High-throughput phenotyping (HTP) identifies seedling root traits linked to variation in seed yield and nutrient capture in field-grown oilseed rape (Brassica napusL.)

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.

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Phenotyping Root Systems in a Set of Japonica Rice Accessions: Can Structural Traits Predict the Response to Drought?

Rice ◽

10.1186/s12284-020-00404-5 ◽

2020 ◽

Vol 13 (1) ◽

Author(s):

Paulo Henrique Ramos Guimarães ◽

Isabela Pereira de Lima ◽

Adriano Pereira de Castro ◽

Anna Cristina Lanna ◽

Patrícia Guimarães Santos Melo ◽

...

Keyword(s):

Root System ◽

Water Deficit ◽

High Throughput ◽

Root Traits ◽

Root Systems ◽

Japonica Rice ◽

Plastic Response ◽

Reproductive Phase ◽

High Throughput Phenotyping ◽

Structural Traits

Abstract Background The root system plays a major role in plant growth and development and root system architecture is reported to be the main trait related to plant adaptation to drought. However, phenotyping root systems in situ is not suited to high-throughput methods, leading to the development of non-destructive methods for evaluations in more or less controlled root environments. This study used a root phenotyping platform with a panel of 20 japonica rice accessions in order to: (i) assess their genetic diversity for a set of structural and morphological root traits and classify the different types; (ii) analyze the plastic response of their root system to a water deficit at reproductive phase and (iii) explore the ability of the platform for high-throughput phenotyping of root structure and morphology. Results High variability for the studied root traits was found in the reduced set of accessions. Using eight selected traits under irrigated conditions, five root clusters were found that differed in root thickness, branching index and the pattern of fine and thick root distribution along the profile. When water deficit occurred at reproductive phase, some accessions significantly reduced root growth compared to the irrigated treatment, while others stimulated it. It was found that root cluster, as defined under irrigated conditions, could not predict the plastic response of roots under drought. Conclusions This study revealed the possibility of reconstructing the structure of root systems from scanned images. It was thus possible to significantly class root systems according to simple structural traits, opening up the way for using such a platform for medium to high-throughput phenotyping. The study also highlighted the uncoupling between root structures under non-limiting water conditions and their response to drought.

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GrowScreen-PaGe, a non-invasive, high-throughput phenotyping system based on germination paper to quantify crop phenotypic diversity and plasticity of root traits under varying nutrient supply

Functional Plant Biology ◽

10.1071/fp16128 ◽

2017 ◽

Vol 44 (1) ◽

pp. 76 ◽

Cited By ~ 22

Author(s):

Tania Gioia ◽

Anna Galinski ◽

Henning Lenz ◽

Carmen Müller ◽

Jonas Lentz ◽

...

Keyword(s):

High Throughput ◽

Phenotypic Diversity ◽

Crop Improvement ◽

Root Traits ◽

Root Systems ◽

Non Invasive ◽

Large Sets ◽

High Throughput Phenotyping ◽

Improvement Programs ◽

Root Phenotyping

New techniques and approaches have been developed for root phenotyping recently; however, rapid and repeatable non-invasive root phenotyping remains challenging. Here, we present GrowScreen-PaGe, a non-invasive, high-throughput phenotyping system (4 plants min–1) based on flat germination paper. GrowScreen-PaGe allows the acquisition of time series of the developing root systems of 500 plants, thereby enabling to quantify short-term variations in root system. The choice of germination paper was found to be crucial and paper ☓ root interaction should be considered when comparing data from different studies on germination paper. The system is suitable for phenotyping dicot and monocot plant species. The potential of the system for high-throughput phenotyping was shown by investigating phenotypic diversity of root traits in a collection of 180 rapeseed accessions and of 52 barley genotypes grown under control and nutrient-starved conditions. Most traits showed a large variation linked to both genotype and treatment. In general, root length traits contributed more than shape and branching related traits in separating the genotypes. Overall, results showed that GrowScreen-PaGe will be a powerful resource to investigate root systems and root plasticity of large sets of plants and to explore the molecular and genetic root traits of various species including for crop improvement programs.

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Phenotyping oilseed rape growth-related traits and their responses to water deficit: the disturbing pot size effect

Functional Plant Biology ◽

10.1071/fp16036 ◽

2017 ◽

Vol 44 (1) ◽

pp. 35 ◽

Cited By ~ 9

Author(s):

Anaëlle Dambreville ◽

Mélanie Griolet ◽

Gaëlle Rolland ◽

Myriam Dauzat ◽

Alexis Bédiée ◽

...

Keyword(s):

Water Deficit ◽

Oilseed Rape ◽

High Throughput ◽

Interactive Effects ◽

Brassica Napus L ◽

Root Shoot Ratio ◽

Whole Plant ◽

Pot Size ◽

High Throughput Phenotyping ◽

Root Restriction

Following the recent development of high-throughput phenotyping platforms for plant research, the number of individual plants grown together in a same experiment has raised, sometimes at the expense of pot size. However, root restriction in excessively small pots affects plant growth and carbon partitioning, and may interact with other stresses targeted in these experiments. In work reported here, we investigated the interactive effects of pot size and soil water deficit on multiple growth-related traits from the cellular to the whole-plant scale in oilseed rape (Brassica napus L.). The effects of pot size on responses to water deficit and allometric relationships revealed strong, multilevel interactions between pot size and watering regime. Notably, water deficit increased the root : shoot ratio in large pots, but not in small pots. At the cellular scale, water deficit decreased epidermal leaf cell area in large pots, but not in small pots. These results were consistent with changes in the level of endoreduplication factor in leaf cells. Our study illustrates the disturbing interaction of pot size with water deficit and raises the need to carefully consider this factor in the frame of the current development of high-throughput phenotyping experiments.

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Ground-Penetrating Radar as phenotyping tool for characterizing intraspecific variability in root traits of a widespread conifer

Plant and Soil ◽

10.1007/s11104-021-05135-0 ◽

2021 ◽

Author(s):

Erica Lombardi ◽

Juan Pedro Ferrio ◽

Ulises Rodríguez-Robles ◽

Víctor Resco de Dios ◽

Jordi Voltas

Keyword(s):

High Throughput ◽

Ground Penetrating Radar ◽

Intraspecific Variability ◽

Root Traits ◽

Root Systems ◽

Mediterranean Forests ◽

High Throughput Phenotyping ◽

The Mediterranean ◽

Ground Penetrating ◽

Root Frequency

Abstract Background and Aim Drought is the main abiotic stress affecting Mediterranean forests. Root systems are responsible for water uptake, but intraspecific variability in tree root morphology is poorly understood mainly owing to sampling difficulties. The aim of this study was to gain knowledge on the adaptive relevance of rooting traits for a widespread pine using a non-invasive, high-throughput phenotyping technique. Methods Ground-Penetrating Radar (GPR) was used to characterize variability in coarse root features (depth, diameter and frequency) among populations of the Mediterranean conifer Pinus halepensis evaluated in a common garden. GPR records were examined in relation to aboveground growth and climate variables at origin of populations. Results Variability was detected for root traits among 56 range-wide populations categorized into 16 ecotypes. Root diameter decreased eastward within the Mediterranean basin. In turn, root frequency, but not depth and diameter, decreased following a northward gradient. Root traits also varied with climatic variables at origin such as the ratio of summer to annual precipitation, summer temperature or solar radiation. Particularly, root frequency increased with aridity, whereas root depth and diameter were maximum for ecotypes occupying the thermal midpoint of the species distribution range. Conclusion GPR is a high-throughput phenotyping tool that allows detection of intraspecific variation in root traits of P. halepensis and its dependencies on eco-geographic characteristics at origin, thereby informing on the adaptive relevance of root systems for the species. It is also potentially suited for inferring population divergence in resource allocation above- and belowground in forest genetic trials.

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High-throughput phenotyping of seminal root traits in wheat

Plant Methods ◽

10.1186/s13007-015-0055-9 ◽

2015 ◽

Vol 11 (1) ◽

pp. 13 ◽

Cited By ~ 76

Author(s):

Cecile Richard ◽

Lee T Hickey ◽

Susan Fletcher ◽

Raeleen Jennings ◽

Karine Chenu ◽

...

Keyword(s):

High Throughput ◽

Root Traits ◽

Seminal Root ◽

High Throughput Phenotyping

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High-throughput Phenotyping of Wheat Seminal Root Traits in a Breeding Context

Procedia Environmental Sciences ◽

10.1016/j.proenv.2015.07.179 ◽

2015 ◽

Vol 29 ◽

pp. 102-103 ◽

Cited By ~ 1

Author(s):

Cecile Richard ◽

Lee Hickey ◽

Susan Fletcher ◽

Karine Chenu ◽

Andrew Borrell ◽

...

Keyword(s):

High Throughput ◽

Root Traits ◽

Seminal Root ◽

High Throughput Phenotyping

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Root and canopy traits and adaptability genes explain drought tolerance mechanism in winter wheat

10.1101/2020.11.04.367904 ◽

2020 ◽

Author(s):

A.S. Nehe ◽

M. J. Foulkes ◽

I. Ozturk ◽

A. Rasheed ◽

L. York ◽

...

Keyword(s):

Drought Tolerance ◽

Grain Yield ◽

High Throughput ◽

Vegetation Index ◽

Root Traits ◽

Wheat Cultivars ◽

Drought Tolerant ◽

Green Area ◽

High Throughput Phenotyping ◽

Semiarid Conditions

AbstractBread wheat (Triticum aestivum L) is one of main staple food crops worldwide contributing 20% calories in human diet. Drought stress is the main factor limiting yields and threatening to food security, with climate change resulting in more frequent and intense drought. Developing drought-tolerant wheat cultivars is a promising way forward. The use of a holistic approaches that include high-throughput phenotyping and genetic makers in selection could help in accelerating genetic gains. Fifty advanced breeding lines were selected from the CIMMYT Turkey winter wheat breeding program and studied under irrigated and semiarid conditions for two years. High-throughput phenotyping were done for wheat crown root traits using shovelomics techniques and canopy green area and senescence dynamics using vegetation indices (green area using RGB images and Normalized Difference Vegetation Index using spectral reflectance). In addition, genotyping by KASP markers for adaptability genes was done. Overall, under semiarid conditions compared to irrigated conditions yield reduced by 3.09 t ha−1 (−46.8%). Significant difference between the treatment and genotype was observed for grain yield and senescence traits. Genotypes responded differently under drought stress. Root traits including shallower nodal root angle under irrigated conditions and root number per shoot under semiarid conditions were associated with increased grain yield. RGB based vegetation index measuring canopy green area at anthesis was more strongly associated with GY than NDVI under drought. Five established functional genes (PRR73.A1 – flowering time, TEF-7A – grain size and weight, TaCwi.4A - yield under drought, Dreb1-drought tolerance, and ISBW11.GY.QTL.CANDIDATE- grain yield) were associated with different drought-tolerance traits in this experiment. We conclude that a combination of high-throughput phenotyping and selection for genetic markers can help to develop drought-tolerant wheat cultivars.

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