Determination of root system architecture variation of drought adapted sorghum genotypes using high throughput root phenotyping

Rhizosphere ◽  
2021 ◽  
pp. 100370
Author(s):  
Habtamu Demelash ◽  
Taye Tadesse ◽  
Temesegen Menamo ◽  
Ahadu Menzir
Keyword(s):  
Root System ◽  
High Throughput ◽  
System Architecture ◽  
Root System Architecture ◽  
Root Phenotyping ◽  
Sorghum Genotypes

scholarly journals ChronoRoot: High-throughput phenotyping by deep segmentation networks reveals novel temporal parameters of plant root system architecture

2020 ◽  
Author(s):  
Nicolás Gaggion ◽  
Federico Ariel ◽  
Vladimir Daric ◽  
Éric Lambert ◽  
Simon Legendre ◽  
...  
Keyword(s):  
Deep Learning ◽  
Root System ◽  
High Throughput ◽  
System Architecture ◽  
Root Traits ◽  
Root System Architecture ◽  
Machine Intelligence ◽  
Reconstruction Process ◽  
High Throughput Phenotyping ◽  
3D Printed

ABSTRACTDeep learning methods have outperformed previous techniques in most computer vision tasks, including image-based plant phenotyping. However, massive data collection of root traits and the development of associated artificial intelligence approaches have been hampered by the inaccessibility of the rhizosphere. Here we present ChronoRoot, a system which combines 3D printed open-hardware with deep segmentation networks for high temporal resolution phenotyping of plant roots in agarized medium. We developed a novel deep learning based root extraction method which leverages the latest advances in convolutional neural networks for image segmentation, and incorporates temporal consistency into the root system architecture reconstruction process. Automatic extraction of phenotypic parameters from sequences of images allowed a comprehensive characterization of the root system growth dynamics. Furthermore, novel time-associated parameters emerged from the analysis of spectral features derived from temporal signals. Altogether, our work shows that the combination of machine intelligence methods and a 3D-printed device expands the possibilities of root high-throughput phenotyping for genetics and natural variation studies as well as the screening of clock-related mutants, revealing novel root traits.

Temperature responses of roots: impact on growth, root system architecture and implications for phenotyping

2009 ◽  
Vol 36 (11) ◽  
pp. 947 ◽  
Author(s):  
Kerstin A. Nagel ◽  
Bernd Kastenholz ◽  
Siegfried Jahnke ◽  
Dagmar van Dusschoten ◽  
Til Aach ◽  
...  
Keyword(s):  
Root System ◽  
High Throughput ◽  
System Architecture ◽  
Root Zone ◽  
Root System Architecture ◽  
Structure And Function ◽  
Soil Conditions ◽  
Root Structure ◽  
Optical Analysis ◽  
And Function

Root phenotyping is a challenging task, mainly because of the hidden nature of this organ. Only recently, imaging technologies have become available that allow us to elucidate the dynamic establishment of root structure and function in the soil. In root tips, optical analysis of the relative elemental growth rates in root expansion zones of hydroponically-grown plants revealed that it is the maximum intensity of cellular growth processes rather than the length of the root growth zone that control the acclimation to dynamic changes in temperature. Acclimation of entire root systems was studied at high throughput in agar-filled Petri dishes. In the present study, optical analysis of root system architecture showed that low temperature induced smaller branching angles between primary and lateral roots, which caused a reduction in the volume that roots access at lower temperature. Simulation of temperature gradients similar to natural soil conditions led to differential responses in basal and apical parts of the root system, and significantly affected the entire root system. These results were supported by first data on the response of root structure and carbon transport to different root zone temperatures. These data were acquired by combined magnetic resonance imaging (MRI) and positron emission tomography (PET). They indicate acclimation of root structure and geometry to temperature and preferential accumulation of carbon near the root tip at low root zone temperatures. Overall, this study demonstrated the value of combining different phenotyping technologies that analyse processes at different spatial and temporal scales. Only such an integrated approach allows us to connect differences between genotypes obtained in artificial high throughput conditions with specific characteristics relevant for field performance. Thus, novel routes may be opened up for improved plant breeding as well as for mechanistic understanding of root structure and function.

scholarly journals Assessing Root System Architecture of Wheat Seedlings Using A High-Throughput Root Phenotyping System

2019 ◽  
Author(s):  
E. Adeleke ◽  
R. Millas ◽  
W. McNeal ◽  
J Faris ◽  
A. Taheri
Keyword(s):  
Root System ◽  
System Architecture ◽  
Root Traits ◽  
Wheat Seedling ◽  
Root System Architecture ◽  
Rapid Screening ◽  
Wheat Seedlings ◽  
Ploidy Levels ◽  
Seedling Traits ◽  
Root Phenotyping

AbstractBackground and aimsRoot system architecture is a vital part of the plant that has been shown to vary between species and within species based on response to genotypic and/or environmental influences. The root traits of wheat seedlings is critical for the establishment and evidently linked to plant height and seed yield. However, plant breeders have not efficiently developed the role of RSA in wheat selection due to the difficulty of studying root traits.MethodsWe set up a root phenotyping platform to characterize RSA in 34 wheat accessions. The phenotyping pipeline consists of the germination paper-based moisture replacement system, image capture units, and root-image processing software. The 34 accessions from two different wheat ploidy levels (hexaploids and tetraploids), were characterized in ten replicates. A total of 19 root traits were quantified from the root architecture generated.ResultsThis pipeline allowed for rapid screening of 340 wheat seedlings within 10days. Also, at least one line from each ploidy (6x and 4x) showed significant differences (P < 0.05) in measured traits except in mean seminal count. Our result also showed strong correlation (0.8) between total root length, maximum depth and convex hull area.ConclusionsThis phenotyping pipeline has the advantage and capacity to increase screening potential at early stages of plant development leading to characterization of wheat seedling traits that can be further examined using QTL analysis in populations generated from the examined accessions.

scholarly journals High-throughput three-dimensional visualization of root system architecture of rice using X-ray computed tomography

Plant Methods ◽  
2020 ◽  
Vol 16 (1) ◽  
Author(s):  
Shota Teramoto ◽  
Satoko Takayasu ◽  
Yuka Kitomi ◽  
Yumiko Arai-Sanoh ◽  
Takanari Tanabata ◽  
...  
Keyword(s):  
Computed Tomography ◽  
Root System ◽  
High Throughput ◽  
System Architecture ◽  
Three Dimensional ◽  
Root System Architecture ◽  
X Ray ◽  
X Ray Computed

scholarly journals GiA Roots: software for the high throughput analysis of plant root system architecture

2012 ◽  
Vol 12 (1) ◽  
pp. 116 ◽  
Author(s):  
Taras Galkovskyi ◽  
Yuriy Mileyko ◽  
Alexander Bucksch ◽  
Brad Moore ◽  
Olga Symonova ◽  
...  
Keyword(s):  
Root System ◽  
High Throughput ◽  
System Architecture ◽  
Plant Root ◽  
Root System Architecture ◽  
High Throughput Analysis ◽  
Throughput Analysis ◽  
Plant Root System

scholarly journals Affordable and robust phenotyping framework to analyse root system architecture of soil-grown plants

2019 ◽  
Author(s):  
Thibaut Bontpart ◽  
Cristobal Concha ◽  
Valerio Giuffrida ◽  
Ingrid Robertson ◽  
Kassahun Admkie ◽  
...  
Keyword(s):  
Root System ◽  
Low Income ◽  
System Architecture ◽  
Imaging System ◽  
Soil Surface ◽  
Root Systems ◽  
Root System Architecture ◽  
Low Income Countries ◽  
Climate Resilience ◽  
Root Phenotyping

AbstractThe analysis of root system growth, root phenotyping, is important to inform efforts to enhance plant resource acquisition from soils. However, root phenotyping remains challenging due to soil opacity and requires systems that optimize root visibility and image acquisition. Previously reported systems require costly and bespoke materials not available in most countries, where breeders need tools to select varieties best adapted to local soils and field conditions. Here, we present an affordable soil-based growth container (rhizobox) and imaging system to phenotype root development in greenhouses or shelters. All components of the system are made from commodity components, locally available worldwide to facilitate the adoption of this affordable technology in low-income countries. The rhizobox is large enough (~6000 cm2 visible soil) to not restrict vertical root system growth for at least seven weeks after sowing, yet light enough (~21 kg) to be routinely moved manually. Support structures and an imaging station, with five cameras covering the whole soil surface, complement the rhizoboxes. Images are acquired via the Phenotiki sensor interface, collected, stitched and analysed. Root system architecture (RSA) parameters are quantified without intervention. RSA of a dicot (chickpea, Cicer arietinum L.) and a monocot (barley, Hordeum vulgare L.) species, which exhibit contrasting root systems, were analysed. The affordable system is relevant for efforts in Ethiopia and elsewhere to enhance yields and climate resilience of chickpea and other crops for improved food security.Significance StatementAn affordable system to characterize root system architecture of soil-grown plants was developed. Using commodity components, this will enable local efforts world-wide to breed for enhanced root systems.

scholarly journals High-throughput imaging and analysis of root system architecture in Brachypodium distachyon under differential nutrient availability

2012 ◽  
Vol 367 (1595) ◽  
pp. 1559-1569 ◽  
Author(s):  
Paul A. Ingram ◽  
Jinming Zhu ◽  
Aabid Shariff ◽  
Ian W. Davis ◽  
Philip N. Benfey ◽  
...  
Keyword(s):  
Root Growth ◽  
Root System ◽  
High Throughput ◽  
Nutrient Availability ◽  
System Architecture ◽  
Brachypodium Distachyon ◽  
Root System Architecture ◽  
Vital Role ◽  
P Deficiency ◽  
Genetic Components

Nitrogen (N) and phosphorus (P) deficiency are primary constraints for plant productivity, and root system architecture (RSA) plays a vital role in the acquisition of these nutrients. The genetic determinants of RSA are poorly understood, primarily owing to the complexity of crop genomes and the lack of sufficient RSA phenotyping methods. The objective of this study was to characterize the RSA of two Brachypodium distachyon accessions under different nutrient availability. To do so, we used a high-throughput plant growth and imaging platform, and developed software that quantified 19 different RSA traits. We found significant differences in RSA between two Brachypodium accessions grown on nutrient-rich, low-N and low-P conditions. More specifically, one accession maintained axile root growth under low N, while the other accession maintained lateral root growth under low P. These traits resemble the RSA of crops adapted to low-N and -P conditions, respectively. Furthermore, we found that a number of these traits were highly heritable. This work lays the foundation for future identification of important genetic components of RSA traits under nutrient limitation using a mapping population derived from these two accessions.

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 &lt; 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.

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