scholarly journals Digital imaging to evaluate root system architectural changes associated with soil biotic factors

2018 ◽  
Author(s):  
Chakradhar Mattupalli ◽  
Anand Seethepalli ◽  
Larry M York ◽  
Carolyn A Young
Keyword(s):  
Root System ◽  
Low Cost ◽  
Root System Architecture ◽  
Line Transect ◽  
Biotic Factors ◽  
Forage Crop ◽  
Growing Seasons ◽  
Segmented Images ◽  
Crown Roots ◽  
Alfalfa Root

Root system architecture (RSA) is critical for plant growth, which is influenced by several edaphic, environmental, genetic and biotic factors including beneficial and pathogenic microbes. Studying root architecture and the dynamic changes that occur during a plant's lifespan, especially for perennial crops growing over multiple growing seasons, is still a challenge because of the nature of their growing environment in soil. We describe the utility of an imaging platform called RhizoVision Crown to study RSA of alfalfa, a perennial forage crop affected by Phymatotrichopsis Root Rot (PRR) disease. Phymatotrichopsis omnivora is the causal agent of PRR disease that reduces alfalfa stand longevity. During the lifetime of the stand, PRR disease rings enlarge and the field can be categorized into three zones based upon plant status: asymptomatic, disease front and survivor. To study root architectural changes associated with PRR, a four-year old 25.6-hectare alfalfa stand infested with PRR was selected at the Red River Farm, Burneyville, OK during October 2017. Line transect sampling was conducted from four actively growing PRR disease rings. At each disease ring, six line transects were positioned spanning 15 m on either side of the disease front with one alfalfa root sampled at every 3 m interval. Each alfalfa root was imaged with the RhizoVision Crown platform using a backlight and a high-resolution monochrome CMOS camera enabling preservation of the natural root architectural integrity. The platform's image analysis software, RhizoVision Analyzer, automatically segmented images, skeletonized, and extracted a suite of features. Data indicated that the survivor plants compensated for damage or loss to the taproot through the development of more lateral and crown roots, and that a suite of multivariate features could be used to automatically classify roots as from survivor or asymptomatic zones. Root growth is a dynamic process adapting to ever changing interactions among various phytobiome components, by utilizing a low-cost, efficient and high-throughput Rhizo-Vision Crown platform we showed quantification of these changes occurring in a mature perennial forage crop.

scholarly journals Digital Imaging to Evaluate Root System Architectural Changes Associated with Soil Biotic Factors

2019 ◽  
Vol 3 (2) ◽  
pp. 102-111 ◽  
Author(s):  
Chakradhar Mattupalli ◽  
Anand Seethepalli ◽  
Larry M. York ◽  
Carolyn A. Young
Keyword(s):  
Root System ◽  
System Architecture ◽  
Low Cost ◽  
Root System Architecture ◽  
Line Transect ◽  
Biotic Factors ◽  
Forage Crop ◽  
System Integrity ◽  
Crown Roots ◽  
Alfalfa Root

Root system architecture is critical for plant growth, which is influenced by several edaphic, environmental, genetic, and biotic factors including beneficial and pathogenic microbes. Studying root system architecture and the dynamic changes that occur during a plant’s lifespan, especially for perennial crops growing over multiple growing seasons, is still a challenge because of the nature of their growing environment. We describe the utility of an imaging platform called RhizoVision Crown to study root system architecture of alfalfa, a perennial forage crop threatened by Phymatotrichopsis root rot (PRR) disease. Phymatotrichopsis omnivora is the causal agent of PRR disease that reduces alfalfa stand longevity. During the lifetime of the stand, PRR disease rings enlarge and the field can be categorized into three zones based upon plant status: asymptomatic, disease front and survivor. To study root system architectural changes associated with PRR, a 4-year-old 25.6-ha alfalfa stand infested with PRR was selected at the Red River Farm, Burneyville, OK during October 2017. Line transect sampling was conducted from four actively growing PRR disease rings. At each disease ring, six line transects were positioned spanning 15 m on either side of the disease front with one alfalfa root crown sampled at every 3 m interval. Each alfalfa root crown was imaged with the RhizoVision Crown platform using a backlight and a high-resolution monochrome CMOS camera enabling preservation of the natural root system integrity. The platform’s image analysis software, RhizoVision Analyzer, automatically segmented images, skeletonized, and extracted a suite of features. Data indicated that the survivor plants compensated for damage or loss to the taproot through the development of more lateral and crown roots, and that a suite of multivariate features could be used to automatically classify roots as from survivor or asymptomatic zones. Root growth is a dynamic process adapting to ever changing interactions among various phytobiome components. By utilizing the low-cost, efficient, and high-throughput RhizoVision Crown platform, we quantified these changes in a mature perennial forage crop.

scholarly journals RSAtrace3D: robust vectorization software for measuring monocot root system architecture

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Shota Teramoto ◽  
Takanari Tanabata ◽  
Yusaku Uga
Keyword(s):  
Root System ◽  
System Architecture ◽  
Three Dimensional ◽  
Root System Architecture ◽  
Ct Images ◽  
X Ray ◽  
Single Root ◽  
Base Points ◽  
Using Data ◽  
Crown Roots

Abstract Background The root distribution in the soil is one of the elements that comprise the root system architecture (RSA). In monocots, RSA comprises radicle and crown roots, each of which can be basically represented by a single curve with lateral root branches or approximated using a polyline. Moreover, RSA vectorization (polyline conversion) is useful for RSA phenotyping. However, a robust software that can enable RSA vectorization while using noisy three-dimensional (3D) volumes is unavailable. Results We developed RSAtrace3D, which is a robust 3D RSA vectorization software for monocot RSA phenotyping. It manages the single root (radicle or crown root) as a polyline (a vector), and the set of the polylines represents the entire RSA. RSAtrace3D vectorizes root segments between the two ends of a single root. By utilizing several base points on the root, RSAtrace3D suits noisy images if it is difficult to vectorize it using only two end nodes of the root. Additionally, by employing a simple tracking algorithm that uses the center of gravity (COG) of the root voxels to determine the tracking direction, RSAtrace3D efficiently vectorizes the roots. Thus, RSAtrace3D represents the single root shape more precisely than straight lines or spline curves. As a case study, rice (Oryza sativa) RSA was vectorized from X-ray computed tomography (CT) images, and RSA traits were calculated. In addition, varietal differences in RSA traits were observed. The vector data were 32,000 times more compact than raw X-ray CT images. Therefore, this makes it easier to share data and perform re-analyses. For example, using data from previously conducted studies. For monocot plants, the vectorization and phenotyping algorithm are extendable and suitable for numerous applications. Conclusions RSAtrace3D is an RSA vectorization software for 3D RSA phenotyping for monocots. Owing to the high expandability of the RSA vectorization and phenotyping algorithm, RSAtrace3D can be applied not only to rice in X-ray CT images but also to other monocots in various 3D images. Since this software is written in Python language, it can be easily modified and will be extensively applied by researchers in this field.

scholarly journals Control of root system architecture by phytohormones and environmental signals in rice

2020 ◽  
Vol 67 (1-2) ◽  
pp. 98-109
Author(s):  
Chen Lin ◽  
Margret Sauter
Keyword(s):  
Root System ◽  
System Architecture ◽  
Crop Production ◽  
Molecular Mechanisms ◽  
Extreme Environments ◽  
Root System Architecture ◽  
Environmental Signals ◽  
Production Water ◽  
Environmental Extremes ◽  
Crown Roots

Drought and flooding are environmental extremes and major threats to crop production. Water uptake is achieved by plant roots which have to explore new soil spaces to alleviate water deficit during drought or to cope with water excess during flooding. Adaptation of the root system architecture helps plants cope with such extreme conditions and is crucial for plant health and survival. While for dicot plants the well studied model plant Arabidopsis thaliana has provided insight into the genetic and molecular regulation of the root system, less information is available for monocot species, which include the agronomically important cereal crops. Rice (Oryza sativa L.) is a semi-aquatic monocot plant that develops strong tolerance to flooding. Flooding tolerance of rice is closely linked to its adaptive root system. The functional root system of rice is mainly composed of crown roots and is shifted to nodal adventitious roots during flooding which allows rice to maintain oxygen supply to the roots and to survive longer periods of partial submergence as compared with other crops. Likewise, a number of drought-tolerance traits of rice are the result of an altered root system architecture. Hence, the structure of the root system adapts to, both, flooding and drought. Understanding the regulatory mechanisms that control root system adaptation to extreme environments is a key task for scientists to accelerate the breeding efforts for stress-tolerant crops. This review summarizes recently identified genes and molecular mechanisms that regulate root system architecture in rice in response to drought and flooding.

scholarly journals Transcriptome diversity among rice root types during asymbiosis and interaction with arbuscular mycorrhizal fungi

2015 ◽  
Vol 112 (21) ◽  
pp. 6754-6759 ◽  
Author(s):  
Caroline Gutjahr ◽  
Ruairidh J. H. Sawers ◽  
Guillaume Marti ◽  
Liliana Andrés-Hernández ◽  
Shu-Yi Yang ◽  
...  
Keyword(s):  
Root System ◽  
System Architecture ◽  
Arbuscular Mycorrhizal ◽  
Root Systems ◽  
Root System Architecture ◽  
Adaptive Plasticity ◽  
Functional Relationships ◽  
Am Symbiosis ◽  
Crown Roots ◽  
Root Types

Root systems consist of different root types (RTs) with distinct developmental and functional characteristics. RTs may be individually reprogrammed in response to their microenvironment to maximize adaptive plasticity. Molecular understanding of such specific remodeling—although crucial for crop improvement—is limited. Here, RT-specific transcriptomes of adult rice crown, large and fine lateral roots were assessed, revealing molecular evidence for functional diversity among individual RTs. Of the three rice RTs, crown roots displayed a significant enrichment of transcripts associated with phytohormones and secondary cell wall (SCW) metabolism, whereas lateral RTs showed a greater accumulation of transcripts related to mineral transport. In nature, arbuscular mycorrhizal (AM) symbiosis represents the default state of most root systems and is known to modify root system architecture. Rice RTs become heterogeneously colonized by AM fungi, with large laterals preferentially entering into the association. However, RT-specific transcriptional responses to AM symbiosis were quantitatively most pronounced for crown roots despite their modest physical engagement in the interaction. Furthermore, colonized crown roots adopted an expression profile more related to mycorrhizal large lateral than to noncolonized crown roots, suggesting a fundamental reprogramming of crown root character. Among these changes, a significant reduction in SCW transcripts was observed that was correlated with an alteration of SCW composition as determined by mass spectrometry. The combined change in SCW, hormone- and transport-related transcript profiles across the RTs indicates a previously overlooked switch of functional relationships among RTs during AM symbiosis, with a potential impact on root system architecture and functioning.

scholarly journals Comprehensive Genome-Wide Association Analysis Reveals the Genetic Basis of Root System Architecture in Soybean

2020 ◽  
Vol 11 ◽  
Author(s):  
Waldiodio Seck ◽  
Davoud Torkamaneh ◽  
François Belzile
Keyword(s):  
Root System ◽  
System Architecture ◽  
Phenotypic Variation ◽  
Genetic Basis ◽  
Genome Wide Association Study ◽  
Primary Root ◽  
Root System Architecture ◽  
Genome Wide Association ◽  
Nucleotide Polymorphisms ◽  
Genome Wide

Increasing the understanding genetic basis of the variability in root system architecture (RSA) is essential to improve resource-use efficiency in agriculture systems and to develop climate-resilient crop cultivars. Roots being underground, their direct observation and detailed characterization are challenging. Here, were characterized twelve RSA-related traits in a panel of 137 early maturing soybean lines (Canadian soybean core collection) using rhizoboxes and two-dimensional imaging. Significant phenotypic variation (P < 0.001) was observed among these lines for different RSA-related traits. This panel was genotyped with 2.18 million genome-wide single-nucleotide polymorphisms (SNPs) using a combination of genotyping-by-sequencing and whole-genome sequencing. A total of 10 quantitative trait locus (QTL) regions were detected for root total length and primary root diameter through a comprehensive genome-wide association study. These QTL regions explained from 15 to 25% of the phenotypic variation and contained two putative candidate genes with homology to genes previously reported to play a role in RSA in other species. These genes can serve to accelerate future efforts aimed to dissect genetic architecture of RSA and breed more resilient varieties.

scholarly journals Genotype-Dependent Tipburn Severity During Lettuce Hydroponic Culture Is Associated with Altered Nutrient Leaf Content

Agronomy ◽  
2021 ◽  
Vol 11 (4) ◽  
pp. 616
Author(s):  
Virginia Birlanga ◽  
José Ramón Acosta-Motos ◽  
José Manuel Pérez-Pérez
Keyword(s):  
Low Cost ◽  
Nutrient Content ◽  
Leafy Vegetables ◽  
Production Methods ◽  
Growing Seasons ◽  
Lactuca Sativa L ◽  
Hydroponic Cultivation ◽  
Highly Correlated ◽  
Nutrient Solutions ◽  
Nutrient Traits

Cultivated lettuce (Lactuca sativa L.) is one of the most important leafy vegetables in the world, and most of the production is concentrated in the Mediterranean Basin. Hydroponics has been successfully utilized for lettuce cultivation, which could contribute to the diversification of production methods and the reduction of water consumption and excessive fertilization. We devised a low-cost procedure for closed hydroponic cultivation and easy phenotyping of root and shoot attributes of lettuce. We studied 12 lettuce genotypes of the crisphead and oak-leaf subtypes, which differed on their tipburn resistance, for three growing seasons (Fall, Winter, and Spring). We found interesting genotype × environment (G × E) interactions for some of the studied traits during early growth. By analyzing tipburn incidence and leaf nutrient content, we were able to identify a number of nutrient traits that were highly correlated with cultivar- and genotype-dependent tipburn. Our experimental setup will allow evaluating different lettuce genotypes in defined nutrient solutions to select for tipburn-tolerant and highly productive genotypes that are suitable for hydroponics.

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