefits modeling science community. extended version SimRoot , established simulate system architecture, nutrient acquisition growth. has a plugin, modular infrastructure, coupling single crop stands soil water transport models. It estimates value traits for in environments species. The flexible design allows...
Root crown phenotyping measures the top portion of crop root systems and can be used for marker-assisted breeding, genetic mapping, understanding how roots influence soil resource acquisition. Several imaging protocols image analysis programs exist, but they are not optimized high-throughput, repeatable, robust phenotyping. The RhizoVision Crown platform integrates an unit, capture software, software that reliable extraction measurements from large numbers crowns. hardware utilizes a...
Abstract Roots are central to the function of natural and agricultural ecosystems by driving plant acquisition soil resources influencing carbon cycle. Root characteristics like length, diameter, volume critical measure understand functions. RhizoVision Explorer is an open-source software designed enable researchers interested in roots providing easy-to-use interface, fast image processing, reliable measurements. The default broken mode intended for sampled from pots or cores, washed,...
We address the complex problem of reliably segmenting root structure from soil in X-ray Computed Tomography (CT) images. utilise a deep learning approach, and propose state-of-the-art multi-resolution architecture based on encoder-decoders. While previous work encoder-decoders implies use multiple resolutions simply by downsampling upsampling images, we make this process explicit, with branches network tasked separately obtaining local high-resolution segmentation, wider low-resolution...
The root economics space is a useful framework for plant ecology but rarely considered crop ecophysiology. In order to understand trait integration in winter wheat, we combined functional phenomics with economic theory, utilizing genetic variation, high-throughput phenotyping, and multivariate analyses. We phenotyped diversity panel of 276 genotypes respiration architectural traits using novel method CO
Phenotyping methods for seed morphology are mostly limited to two-dimensional imaging or manual measures. In this study, we present a novel phenotyping approach utilizing lab-based X-ray microscopy (XRM) characterize 3D morphology, internal structures, and cellular analysis from single scan. Seeds of pennycress (Thlaspi arvense L.) an oilseed cover crop, were scanned segmented using machine learning model. Seed morphological coat thickness map was applied compare volumes four genotypes....
Pennycress (Thlaspi arvense) is under development to be grown as a winter annual intermediate oil seed bioenergy crop in the Midwest during typical fallow periods. Crucial work remains domesticate and optimize pennycress for incorporation into cropping systems increasing resilience rising temperatures. We found that increased planting density reduces biomass swiftens time flowering maturity, which are features associated with shade avoidance responses. In controlled conditions, we elongates...
Pennycress ( Thlaspi arvense ) is a promising intermediate oilseed crop, producing oil suitable for conversion to biofuels—including aviation fuels. While domestication efforts are ongoing, deeper understanding of the genetic architecture traits crucial informing future breeding efforts. Here, we conducted largest genomic and phenotypic survey pennycress date, analyzing 739 accessions collected across four continents. Leveraging whole-genome sequencing field-collected phenotypes,...
Abstract Deep learning is an emerging field that promises unparalleled results on many data analysis problems. We show the success offered by such techniques when applied to challenging problem of image-based plant phenotyping, and demonstrate state-of-the-art for root shoot feature identification localisation. predict a paradigm shift in phenotyping thanks deep approaches.
Abstract Nutrient uptake is critical for crop growth and determined by root foraging in soil. Growth branching of roots lead to effective placement acquire nutrients, but relatively little known about absorption nutrients at the surface from soil solution. This knowledge gap could be alleviated understanding sources genetic variation short-term nutrient on a length basis. A modular platform called RhizoFlux was developed high-throughput phenotyping multiple ion-uptake rates maize (Zea mays...
Abstract The spatial arrangement of the root system, termed system architecture , is important for resource acquisition as it directly affects soil zone explored. Methods phenotyping roots are mostly destructive, which prevents analysis over time they grow. Here, we used X‐ray microcomputed tomography (μCT) to non‐invasively characterize wheat ( Triticum aestivum L.) seedling development across under high and low nitrate nutrition. Roots were imaged multiple times with 3D models co‐aligned...
The root system of a plant provides vital functions including resource uptake, storage, and anchorage in soil. uptake macro-nutrients like nitrogen (N), phosphorus (P), potassium (K), sulphur (S) from the soil is critical for growth development. Small signaling peptide (SSP) hormones are best known as potent regulators development with few also to have specialized roles macronutrient utilization. Here we describe high throughput phenotyping platform testing SSP effects on multiple nutrients....
Abstract Genetic analyses of plant root systems require large datasets extracted architectural traits. To quantify such traits from images systems, researchers often have to choose between automated tools (that are prone error and extract only a limited number traits) or semi-automated ones highly time consuming). We trained Random Forest algorithm infer automatically image descriptors. The training was performed on subset the dataset, then applied its entirety. This strategy allowed us (i)...
The response of plant growth and development to nutrient water availability is an important adaptation for abiotic stress tolerance. Roots need intercept both passing nutrients while foraging into new soil layers further resources. Substantial amounts nitrate can be lost in the field when leaching groundwater, yet very little known about how deep rooting affects this process. Here, we phenotyped root system traits 15N capture across 1.5 m vertical profiles solid media using tall mesocosms...
Iron–sulfur (Fe–S) clusters are inorganic cofactors that present in all kingdoms of life as part a large number proteins involved several cellular processes, including DNA replication and metabolism. In this work, we demonstrate an additional role for two Fe–S cluster genes biotic stress responses plants. Eleven genes, the NITROGEN FIXATION S-LIKE1 (NFS1) its interactor FRATAXIN (FH), when silenced Nicotiana benthamiana, compromised nonhost resistance to Pseudomonas syringae pv. tomato T1....
Abstract Background and aims Cover crops have the potential to aid in adapting agricultural systems climate change impacts through their ecosystem services, such as preventing soil erosion, remediating structure, storing carbon belowground. Though roots are integral these processes, there is a lack of cover crop root trait data. This study characterize rooting behavior several commercially available assess how differences system architecture potentially impact selection for services. Methods...
The root system architecture (RSA) of a crop has profound effect on the uptake nutrients and consequently potential yield. However, little is known about genetic basis RSA resource adaptive responses in wheat (Triticum aestivum L.). Here, high-throughput germination paper-based plant phenotyping was used to identify seedling traits doubled haploid mapping population, Savannah×Rialto. Significant genotypic nitrate-N treatment variation found across population for with distinct trait grouping...