A Statistical Growth Property of Plant Root Architectures.
Ontology highlight
ABSTRACT:
SUBMITTER: Sultan S
PROVIDER: S-EPMC7706341 | biostudies-literature | 2020
REPOSITORIES: biostudies-literature
Publications
A Statistical Growth Property of Plant Root Architectures.
Sultan Sam S Snider Joseph J Conn Adam A Li Mao M Topp Christopher N CN Navlakha Saket S
Plant phenomics (Washington, D.C.) 20201108
Numerous types of biological branching networks, with varying shapes and sizes, are used to acquire and distribute resources. Here, we show that plant root and shoot architectures share a fundamental design property. We studied the spatial density function of plant architectures, which specifies the probability of finding a branch at each location in the 3-dimensional volume occupied by the plant. We analyzed 1645 root architectures from four species and discovered that the spatial density funct ...[more]
Similar Datasets
Project description:BACKGROUND:In recent years quantitative analysis of root growth has become increasingly important as a way to explore the influence of abiotic stress such as high temperature and drought on a plant's ability to take up water and nutrients. Segmentation and feature extraction of plant roots from images presents a significant computer vision challenge. Root images contain complicated structures, variations in size, background, occlusion, clutter and variation in lighting conditions. We present a new image analysis approach that provides fully automatic extraction of complex root system architectures from a range of plant species in varied imaging set-ups. Driven by modern deep-learning approaches, RootNav 2.0 replaces previously manual and semi-automatic feature extraction with an extremely deep multi-task convolutional neural network architecture. The network also locates seeds, first order and second order root tips to drive a search algorithm seeking optimal paths throughout the image, extracting accurate architectures without user interaction. RESULTS:We develop and train a novel deep network architecture to explicitly combine local pixel information with global scene information in order to accurately segment small root features across high-resolution images. The proposed method was evaluated on images of wheat (Triticum aestivum L.) from a seedling assay. Compared with semi-automatic analysis via the original RootNav tool, the proposed method demonstrated comparable accuracy, with a 10-fold increase in speed. The network was able to adapt to different plant species via transfer learning, offering similar accuracy when transferred to an Arabidopsis thaliana plate assay. A final instance of transfer learning, to images of Brassica napus from a hydroponic assay, still demonstrated good accuracy despite many fewer training images. CONCLUSIONS:We present RootNav 2.0, a new approach to root image analysis driven by a deep neural network. The tool can be adapted to new image domains with a reduced number of images, and offers substantial speed improvements over semi-automatic and manual approaches. The tool outputs root architectures in the widely accepted RSML standard, for which numerous analysis packages exist (http://rootsystemml.github.io/), as well as segmentation masks compatible with other automated measurement tools. The tool will provide researchers with the ability to analyse root systems at larget scales than ever before, at a time when large scale genomic studies have made this more important than ever.
| S-EPMC6839032 | biostudies-literature
Project description:In present study free radical scavenging potential of aerial parts and root of Phyllanthus fraternus was investigated. Extraction was done in water and ethanol. Total antioxidant capacity was measured by DPPH free radical scavenging method; ethanolic extract of aerial part was most potent in activity with 50% inhibition at 258 μg/mL concentration. Lipid peroxidation (LPO) was measured in terms of thiobarbituric acid-reactive substances (TBARS) by using egg-yolk homogenates as lipid-rich media with EC₅₀ of aerial part (ethanolic) 1522 μg/mL which was found to be most active. Superoxide (SO) radical scavenging activity was measured using riboflavin-light-nitroblue tetrazolium assay. Ethanolic and aqueous extract of both aerial part and root was almost similar in superoxide radical scavenging activity. Reducing power was determined on the basis of Fe³⁺-Fe⁺ transformation in the presence of extract. Total phenolic and flavonoid contents were also measured by spectroscopic method. Results showed that the ethanolic fraction of aerial part is most active towards antioxidant potential and this activity is related to its polyphenolic content and reducing potential. Thus, P. fraternus extract can be used as potent natural antioxidant.
| S-EPMC3921995 | biostudies-other
Project description:Volatile organic compounds (VOCs) emitted by plant leaves can influence the physiology of neighbouring plants. In contrast to leaf VOCs, little is known about the role of root VOCs in plant-plant interactions. Here, we characterize constitutive root VOC emissions of the spotted knapweed (Centaurea stoebe) and explore the impact of these VOCs on the germination and growth of different sympatric plant species. We show that C. stoebe roots emit high amounts of sesquiterpenes, with estimated release rates of (E)-?-caryophyllene above 3 ?g g-1 dw hr-1 . Sesquiterpene emissions show little variation between different C. stoebe populations but vary substantially between different Centaurea species. Through root transcriptome sequencing, we identify six root-expressed sesquiterpene synthases (TPSs). Two root-specific TPSs, CsTPS4 and CsTPS5, are sufficient to produce the full blend of emitted root sesquiterpenes. VOC-exposure experiments demonstrate that C. stoebe root VOCs have neutral to positive effects on the germination and growth of different sympatric neighbours. Thus, constitutive root sesquiterpenes produced by two C. stoebe TPSs are associated with facilitation of sympatric neighbouring plants. The release of root VOCs may thus influence plant community structure in nature.
| S-EPMC6850102 | biostudies-literature
Project description:Maize is a globally important food, feed crop and raw material for the food and energy industry. Plant architecture optimization plays important roles in maize yield improvement. PIN-FORMED (PIN) proteins are important for regulating auxin spatiotemporal asymmetric distribution in multiple plant developmental processes. In this study, ZmPIN1a overexpression in maize increased the number of lateral roots and inhibited their elongation, forming a developed root system with longer seminal roots and denser lateral roots. ZmPIN1a overexpression reduced plant height, internode length and ear height. This modification of the maize phenotype increased the yield under high-density cultivation conditions, and the developed root system improved plant resistance to drought, lodging and a low-phosphate environment. IAA concentration, transport capacity determination and application of external IAA indicated that ZmPIN1a overexpression led to increased IAA transport from shoot to root. The increase in auxin in the root enabled the plant to allocate more carbohydrates to the roots, enhanced the growth of the root and improved plant resistance to environmental stress. These findings demonstrate that maize plant architecture can be improved by root breeding to create an ideal phenotype for further yield increases.
| S-EPMC5785362 | biostudies-literature
Project description:ATTED-II (http://atted.jp) is a coexpression database for plant species to aid in the discovery of relationships of unknown genes within a species. As an advanced coexpression analysis method, multispecies comparisons have the potential to detect alterations in gene relationships within an evolutionary context. However, determining the validity of comparative coexpression studies is difficult without quantitative assessments of the quality of coexpression data. ATTED-II (version 9) provides 16 coexpression platforms for nine plant species, including seven species supported by both microarray- and RNA sequencing (RNAseq)-based coexpression data. Two independent sources of coexpression data enable the assessment of the reproducibility of coexpression. The latest coexpression data for Arabidopsis (Ath-m.c7-1 and Ath-r.c3-0) showed the highest reproducibility (Jaccard coefficient = 0.13) among previous coexpression data in ATTED-II. We also investigated the statistical basis of the mutual rank (MR) index as a coexpression measure by bootstrap sampling of experimental units. We found that the error distribution of the logit-transformed MR index showed normality with equal variances for each coexpression platform. Because the MR error was strongly correlated with the number of samples for the coexpression data, typical confidence intervals for the MR index can be estimated for any coexpression platform. These new, high-quality coexpression data can be analyzed with any tool in ATTED-II and combined with external resources to obtain insight into plant biology.
| S-EPMC5914358 | biostudies-literature
Project description:Volatile compounds produced by plant-associated microorganisms represent a diverse resource to promote plant growth and health. Here, we investigated the effect of volatiles from root-associated Microbacterium species on plant growth and development. Volatiles of eight strains induced significant increases in shoot and root biomass of Arabidopsis but differed in their effects on root architecture. Microbacterium strain EC8 also enhanced root and shoot biomass of lettuce and tomato. Biomass increases were also observed for plants exposed only briefly to volatiles from EC8 prior to transplantation of the seedlings to soil. These results indicate that volatiles from EC8 can prime plants for growth promotion without direct and prolonged contact. We further showed that the induction of plant growth promotion is tissue specific; that is, exposure of roots to volatiles from EC8 led to an increase in plant biomass, whereas shoot exposure resulted in no or less growth promotion. Gas chromatography-quadrupole time of flight mass spectometry (GC-QTOF-MS) analysis revealed that EC8 produces a wide array of sulfur-containing compounds, as well as ketones. Bioassays with synthetic sulfur volatile compounds revealed that the plant growth response to dimethyl trisulfide was concentration-dependent, with a significant increase in shoot weight at 1 ?M and negative effects on plant biomass at concentrations higher than 1 mM. Genome-wide transcriptome analysis of volatile-exposed Arabidopsis seedlings showed upregulation of genes involved in assimilation and transport of sulfate and nitrate. Collectively, these results show that root-associated Microbacterium primes plants, via the roots, for growth promotion, most likely via modulation of sulfur and nitrogen metabolism.IMPORTANCE In the past decade, various studies have described the effects of microbial volatiles on other (micro)organisms in vitro, but their broad-spectrum activity in vivo and the mechanisms underlying volatile-mediated plant growth promotion have not been addressed in detail. Here, we revealed that volatiles from root-associated bacteria of the genus Microbacterium can enhance the growth of different plant species and can prime plants for growth promotion without direct and prolonged contact between the bacterium and the plant. Collectively, these results provide new opportunities for sustainable agriculture and horticulture by exposing roots of plants only briefly to a specific blend of microbial volatile compounds prior to transplantation of the seedlings to the greenhouse or field. This strategy has no need for large-scale introduction or root colonization and survival of the microbial inoculant.
| S-EPMC6210106 | biostudies-literature
Project description:Background and aimsAuxin response factors (ARFs) as transcription activators or repressors have important roles in plant growth and development, but knowledge about the functions of wheat ARF members is limited. A novel ARF member in wheat (Triticum aestivum), TaARF4, was identified, and its protein function, haplotype geographic distribution and allelic frequencies were investigated.MethodsTissue expression of TaARF4 was analysed by real-time PCR. Sub-cellular localization was performed using green fluorescent protein (GFP)-tagged TaARF4. Ectopic expression of TaARF4-A in arabidopsis was used to study its functions. Electrophoretic mobility shift assays (EMSAs), chromatin immunoprecipitation (ChIP) analyses and gene expression were performed to detect TaARF4 target genes. A dCAPS (derived cleaved amplified polymorphic sequence) marker developed from TaARF4-B was used to identify haplotypes and association analysis between haplotypes and agronomic traits.Key resultsTaARF4-A was constitutively expressed and its protein was localized in the nucleus. Ectopic expression of TaARF4-A in arabidopsis caused abscisic acid (ABA) insensitivity, shorter primary root length and reduced plant height (PH). Through expression studies and ChIP assays, TaARF4-A was shown to regulate HB33 expression which negatively responded to ABA, and reduced root length and plant height by repressing expression of Gretchen Hagen 3 (GH3) genes that in turn upregulated indole-3-acetic acid content in arabidopsis. Association analysis showed that TaARF4-B was strongly associated with PH and root depth at the tillering, jointing and grain fill stages. Geographic distribution and allelic frequencies suggested that TaARF4-B haplotypes were selected in Chinese wheat breeding programmes. An amino acid change (threonine to alanine) at position 158 might be the cause of phenotype variation in accessions possessing different haplotypes.ConclusionsEctopic expression and association analysis indicate that TaARF4 may be involved in root length and plant height determination in wheat. This work is helpful for selection of wheat genotypes with optimal root and plant architecture.
| S-EPMC6881231 | biostudies-literature
Project description:Plant growth regulating properties of brevicompanines (Brvs), natural products of the fungus Penicillium brevicompactum, have been known for several years, but further investigations into the molecular mechanism of their bioactivity have not been performed. Following chemical synthesis of brevicompanine derivatives, we studied their activity in the model plant Arabidopsis by a combination of plant growth assays, transcriptional profiling, and numerous additional bioassays. These studies demonstrated that brevicompanines cause transcriptional misregulation of core components of the circadian clock, whereas other biological read-outs were not affected. Brevicompanines thus represent promising chemical tools for investigating the regulation of the plant circadian clock. In addition, our study also illustrates the potential of an unbiased -omics-based characterization of bioactive compounds for identifying the often cryptic modes of action of small molecules.
| S-EPMC5477000 | biostudies-literature
Project description:Various types of flat rhizoboxes aid in root visualization and tracking in experiments where the focus is upon root system growth and development. While size of the pot is known to affect experiments, nothing is known about the impact of rhizoboxes-not only their volume, but also their shape might affect root and shoot growth. Therefore, we investigated how rhizoboxes change plant biomass and root:shoot biomass partitioning. We compared biomass and root:shoot ratio of plants growing in the pots with different geometry-usual three-dimensional, cuboid plant pots and flat two-dimensional rhizoboxes about the same volume. We used two different nutritional treatments (deionized water and additional nutrients) for investigating whether the nutrient availability in the substrate changed the impact of rhizoboxes on plant growth. We used 15 species for the generalizability of our results across the phylogenetic tree. Proportional investment of plants into roots was similar in usual pots and in rhizoboxes. This pattern was stable across nutrition treatments and across species. Further, we found no differences in total biomass of plants between pot type within nutrient treatments. With added nutrients, the plants had a higher biomass and lower root:shoot ratio compared to treatments without nutrient addition. Thus, species can be safely compared when grown in the rhizoboxes; rhizoboxes did not affect root system growth comparisons among species and nutrient levels. Also, they did not affect plant growth in terms of total biomass.
| S-EPMC6978282 | biostudies-literature
Project description:Glyphosate is a commonly used herbicide with a broad action spectrum. However, at sublethal doses, glyphosate can induce plant growth, a phenomenon known as hormesis. Most glyphosate hormesis studies have been performed under microbe-free or reduced-microbial-diversity conditions; only a few were performed in open systems or agricultural fields, which include a higher diversity of soil microorganisms. Here, we investigated how microbes affect the hormesis induced by low doses of glyphosate. To this end, we used Arabidopsis thaliana and a well-characterized synthetic bacterial community of 185 strains (SynCom) that mimics the root-associated microbiome of Arabidopsis We found that a dose of 3.6 × 10-6 g acid equivalent/liter (low dose of glyphosate, or LDG) produced an ∼14% increase in the shoot dry weight (i.e., hormesis) of uninoculated plants. Unexpectedly, in plants inoculated with the SynCom, LDG reduced shoot dry weight by ∼17%. We found that LDG enriched two Firmicutes and two Burkholderia strains in the roots. These specific strains are known to act as root growth inhibitors (RGI) in monoassociation assays. We tested the link between RGI and shoot dry weight reduction in LDG by assembling a new synthetic community lacking RGI strains. Dropping RGI strains out of the community restored growth induction by LDG. Finally, we showed that individual RGI strains from a few specific phyla were sufficient to switch the response to LDG from growth promotion to growth inhibition. Our results indicate that glyphosate hormesis was completely dependent on the root microbiome composition, specifically on the presence of root growth inhibitor strains.IMPORTANCE Since the introduction of glyphosate-resistant crops, glyphosate has become the most common and widely used herbicide around the world. Due to its intensive use and ability to bind to soil particles, it can be found at low concentrations in the environment. The effect of these remnants of glyphosate in plants has not been broadly studied; however, glyphosate 1,000 to 100,000 times less concentrated than the recommended field dose promoted growth in several species in laboratory and greenhouse experiments. However, this effect is rarely observed in agricultural fields, where complex communities of microbes have a central role in the way plants respond to external cues. Our study reveals how root-associated bacteria modulate the responses of Arabidopsis to low doses of glyphosate, shifting between growth promotion and growth inhibition.
| S-EPMC7426167 | biostudies-literature