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Vleugels T, Saleem A, Dubey R, Muylle H, Borra-Serrano I, Lootens P, De Swaef T, Roldán-Ruiz I. Phenotypic characterization of drought responses in red clover ( Trifolium pratense L.). Front Plant Sci 2024; 14:1304411. [PMID: 38283975 PMCID: PMC10811260 DOI: 10.3389/fpls.2023.1304411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 12/18/2023] [Indexed: 01/30/2024]
Abstract
Introduction Red clover (Trifolium pratense) is a protein-rich, short-lived perennial forage crop that can achieve high yields, but suffers increasingly from drought in different cultivation areas. Breeding for increased adaptation to drought is becoming essential, but at this stage it is unclear which traits breeders should target to phenotype responses to drought that allow them to identify the most promising red clover genotypes. In this study, we assessed how prolonged periods of drought affected plant growth in field conditions, and which traits could be used to distinguish better adapted plant material. Methods A diverse panel of 395 red clover accessions was evaluated during two growing seasons. We simulated 6-to-8-week drought periods during two consecutive summers, using mobile rain-out shelters, while an irrigated control field was established in an adjacent parcel. Plant growth was monitored throughout both growing seasons using multiple flights with a drone equipped with RGB and thermal sensors. At various observation moments throughout both growing seasons, we measured canopy cover (CC) and canopy height (CH). The crop water stress index (CWSI) was determined at two moments, during or shortly after the drought event. Results Manual and UAV-derived measurements for CH were well correlated, indicating that UAV-derived measurements can be reliably used in red clover. In both years, CC, CH and CWSI were affected by drought, with measurable growth reductions by the end of the drought periods, and during the recovery phase. We found that the end of the drought treatment and the recovery phase of approximately 20 days after drought were suitable periods to phenotype drought responses and to distinguish among genotypes. Discussion Multifactorial analysis of accession responses revealed interactions of the maturity type with drought responses, which suggests the presence of two independent strategies in red clover: 'drought tolerance' and 'drought recovery'. We further found that a large proportion of the accessions able to perform well under well-watered conditions were also the ones that were less affected by drought. The results of this investigation are interpreted in view of the development of breeding for adaptation to drought in red clover.
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Affiliation(s)
- Tim Vleugels
- ILVO (Flanders Research Institute for Agriculture, Fisheries and Food), Plant Sciences Unit, Melle, Belgium
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Van den Broeck L, Bhosale DK, Song K, Fonseca de Lima CF, Ashley M, Zhu T, Zhu S, Van De Cotte B, Neyt P, Ortiz AC, Sikes TR, Aper J, Lootens P, Locke AM, De Smet I, Sozzani R. Functional annotation of proteins for signaling network inference in non-model species. Nat Commun 2023; 14:4654. [PMID: 37537196 PMCID: PMC10400656 DOI: 10.1038/s41467-023-40365-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 07/25/2023] [Indexed: 08/05/2023] Open
Abstract
Molecular biology aims to understand cellular responses and regulatory dynamics in complex biological systems. However, these studies remain challenging in non-model species due to poor functional annotation of regulatory proteins. To overcome this limitation, we develop a multi-layer neural network that determines protein functionality directly from the protein sequence. We annotate kinases and phosphatases in Glycine max. We use the functional annotations from our neural network, Bayesian inference principles, and high resolution phosphoproteomics to infer phosphorylation signaling cascades in soybean exposed to cold, and identify Glyma.10G173000 (TOI5) and Glyma.19G007300 (TOT3) as key temperature regulators. Importantly, the signaling cascade inference does not rely upon known kinase motifs or interaction data, enabling de novo identification of kinase-substrate interactions. Conclusively, our neural network shows generalization and scalability, as such we extend our predictions to Oryza sativa, Zea mays, Sorghum bicolor, and Triticum aestivum. Taken together, we develop a signaling inference approach for non-model species leveraging our predicted kinases and phosphatases.
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Affiliation(s)
- Lisa Van den Broeck
- Plant and Microbial Biology Department and NC Plant Sciences Initiative, North Carolina State University, Raleigh, NC, 27695, USA.
| | - Dinesh Kiran Bhosale
- Electrical and Computer Engineering Department, North Carolina State University, Raleigh, NC, 27695, USA
| | - Kuncheng Song
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, 27695, USA
| | - Cássio Flavio Fonseca de Lima
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, B-9052, Ghent, Belgium
| | - Michael Ashley
- Electrical and Computer Engineering Department, North Carolina State University, Raleigh, NC, 27695, USA
| | - Tingting Zhu
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, B-9052, Ghent, Belgium
| | - Shanshuo Zhu
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, B-9052, Ghent, Belgium
| | - Brigitte Van De Cotte
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, B-9052, Ghent, Belgium
| | - Pia Neyt
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, B-9052, Ghent, Belgium
| | - Anna C Ortiz
- USDA-ARS Soybean & Nitrogen Fixation Research Unit, Raleigh, NC, 27607, Belgium
| | - Tiffany R Sikes
- USDA-ARS Soybean & Nitrogen Fixation Research Unit, Raleigh, NC, 27607, Belgium
| | - Jonas Aper
- Protealis NV, Technologiepark-Zwijnaarde 94, 9052, Ghent, Belgium
| | - Peter Lootens
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), 9090, Melle, Belgium
| | - Anna M Locke
- USDA-ARS Soybean & Nitrogen Fixation Research Unit, Raleigh, NC, 27607, Belgium
- Department of Crop and Soil Sciences and NC Plant Sciences Initiative, North Carolina State University, Raleigh, NC, 27695, USA
| | - Ive De Smet
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, B-9052, Ghent, Belgium
| | - Rosangela Sozzani
- Plant and Microbial Biology Department and NC Plant Sciences Initiative, North Carolina State University, Raleigh, NC, 27695, USA.
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De Meyer S, Cruz DF, De Swaef T, Lootens P, De Block J, Bird K, Sprenger H, Van de Voorde M, Hawinkel S, Van Hautegem T, Inzé D, Nelissen H, Roldán-Ruiz I, Maere S. Predicting yield of individual field-grown rapeseed plants from rosette-stage leaf gene expression. PLoS Comput Biol 2023; 19:e1011161. [PMID: 37253069 DOI: 10.1371/journal.pcbi.1011161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 05/05/2023] [Indexed: 06/01/2023] Open
Abstract
In the plant sciences, results of laboratory studies often do not translate well to the field. To help close this lab-field gap, we developed a strategy for studying the wiring of plant traits directly in the field, based on molecular profiling and phenotyping of individual plants. Here, we use this single-plant omics strategy on winter-type Brassica napus (rapeseed). We investigate to what extent early and late phenotypes of field-grown rapeseed plants can be predicted from their autumnal leaf gene expression, and find that autumnal leaf gene expression not only has substantial predictive power for autumnal leaf phenotypes but also for final yield phenotypes in spring. Many of the top predictor genes are linked to developmental processes known to occur in autumn in winter-type B. napus accessions, such as the juvenile-to-adult and vegetative-to-reproductive phase transitions, indicating that the yield potential of winter-type B. napus is influenced by autumnal development. Our results show that single-plant omics can be used to identify genes and processes influencing crop yield in the field.
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Affiliation(s)
- Sam De Meyer
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Daniel Felipe Cruz
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Tom De Swaef
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Melle, Belgium
| | - Peter Lootens
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Melle, Belgium
| | - Jolien De Block
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Kevin Bird
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Heike Sprenger
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Michael Van de Voorde
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Stijn Hawinkel
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Tom Van Hautegem
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Dirk Inzé
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Hilde Nelissen
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Isabel Roldán-Ruiz
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Melle, Belgium
| | - Steven Maere
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
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Coudron W, De Frenne P, Verheyen K, Gobin A, Boeckaert C, De Cuypere T, Lootens P, Pollet S, De Swaef T. Usefulness of cultivar-level calibration of AquaCrop for vegetables depends on the crop and data availability. Front Plant Sci 2023; 14:1094677. [PMID: 36968371 PMCID: PMC10034377 DOI: 10.3389/fpls.2023.1094677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 02/17/2023] [Indexed: 06/18/2023]
Abstract
As a result of climate change, climatic extremes are expected to increase. For high-value crops like vegetables, irrigation is a potentially economically viable adaptation measure in western Europe. To optimally schedule irrigation, decision support systems based on crop models like AquaCrop are increasingly used by farmers. High value vegetable crops like cauliflower or spinach are grown in two distinct growth cycles per year and, additionally, have a high turnover rate of new varieties. To successfully deploy the AquaCrop model in a decision support system, it requires a robust calibration. However, it is not known whether parameters can be conserved over both growth periods, nor whether a cultivar dependent model calibration is always required. Furthermore, when data are collected from farmers' fields, there are constraints in data availability and uncertainty. We collected data from commercial cauliflower and spinach fields in Belgium in 2019, 2020 and 2021 during different growing periods and of different cultivars. With the use of a Bayesian calibration, we confirmed the need for a condition or cultivar specific calibration for cauliflower, while for spinach, splitting the data per cultivar or pooling the data together did not improve uncertainty on the model simulations. However, due to uncertainties arising from field specific soil and weather conditions, or measurement errors from calibration data, real time field specific adjustments are advised to simulations when using AquaCrop as decision support tool. Remotely sensed or in situ ground data may be invaluable information to reduce uncertainty on model simulations.
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Affiliation(s)
- Willem Coudron
- Plant Science Unit, Research Institute for Agriculture, Fisheries and Food (ILVO), Melle, Belgium
- Forest & Nature Lab, Department of Environment, Ghent University, Gontrode, Belgium
| | - Pieter De Frenne
- Forest & Nature Lab, Department of Environment, Ghent University, Gontrode, Belgium
| | - Kris Verheyen
- Forest & Nature Lab, Department of Environment, Ghent University, Gontrode, Belgium
| | - Anne Gobin
- Remote Sensing, Flemish Institute for Technological Research (VITO), Mol, Belgium
- Department of Earth and Environmental Sciences, Faculty of Bioscience Engineering, KU Leuven, Leuven, Belgium
| | - Charlotte Boeckaert
- Vlaams Kenniscentrum Water (VLAKWA), Flemish Institute for Technological Research (VITO), Kortrijk, Belgium
| | - Tim De Cuypere
- Department of Outdoor Horticulture And Precision Agriculture, Inagro, Rumbeke-Beitem, Belgium
| | - Peter Lootens
- Plant Science Unit, Research Institute for Agriculture, Fisheries and Food (ILVO), Melle, Belgium
| | - Sabien Pollet
- Department of Outdoor Horticulture And Precision Agriculture, Inagro, Rumbeke-Beitem, Belgium
| | - Tom De Swaef
- Plant Science Unit, Research Institute for Agriculture, Fisheries and Food (ILVO), Melle, Belgium
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Saleem A, Aper J, Muylle H, Borra-Serrano I, Quataert P, Lootens P, De Swaef T, Roldán-Ruiz I. Response of a Diverse European Soybean Collection to "Short Duration" and "Long Duration" Drought Stress. Front Plant Sci 2022; 13:818766. [PMID: 35251088 PMCID: PMC8891225 DOI: 10.3389/fpls.2022.818766] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 01/24/2022] [Indexed: 06/14/2023]
Abstract
Drought causes significant damage to a high value crop of soybean. Europe has an increasing demand for soybean and its own production is insufficient. Selection and breeding of cultivars adapted to European growth conditions is therefore urgently needed. These new cultivars must have a shorter growing cycle (specifically for adaptation to North-West Europe), high yield potential under European growing conditions, and sufficient drought resistance. We have evaluated the performance of a diverse collection of 359 soybean accessions under drought stress using rain-out shelters for 2 years. The contrasting weather conditions between years and correspondingly the varying plant responses demonstrated that the consequences of drought for an individual accession can vary strongly depending on the characteristics (e.g., duration and intensity) of the drought period. Short duration drought stress, for a period of four to 7 weeks, caused an average reduction of 11% in maximum canopy height (CH), a reduction of 17% in seed number per plant (SN) and a reduction of 16% in seed weight per plant (SW). Long duration drought stress caused an average reduction of 29% in CH, a reduction of 38% in SN and a reduction of 43% in SW. Drought accelerated plant development and caused an earlier cessation of flowering and pod formation. This seemed to help some accessions to better protect the seed yield, under short duration drought stress. Drought resistance for yield-related traits was associated with the maintenance of growth under long duration drought stress. The collection displayed a broad range of variation for canopy wilting and leaf senescence but a very narrow range of variation for crop water stress index (CWSI; derived from canopy temperature data). To the best of our knowledge this is the first study reporting a detailed investigation of the response to drought within a diverse soybean collection relevant for breeding in Europe.
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Affiliation(s)
- Aamir Saleem
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Merelbeke, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | - Jonas Aper
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Merelbeke, Belgium
| | - Hilde Muylle
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Merelbeke, Belgium
| | - Irene Borra-Serrano
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Merelbeke, Belgium
| | - Paul Quataert
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Merelbeke, Belgium
| | - Peter Lootens
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Merelbeke, Belgium
| | - Tom De Swaef
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Merelbeke, Belgium
| | - Isabel Roldán-Ruiz
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Merelbeke, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
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Coussement JR, De Swaef T, Lootens P, Steppe K. Turgor-driven plant growth applied in a soybean functional-structural plant model. Ann Bot 2020; 126:729-744. [PMID: 32304206 PMCID: PMC7489068 DOI: 10.1093/aob/mcaa076] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Accepted: 04/16/2020] [Indexed: 05/28/2023]
Abstract
BACKGROUND AND AIMS Turgor pressure within a plant cell represents the key to the mechanistical descriptiion of plant growth, combining the effects of both water and carbon availability. The high level of spatio-temporal variation and diurnal dynamics in turgor pressure within a single plant make it a challenge to model these on the fine spatial scale required for functional-structural plant models (FSPMs). A conceptual model for turgor-driven growth in FSPMs has been established previously, but its practical use has not yet been explored. METHODS A turgor-driven growth model was incorporated in a newly established FSPM for soybean. The FSPM simulates dynamics in photosynthesis, transpiration and turgor pressure in direct relation to plant growth. Comparisons of simulations with field data were used to evaluate the potential and shortcomings of the modelling approach. KEY RESULTS Model simulations revealed the need to include an initial seed carbon contribution, a more realistic sink function, an estimation of respiration, and the distinction between osmotic and structural sugars, in order to achieve a realistic model of plant growth. However, differences between simulations and observations remained in individual organ growth patterns and under different environmental conditions. This exposed the need to further investigate the assumptions of developmental and environmental (in)sensitivity of the parameters, which represent physiological and biophysical organ properties in the model, in future research. CONCLUSIONS The model in its current form is primarily a diagnostic tool, to better understand and model the behaviour of water relations on the scale of individual plant organs throughout the plant life cycle. Potential future applications include its use as a phenotyping tool to capture differences in plant performance between genotypes and growing environments in terms of specific plant characteristics. Additionally, focused experiments can be used to further improve the model mechanisms to lead to better predictive FSPMs, including scenarios of water deficit.
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Affiliation(s)
- Jonas R Coussement
- Laboratory of Plant Ecology, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Coupure links 653, Gent, Belgium
- Plant Sciences Unit, Institute of Agricultural, Fisheries and Food Research (ILVO), Caritasstraat 39, Melle, Belgium
| | - Tom De Swaef
- Plant Sciences Unit, Institute of Agricultural, Fisheries and Food Research (ILVO), Caritasstraat 39, Melle, Belgium
| | - Peter Lootens
- Plant Sciences Unit, Institute of Agricultural, Fisheries and Food Research (ILVO), Caritasstraat 39, Melle, Belgium
| | - Kathy Steppe
- Laboratory of Plant Ecology, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Coupure links 653, Gent, Belgium
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Fernandez-Gallego JA, Lootens P, Borra-Serrano I, Derycke V, Haesaert G, Roldán-Ruiz I, Araus JL, Kefauver SC. Automatic wheat ear counting using machine learning based on RGB UAV imagery. Plant J 2020; 103:1603-1613. [PMID: 32369641 DOI: 10.1111/tpj.14799] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 04/15/2020] [Accepted: 04/23/2020] [Indexed: 06/11/2023]
Abstract
In wheat (Triticum aestivum L) and other cereals, the number of ears per unit area is one of the main yield-determining components. An automatic evaluation of this parameter may contribute to the advance of wheat phenotyping and monitoring. There is no standard protocol for wheat ear counting in the field, and moreover it is time consuming. An automatic ear-counting system is proposed using machine learning techniques based on RGB (red, green, blue) images acquired from an unmanned aerial vehicle (UAV). Evaluation was performed on a set of 12 winter wheat cultivars with three nitrogen treatments during the 2017-2018 crop season. The automatic system uses a frequency filter, segmentation and feature extraction, with different classification techniques, to discriminate wheat ears in micro-plot images. The relationship between the image-based manual counting and the algorithm counting exhibited high levels of accuracy and efficiency. In addition, manual ear counting was conducted in the field for secondary validation. The correlations between the automatic and the manual in-situ ear counting with grain yield were also compared. Correlations between the automatic ear counting and grain yield were stronger than those between manual in-situ counting and GY, particularly for the lower nitrogen treatment. Methodological requirements and limitations are discussed.
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Affiliation(s)
- Jose A Fernandez-Gallego
- Plant Physiology Section, Department of Evolutionary Biology, Ecology and Environmental Sciences, Faculty of Biology, University of Barcelona, Diagonal 643, Barcelona, 08028, Spain
- AGROTECNIO (Center for Research in Agrotechnology), Av. Rovira Roure 191, Lleida, 25198, Spain
- Programa de Ingeniería Electrónica, Facultad de Ingeniería, Universidad de Ibagué, Carrera 22 Calle 67, Ibagué, 730001, Colombia
| | - Peter Lootens
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Caritasstraat 39, Melle, 9090, Belgium
| | - Irene Borra-Serrano
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Caritasstraat 39, Melle, 9090, Belgium
- Division of Forest, Nature and Landscape, KU Leuven, Celestijnenlaan 200E, Leuven, 3001, Belgium
| | - Veerle Derycke
- Department Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Valentin Vaerwyckweg 1, Ghent, 9000, Belgium
| | - Geert Haesaert
- Department Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Valentin Vaerwyckweg 1, Ghent, 9000, Belgium
| | - Isabel Roldán-Ruiz
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Caritasstraat 39, Melle, 9090, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, Ghent, 9052, Belgium
| | - Jose L Araus
- Plant Physiology Section, Department of Evolutionary Biology, Ecology and Environmental Sciences, Faculty of Biology, University of Barcelona, Diagonal 643, Barcelona, 08028, Spain
- AGROTECNIO (Center for Research in Agrotechnology), Av. Rovira Roure 191, Lleida, 25198, Spain
| | - Shawn C Kefauver
- Plant Physiology Section, Department of Evolutionary Biology, Ecology and Environmental Sciences, Faculty of Biology, University of Barcelona, Diagonal 643, Barcelona, 08028, Spain
- AGROTECNIO (Center for Research in Agrotechnology), Av. Rovira Roure 191, Lleida, 25198, Spain
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Pieters O, De Swaef T, Lootens P, Stock M, Roldán-Ruiz I, wyffels F. Gloxinia-An Open-Source Sensing Platform to Monitor the Dynamic Responses of Plants. Sensors (Basel) 2020; 20:s20113055. [PMID: 32481619 PMCID: PMC7309107 DOI: 10.3390/s20113055] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 05/20/2020] [Accepted: 05/26/2020] [Indexed: 11/28/2022]
Abstract
The study of the dynamic responses of plants to short-term environmental changes is becoming increasingly important in basic plant science, phenotyping, breeding, crop management, and modelling. These short-term variations are crucial in plant adaptation to new environments and, consequently, in plant fitness and productivity. Scalable, versatile, accurate, and low-cost data-logging solutions are necessary to advance these fields and complement existing sensing platforms such as high-throughput phenotyping. However, current data logging and sensing platforms do not meet the requirements to monitor these responses. Therefore, a new modular data logging platform was designed, named Gloxinia. Different sensor boards are interconnected depending upon the needs, with the potential to scale to hundreds of sensors in a distributed sensor system. To demonstrate the architecture, two sensor boards were designed—one for single-ended measurements and one for lock-in amplifier based measurements, named Sylvatica and Planalta, respectively. To evaluate the performance of the system in small setups, a small-scale trial was conducted in a growth chamber. Expected plant dynamics were successfully captured, indicating proper operation of the system. Though a large scale trial was not performed, we expect the system to scale very well to larger setups. Additionally, the platform is open-source, enabling other users to easily build upon our work and perform application-specific optimisations.
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Affiliation(s)
- Olivier Pieters
- IDLab-AIRO—Ghent University—imec, Technologiepark-Zwijnaarde 126, 9052 Zwijnaarde, Belgium;
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food, Caritasstraat 39, 9090 Melle, Belgium; (T.D.S.); (P.L.); (I.R.-R.)
- Correspondence:
| | - Tom De Swaef
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food, Caritasstraat 39, 9090 Melle, Belgium; (T.D.S.); (P.L.); (I.R.-R.)
| | - Peter Lootens
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food, Caritasstraat 39, 9090 Melle, Belgium; (T.D.S.); (P.L.); (I.R.-R.)
| | - Michiel Stock
- KERMIT, Department of Data Analysis and Mathematical Modelling, Ghent University, Coupure links 653, 9000 Ghent, Belgium;
| | - Isabel Roldán-Ruiz
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food, Caritasstraat 39, 9090 Melle, Belgium; (T.D.S.); (P.L.); (I.R.-R.)
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ledeganckstraat 35, 9000 Gent, Belgium
| | - Francis wyffels
- IDLab-AIRO—Ghent University—imec, Technologiepark-Zwijnaarde 126, 9052 Zwijnaarde, Belgium;
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De Swaef T, Bellocchi G, Aper J, Lootens P, Roldán-Ruiz I. Use of identifiability analysis in designing phenotyping experiments for modelling forage production and quality. J Exp Bot 2019; 70:2587-2604. [PMID: 30753587 DOI: 10.1093/jxb/erz049] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Accepted: 01/31/2019] [Indexed: 06/09/2023]
Abstract
Agricultural systems models are complex and tend to be over-parameterized with respect to observational datasets. Practical identifiability analysis based on local sensitivity analysis has proved effective in investigating identifiable parameter sets in environmental models, but has not been applied to agricultural systems models. Here, we demonstrate that identifiability analysis improves experimental design to ensure independent parameter estimation for yield and quality outputs of a complex grassland model. The Pasture Simulation model (PaSim) was used to demonstrate the effectiveness of practical identifiability analysis in designing experiments and measurement protocols within phenotyping experiments with perennial ryegrass. Virtual experiments were designed combining three factors: frequency of measurements, duration of the experiment. and location of trials. Our results demonstrate that (i) PaSim provides sufficient detail in terms of simulating biomass yield and quality of perennial ryegrass for use in breeding, (ii) typical breeding trials are insufficient to parameterize all influential parameters, (iii) the frequency of measurements is more important than the number of growing seasons to improve the identifiability of PaSim parameters, and (iv) identifiability analysis provides a sound approach for optimizing the design of multi-location trials. Practical identifiability analysis can play an important role in ensuring proper exploitation of phenotypic data and cost-effective multi-location experimental designs. Considering the growing importance of simulation models, this study supports the design of experiments and measurement protocols in the phenotyping networks that have recently been organized.
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Affiliation(s)
- Tom De Swaef
- Plant Sciences Unit, Institute for Agricultural Fisheries and Food Research (ILVO), Melle, Belgium
| | - Gianni Bellocchi
- UCA, INRA, VetAgro Sup, Unité Mixte de Recherche sur Écosystème Prairial (UREP), Clermont-Ferrand, France
| | - Jonas Aper
- Plant Sciences Unit, Institute for Agricultural Fisheries and Food Research (ILVO), Melle, Belgium
| | - Peter Lootens
- Plant Sciences Unit, Institute for Agricultural Fisheries and Food Research (ILVO), Melle, Belgium
| | - Isabel Roldán-Ruiz
- Plant Sciences Unit, Institute for Agricultural Fisheries and Food Research (ILVO), Melle, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
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Coussement J, Henke M, Lootens P, Roldán-Ruiz I, Steppe K, De Swaef T. Modelling leaf spectral properties in a soybean functional-structural plant model by integrating the prospect radiative transfer model. Ann Bot 2018; 122:669-676. [PMID: 29905760 PMCID: PMC6153468 DOI: 10.1093/aob/mcy105] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Accepted: 05/23/2018] [Indexed: 05/30/2023]
Abstract
Background and Aims Currently, functional-structural plant models (FSPMs) mostly resort to static descriptions of leaf spectral characteristics, which disregard the influence of leaf physiological changes over time. In many crop species, including soybean, these time-dependent physiological changes are of particular importance as leaf chlorophyll content changes with leaf age and vegetative nitrogen is remobilized to the developing fruit during pod filling. Methods PROSPECT, a model developed to estimate leaf biochemical composition from remote sensing data, is well suited to allow a dynamic approximation of leaf spectral characteristics in terms of leaf composition. In this study, measurements of the chlorophyll content index (CCI) were linked to leaf spectral characteristics within the 400-800 nm range by integrating the PROSPECT model into a soybean FSPM alongside a wavelength-specific light model. Key Results Straightforward links between the CCI and the parameters of the PROSPECT model allowed us to estimate leaf spectral characteristics with high accuracy using only the CCI as an input. After integration with an FSPM, this allowed digital reconstruction of leaf spectral characteristics on the scale of both individual leaves and the whole canopy. As a result, accurate simulations of light conditions within the canopy were obtained. Conclusions The proposed approach resulted in a very accurate representation of leaf spectral properties, based on fast and simple measurements of the CCI. Integration of accurate leaf spectral characteristics into a soybean FSPM leads to a better, dynamic understanding of the actual perceived light within the canopy in terms of both light quantity and quality.
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Affiliation(s)
- Jonas Coussement
- Plant Sciences Unit, Institute of Agricultural, Fisheries and Food Research (ILVO), Melle, Belgium
- Laboratory of Plant Ecology, Faculty of Bioscience Engineering, Ghent University, Gent, Belgium
| | - Michael Henke
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Stadt Seeland, Germany
| | - Peter Lootens
- Plant Sciences Unit, Institute of Agricultural, Fisheries and Food Research (ILVO), Melle, Belgium
| | - Isabel Roldán-Ruiz
- Plant Sciences Unit, Institute of Agricultural, Fisheries and Food Research (ILVO), Melle, Belgium
- Department of Plant Biotechnology and Bioinformatics, Faculty of Sciences, Ghent University, Zwijnaarde, Belgium
| | - Kathy Steppe
- Laboratory of Plant Ecology, Faculty of Bioscience Engineering, Ghent University, Gent, Belgium
| | - Tom De Swaef
- Plant Sciences Unit, Institute of Agricultural, Fisheries and Food Research (ILVO), Melle, Belgium
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Coussement JR, De Swaef T, Lootens P, Roldán-Ruiz I, Steppe K. Introducing turgor-driven growth dynamics into functional-structural plant models. Ann Bot 2018; 121:849-861. [PMID: 29324998 PMCID: PMC5906928 DOI: 10.1093/aob/mcx144] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Accepted: 10/12/2017] [Indexed: 05/18/2023]
Abstract
Background and Aims In many scenarios the availability of assimilated carbon is not the constraining factor of plant growth. Rather, organ growth appears driven by sink activity in which water availability plays a determinant role. Current functional-structural plant models (FSPMs) mainly focus on plant-carbon relations and largely disregard the importance of plant water status in organogenesis. Consequently, incorporating a turgor-driven growth concept, coupling carbon and water dynamics in an FSPM, presents a significant improvement towards capturing plant development in a more mechanistic manner. Methods An existing process-based water flow and storage model served as a basis for implementing water control in FSPMs. Its concepts were adjusted to the scale of individual plant organs and interwoven with the basic principles of modelling carbon dynamics to allow evaluation of turgor pressure across the entire plant. This was then linked to plant organ growth by applying the principles of the widely used Lockhart equation. Key results This model successfully integrates a mechanistic understanding of plant water transport dynamics coupled with simple carbon dynamics within a dynamically developing plant architecture. It allows evaluation of turgor pressure on the scale of plant organs, resulting in clear diel and long-term patterns, directly linked to plant organ growth. Conclusions A conceptual sap flow and turgor-driven growth model was introduced for functional-structural plant modelling. It is applicable to any plant architecture and allows visual exploration of the diel patterns of organ water content and growth. Integrated in existing FSPMs, this new concept fosters an array of possibilities for FSPMs, as it presents a different formulation of growth in terms of local processes, influenced by local and external conditions.
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Affiliation(s)
- Jonas R Coussement
- Laboratory of Plant Ecology, Department of Applied Ecology and Environmental Biology, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
- Plant Sciences Unit, Institute of Agricultural, Fisheries and Food Research (ILVO), Melle, Belgium
| | - Tom De Swaef
- Plant Sciences Unit, Institute of Agricultural, Fisheries and Food Research (ILVO), Melle, Belgium
| | - Peter Lootens
- Plant Sciences Unit, Institute of Agricultural, Fisheries and Food Research (ILVO), Melle, Belgium
| | - Isabel Roldán-Ruiz
- Plant Sciences Unit, Institute of Agricultural, Fisheries and Food Research (ILVO), Melle, Belgium
- Department of Plant Biotechnology and Bioinformatics, Faculty of Sciences, Ghent University, Zwijnaarde, Belgium
| | - Kathy Steppe
- Laboratory of Plant Ecology, Department of Applied Ecology and Environmental Biology, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
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Denaeghel HER, Van Laere K, Leus L, Lootens P, Van Huylenbroeck J, Van Labeke MC. The Variable Effect of Polyploidization on the Phenotype in Escallonia. Front Plant Sci 2018; 9:354. [PMID: 29616065 PMCID: PMC5869194 DOI: 10.3389/fpls.2018.00354] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Accepted: 03/02/2018] [Indexed: 05/22/2023]
Abstract
To induce new variation within the Escallonia genus, chromosome doubling was performed in E. rubra, E. rosea, and E. illinita, three important species within this genus of mainly evergreen woody ornamental species. Obtained tetraploids and diploid controls were analyzed for rooting capacity, leaf and flower characteristics, and plant architecture using image analysis and cold tolerance. In the present study, a breeders' collection of 23 accessions was characterized cytogenetically and described morphologically. All analyzed species and cultivars were diploid (2n = 2x = 24), with exception of E. pendula, a tetraploid. Today, breeding in Escallonia is limited to lucky finds in seedling populations and few efforts in interspecific hybridization. Three selected Escallonia species underwent an in vitro chromosome doubling with both oryzalin and trifluralin applied as either a continuous or shock treatment. The treatments successfully induced polyploids in all three species. Image analysis revealed that tetraploid E. rosea had decreased shoot length (from 3.8 to 1.3 cm), higher circularity and more dense growth habit compared to diploids. No significant changes in cold tolerance were seen. Tetraploid E. illinita did not differ in shoot length, but an increased outgrowth of axillary buds on the main axis led to denser plants. For tetraploid E. rubra, an increase in plant height (from 4.9 to 5.5 cm) was observed together with a large decrease in circularity and density due to a more polar outgrowth of branches on the main axis. E. rubra tetraploids bore larger flowers than diploids and had an increased cold tolerance (from -7.7 to -11.8°C). Leaf width and area of tetraploids increased for both E. illinita and E. rubra, while a decrease was seen in E. rosea genotypes. For all three species, the rooting capacity of the tetraploids did not differ from the diploids. We conclude that the effect of polyploidization on Escallonia was highly variable and species dependent.
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Affiliation(s)
- Hanne E. R. Denaeghel
- Applied Genetics and Breeding, Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food, Melle, Belgium
- Department of Plant Production, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Katrijn Van Laere
- Applied Genetics and Breeding, Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food, Melle, Belgium
| | - Leen Leus
- Applied Genetics and Breeding, Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food, Melle, Belgium
| | - Peter Lootens
- Applied Genetics and Breeding, Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food, Melle, Belgium
| | - Johan Van Huylenbroeck
- Applied Genetics and Breeding, Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food, Melle, Belgium
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Fonteyne S, Muylle H, Lootens P, Kerchev P, Van den Ende W, Staelens A, Reheul D, Roldán-Ruiz I. Physiological basis of chilling tolerance and early-season growth in miscanthus. Ann Bot 2018; 121:281-295. [PMID: 29300823 PMCID: PMC5808799 DOI: 10.1093/aob/mcx159] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Accepted: 10/26/2017] [Indexed: 05/23/2023]
Abstract
BACKGROUND AND AIMS The high productivity of Miscanthus × giganteus has been at least partly ascribed to its high chilling tolerance compared with related C4 crops, allowing for a longer productive growing season in temperate climates. However, the chilling tolerance of M. × giganteus has been predominantly studied under controlled environmental conditions. The understanding of the underlying mechanisms contributing to chilling tolerance in the field and their variation in different miscanthus genotypes is largely unexplored. METHODS Five miscanthus genotypes with different sensitivities to chilling were grown in the field and scored for a comprehensive set of physiological traits throughout the spring season. Chlorophyll fluorescence was measured as an indication of photosynthesis, and leaf samples were analysed for biochemical traits related to photosynthetic activity (chlorophyll content and pyruvate, Pi dikinase activity), redox homeostasis (malondialdehyde, glutathione and ascorbate contents, and catalase activity) and water-soluble carbohydrate content. KEY RESULTS Chilling-tolerant genotypes were characterized by higher levels of malondialdehyde, raffinose and sucrose, and higher catalase activity, while the chilling-sensitive genotypes were characterized by higher concentrations of glucose and fructose, and higher pyruvate, Pi dikinase activity later in the growing season. On the early sampling dates, the biochemical responses of M. × giganteus were similar to those of the chilling-tolerant genotypes, but later in the season they became more similar to those of the chilling-sensitive genotypes. CONCLUSIONS The overall physiological response of chilling-tolerant genotypes was distinguishable from that of chilling-sensitive genotypes, while M. × giganteus was intermediate between the two. There appears to be a trade-off between high and efficient photosynthesis and chilling stress tolerance. Miscanthus × giganteus is able to overcome this trade-off and, while it is more similar to the chilling-sensitive genotypes in early spring, its photosynthetic capacity is similar to that of the chilling-tolerant genotypes later on.
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Affiliation(s)
- Simon Fonteyne
- Research Institute for Agriculture, Fisheries and Food (ILVO), Plant Sciences Unit, Melle, Belgium
- Ghent University, Department of Plant Production, Ghent, Belgium
| | - Hilde Muylle
- Research Institute for Agriculture, Fisheries and Food (ILVO), Plant Sciences Unit, Melle, Belgium
| | - Peter Lootens
- Research Institute for Agriculture, Fisheries and Food (ILVO), Plant Sciences Unit, Melle, Belgium
| | - Pavel Kerchev
- Ghent University, VIB Department of Plant Systems Biology, Ghent, Belgium
| | - Wim Van den Ende
- KU Leuven, Laboratory of Molecular Plant Biology, Leuven, Belgium
| | - Ariane Staelens
- Research Institute for Agriculture, Fisheries and Food (ILVO), Plant Sciences Unit, Melle, Belgium
| | - Dirk Reheul
- Ghent University, Department of Plant Production, Ghent, Belgium
| | - Isabel Roldán-Ruiz
- Research Institute for Agriculture, Fisheries and Food (ILVO), Plant Sciences Unit, Melle, Belgium
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium
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Lewandowski I, Clifton-Brown J, Trindade LM, van der Linden GC, Schwarz KU, Müller-Sämann K, Anisimov A, Chen CL, Dolstra O, Donnison IS, Farrar K, Fonteyne S, Harding G, Hastings A, Huxley LM, Iqbal Y, Khokhlov N, Kiesel A, Lootens P, Meyer H, Mos M, Muylle H, Nunn C, Özgüven M, Roldán-Ruiz I, Schüle H, Tarakanov I, van der Weijde T, Wagner M, Xi Q, Kalinina O. Progress on Optimizing Miscanthus Biomass Production for the European Bioeconomy: Results of the EU FP7 Project OPTIMISC. Front Plant Sci 2016; 7:1620. [PMID: 27917177 PMCID: PMC5114296 DOI: 10.3389/fpls.2016.01620] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Accepted: 10/13/2016] [Indexed: 05/23/2023]
Abstract
This paper describes the complete findings of the EU-funded research project OPTIMISC, which investigated methods to optimize the production and use of miscanthus biomass. Miscanthus bioenergy and bioproduct chains were investigated by trialing 15 diverse germplasm types in a range of climatic and soil environments across central Europe, Ukraine, Russia, and China. The abiotic stress tolerances of a wider panel of 100 germplasm types to drought, salinity, and low temperatures were measured in the laboratory and a field trial in Belgium. A small selection of germplasm types was evaluated for performance in grasslands on marginal sites in Germany and the UK. The growth traits underlying biomass yield and quality were measured to improve regional estimates of feedstock availability. Several potential high-value bioproducts were identified. The combined results provide recommendations to policymakers, growers and industry. The major technical advances in miscanthus production achieved by OPTIMISC include: (1) demonstration that novel hybrids can out-yield the standard commercially grown genotype Miscanthus x giganteus; (2) characterization of the interactions of physiological growth responses with environmental variation within and between sites; (3) quantification of biomass-quality-relevant traits; (4) abiotic stress tolerances of miscanthus genotypes; (5) selections suitable for production on marginal land; (6) field establishment methods for seeds using plugs; (7) evaluation of harvesting methods; and (8) quantification of energy used in densification (pellet) technologies with a range of hybrids with differences in stem wall properties. End-user needs were addressed by demonstrating the potential of optimizing miscanthus biomass composition for the production of ethanol and biogas as well as for combustion. The costs and life-cycle assessment of seven miscanthus-based value chains, including small- and large-scale heat and power, ethanol, biogas, and insulation material production, revealed GHG-emission- and fossil-energy-saving potentials of up to 30.6 t CO2eq C ha-1y-1 and 429 GJ ha-1y-1, respectively. Transport distance was identified as an important cost factor. Negative carbon mitigation costs of -78€ t-1 CO2eq C were recorded for local biomass use. The OPTIMISC results demonstrate the potential of miscanthus as a crop for marginal sites and provide information and technologies for the commercial implementation of miscanthus-based value chains.
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Affiliation(s)
- Iris Lewandowski
- Department of Biobased Products and Energy Crops, Institute of Crop Science, University of HohenheimStuttgart, Germany
| | - John Clifton-Brown
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth UniversityAberystwyth, UK
| | - Luisa M. Trindade
- Department of Plant Breeding, Wageningen UniversityWageningen, Netherlands
| | | | | | - Karl Müller-Sämann
- ANNA - The Agency for Sustainable Management of Agricultural LandscapeFreiburg, Germany
| | - Alexander Anisimov
- Department of Plant Physiology, Russian State Agrarian University–Moscow Timiryazev Agricultural AcademyMoscow, Russia
| | - C.-L. Chen
- Department of Plant Breeding, Wageningen UniversityWageningen, Netherlands
| | - Oene Dolstra
- Department of Plant Breeding, Wageningen UniversityWageningen, Netherlands
| | - Iain S. Donnison
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth UniversityAberystwyth, UK
| | - Kerrie Farrar
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth UniversityAberystwyth, UK
| | - Simon Fonteyne
- Plant Sciences Unit, Institute for Agricultural and Fisheries ResearchMelle, Belgium
| | | | - Astley Hastings
- The Institute of Biological and Environmental Sciences, University of AberdeenAberdeen, UK
| | - Laurie M. Huxley
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth UniversityAberystwyth, UK
| | - Yasir Iqbal
- Department of Biobased Products and Energy Crops, Institute of Crop Science, University of HohenheimStuttgart, Germany
| | - Nikolay Khokhlov
- Department of Plant Physiology, Russian State Agrarian University–Moscow Timiryazev Agricultural AcademyMoscow, Russia
| | - Andreas Kiesel
- Department of Biobased Products and Energy Crops, Institute of Crop Science, University of HohenheimStuttgart, Germany
| | - Peter Lootens
- Plant Sciences Unit, Institute for Agricultural and Fisheries ResearchMelle, Belgium
| | | | | | - Hilde Muylle
- Plant Sciences Unit, Institute for Agricultural and Fisheries ResearchMelle, Belgium
| | - Chris Nunn
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth UniversityAberystwyth, UK
| | - Mensure Özgüven
- Faculty of Agriculture and Natural Sciences, Konya Food and Agriculture UniversityKonya, Turkey
| | - Isabel Roldán-Ruiz
- Plant Sciences Unit, Institute for Agricultural and Fisheries ResearchMelle, Belgium
| | | | - Ivan Tarakanov
- Department of Plant Physiology, Russian State Agrarian University–Moscow Timiryazev Agricultural AcademyMoscow, Russia
| | - Tim van der Weijde
- Department of Plant Breeding, Wageningen UniversityWageningen, Netherlands
| | - Moritz Wagner
- Department of Biobased Products and Energy Crops, Institute of Crop Science, University of HohenheimStuttgart, Germany
| | - Qingguo Xi
- Dongying Agricultural InstituteDongying, China
| | - Olena Kalinina
- Department of Biobased Products and Energy Crops, Institute of Crop Science, University of HohenheimStuttgart, Germany
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Lootens P, Ruttink T, Rohde A, Combes D, Barre P, Roldán-Ruiz I. High-throughput phenotyping of lateral expansion and regrowth of spaced Lolium perenne plants using on-field image analysis. Plant Methods 2016; 12:32. [PMID: 27293473 PMCID: PMC4902915 DOI: 10.1186/s13007-016-0132-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Accepted: 05/31/2016] [Indexed: 05/04/2023]
Abstract
BACKGROUND Genetic studies and breeding of agricultural crops frequently involve phenotypic characterization of large collections of genotypes grown in field conditions. These evaluations are typically based on visual observations and manual (destructive) measurements. Robust image capture and analysis procedures that allow phenotyping large collections of genotypes in time series during developmental phases represent a clear advantage as they allow non-destructive monitoring of plant growth and performance. A L. perenne germplasm panel including wild accessions, breeding material and commercial varieties has been used to develop a low-cost, high-throughput phenotyping tool for determining plant growth based on images of individual plants during two consecutive growing seasons. Further we have determined the correlation between image analysis-based estimates of the plant's base area and the capacity to regrow after cutting, with manual counts of tiller number and measurements of leaf growth 2 weeks after cutting, respectively. When working with field-grown plants, image acquisition and image segmentation are particularly challenging as outdoor light conditions vary throughout the day and the season, and variable soil colours hamper the delineation of the object of interest in the image. Therefore we have used several segmentation methods including colour-, texture- and edge-based approaches, and factors derived after a fast Fourier transformation. The performance of the procedure developed has been analysed in terms of effectiveness across different environmental conditions and time points in the season. RESULTS The procedure developed was able to analyse correctly 77.2 % of the 24,048 top view images processed. High correlations were found between plant's base area (image analysis-based) and tiller number (manual measurement) and between regrowth after cutting (image analysis-based) and leaf growth 2 weeks after cutting (manual measurement), with r values up to 0.792 and 0.824, respectively. Nevertheless, these relations depend on the origin of the plant material (forage breeding lines, current forage varieties, current turf varieties, and wild accessions) and the period in the season. CONCLUSIONS The image-derived parameters presented here deliver reliable, objective data, complementary to the breeders' scores, and are useful for genetic studies. Furthermore, large variation was shown among genotypes for the parameters investigated.
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Affiliation(s)
- Peter Lootens
- />Plant Sciences Unit - Growth and Development, ILVO, Caritasstraat 39, 9090 Melle, Belgium
| | - Tom Ruttink
- />Plant Sciences Unit - Growth and Development, ILVO, Caritasstraat 39, 9090 Melle, Belgium
| | - Antje Rohde
- />Plant Sciences Unit - Growth and Development, ILVO, Caritasstraat 39, 9090 Melle, Belgium
- />Bayer CropScience, Technologiepark 38, 9052 Ghent, Belgium
| | | | | | - Isabel Roldán-Ruiz
- />Plant Sciences Unit - Growth and Development, ILVO, Caritasstraat 39, 9090 Melle, Belgium
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Christiaens A, De Keyser E, Lootens P, Pauwels E, Roldán-Ruiz I, De Riek J, Gobin B, Van Labeke MC. Cold storage to overcome dormancy affects the carbohydrate status and photosynthetic capacity of Rhododendron simsii. Plant Biol (Stuttg) 2015; 17:97-105. [PMID: 24854016 DOI: 10.1111/plb.12195] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2014] [Accepted: 03/20/2014] [Indexed: 05/16/2023]
Abstract
Global warming leads to increasing irregular and unexpected warm spells during autumn, and therefore natural chilling requirements to break dormancy are at risk. Controlled cold treatment can provide an answer to this problem. Nevertheless, artificial cold treatment will have consequences for carbon reserves and photosynthesis. In this paper, the effect of dark cold storage at 7 °C to break flower bud dormancy in the evergreen Rhododendron simsii was quantified. Carbohydrate and starch content in leaves and flower buds of an early ('Nordlicht'), semi-early ('M. Marie') and late ('Mw. G. Kint') flowering cultivar showed that carbon loss due to respiration was lowest in 'M. Marie', while 'Mw. G. Kint' was completely depleted of starch reserves at the end of cold treatment. Gene isolation resulted in a candidate gene for sucrose synthase (SUS) RsSus, which appears to be homologous to AtSus3 and had a clear increase in expression in leaves during cold treatment. Photosynthesis measurements on 'Nordlicht' and the late-flowering cultivar 'Thesla' showed that during cold treatment, dark respiration decreased 58% and 63%, respectively. Immediately after cold treatment, dark respiration increased and stabilised after 3 days. The light compensation point followed the same trend as dark respiration. Quantum efficiency showed no significant changes during the first days after cold treatment, but was significantly higher than in plants with dormant flower buds at the start of cold treatment. In conclusion, photosynthesis stabilised 3 days after cold treatment and was improved compared to the level before cold treatment.
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Affiliation(s)
- A Christiaens
- Department of Plant Production, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium; PCS Ornamental Plant Research, Destelbergen, Belgium
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Voorend W, Lootens P, Nelissen H, Roldán-Ruiz I, Inzé D, Muylle H. LEAF-E: a tool to analyze grass leaf growth using function fitting. Plant Methods 2014; 10:37. [PMID: 25435898 PMCID: PMC4246515 DOI: 10.1186/1746-4811-10-37] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2014] [Accepted: 09/26/2014] [Indexed: 05/18/2023]
Abstract
In grasses, leaf growth is often monitored to gain insights in growth processes, biomass accumulation, regrowth after cutting, etc. To study the growth dynamics of the grass leaf, its length is measured at regular time intervals to derive the leaf elongation rate (LER) profile over time. From the LER profile, parameters such as maximal LER and leaf elongation duration (LED), which are essential for detecting inter-genotype growth differences and/or quantifying plant growth responses to changing environmental conditions, can be determined. As growth is influenced by the circadian clock and, especially in grasses, changes in environmental conditions such as temperature and evaporative demand, the LER profiles show considerable experimental variation and thus often do not follow a smooth curve. Hence it is difficult to quantify the duration and timing of growth. For these reasons, the measured data points should be fitted using a suitable mathematical function, such as the beta sigmoid function for leaf elongation. In the context of high-throughput phenotyping, we implemented the fitting of leaf growth measurements into a user-friendly Microsoft Excel-based macro, a tool called LEAF-E. LEAF-E allows to perform non-linear regression modeling of leaf length measurements suitable for robust and automated extraction of leaf growth parameters such as LER and LED from large datasets. LEAF-E is particularly useful to quantify the timing of leaf growth, which forms an important added value for detecting differences in leaf growth development. We illustrate the broad application range of LEAF-E using published and unpublished data sets of maize, Miscanthus spp. and Brachypodium distachyon, generated in independent experiments and for different purposes. In addition, we show that LEAF-E could also be used to fit datasets of other growth-related processes that follow the sigmoidal profile, such as cell length measurements along the leaf axis. Given its user-friendliness, ability to quantify duration and timing of leaf growth and broad application range, LEAF-E is a tool that could be routinely used to study growth processes following the sigmoidal profile.
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Affiliation(s)
- Wannes Voorend
- />Department of Plant Systems Biology, VIB, Technologiepark 927, 9052 Gent, Belgium
- />Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052 Gent, Belgium
- />Plant Sciences Unit – Growth and Development, Institute for Agricultural and Fisheries Research (ILVO), Caritasstraat 21, 9090 Melle, Belgium
| | - Peter Lootens
- />Plant Sciences Unit – Growth and Development, Institute for Agricultural and Fisheries Research (ILVO), Caritasstraat 21, 9090 Melle, Belgium
| | - Hilde Nelissen
- />Department of Plant Systems Biology, VIB, Technologiepark 927, 9052 Gent, Belgium
- />Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052 Gent, Belgium
| | - Isabel Roldán-Ruiz
- />Plant Sciences Unit – Growth and Development, Institute for Agricultural and Fisheries Research (ILVO), Caritasstraat 21, 9090 Melle, Belgium
| | - Dirk Inzé
- />Department of Plant Systems Biology, VIB, Technologiepark 927, 9052 Gent, Belgium
- />Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052 Gent, Belgium
| | - Hilde Muylle
- />Plant Sciences Unit – Growth and Development, Institute for Agricultural and Fisheries Research (ILVO), Caritasstraat 21, 9090 Melle, Belgium
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Christiaens A, De Keyser E, Lootens P, Pauwels E, Roldan-Ruiz I, De Riek J, Gobin B, Van Labeke MC. Cold storage to overcome dormancy affects the carbon balance of azalea. Commun Agric Appl Biol Sci 2014; 79:45-49. [PMID: 25864312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Flower bud dormancy in azalea (Rhododendron simsii) is broken by artificial cold treatment and this will have its consequences on carbon reserves and photosynthesis. The effect of cold storage at 7 °C on carbohydrate and starch content in leaves and flower buds of an early ('Nordlicht') and semi-early ('M. Marie) flowering cultivar was quantified. Carbon loss due to respiration was lowest for 'M. Marie'. Photosynthetic measurements on 'Nordlicht' showed that photosynthesis 3 days after cold treatment (plants ready to flower) was improved compared to before cold treatment (plants with dormant flower buds).
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Pollet B, Vanhaecke L, Dambre P, Lootens P, Steppe K. Low night temperature acclimation of Phalaenopsis. Plant Cell Rep 2011; 30:1125-34. [PMID: 21305300 DOI: 10.1007/s00299-011-1021-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2010] [Revised: 01/05/2011] [Accepted: 01/19/2011] [Indexed: 05/16/2023]
Abstract
The capability of Phalaenopsis to acclimate its photosynthetic capacity and metabolic activity to cool night temperature conditions is crucial for improving orchid production in terms of efficient greenhouse heating. The extent to which Phalaenopsis possesses acclimation potential and the mechanistic background of the metabolic processes involved, have, however, not been studied before. Plants were subjected to a direct and gradual shift from a day to night temperature regime of 28/28-28/16°C, the cold stress and cold acclimation treatment, respectively. In comparison with the cold stress treatment, the cold acclimation treatment led to a higher malate accumulation and a reduction in leaf net CO(2) uptake. Consistently, the contribution of respiratory CO(2) recycling to nocturnal malate synthesis was calculated to be 23.5 and 47.0% for the cold stress and cold acclimation treatment, respectively. Moreover, the lower levels of starch measured in the cold acclimated leaves confirmed the suggested enhanced respiratory CO(2) recycling, implying that Phalaenopsis CAM operation evolved towards CAM idling. It is, however, plausible that this adjustment was not an effect of the low night temperature per se but a consequence of cool-root induced drought stress. Apart from that, at the start of the photoperiod, membrane stability showed a depression which was directly counteracted by an increased generation of glucose, fructose and sucrose. From these observations, it can be concluded that the observed plasticity in CAM operation and metabolic flexibility may be recognized as important steps in the low night temperature acclimation of Phalaenopsis.
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Affiliation(s)
- Bruno Pollet
- Laboratory of Plant Ecology, Department of Applied Ecology and Environmental Biology, Faculty of Bioscience Engineering, Ghent University, Coupure links 653, 9000 Ghent, Belgium.
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20
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Devacht S, Lootens P, Baert J, Van Waes J, Van Bockstaele E, Roldan-Ruiz I. Influence of anthocyanin on the photosynthetic performance of industrial chicory under cold stress conditions. Commun Agric Appl Biol Sci 2009; 74:121-6. [PMID: 20420233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Affiliation(s)
- S Devacht
- Institute for Agricultural and Fisheries Research, Plant Sciences Unit, Burgemeester Van Gansberghelaan 109, BE-9820 Merelbeke, Belgium
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21
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Devacht S, Lootens P, Roldan-Ruiz I, Carlier L, Baert J, Van Huylenbroeck J, Van Waes J, Van Bockstaele E. The use of chlorophyll fluorescence imaging to evaluate the effect of cold stress for industrial chicory. Commun Agric Appl Biol Sci 2008; 73:137-40. [PMID: 18831260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Affiliation(s)
- S Devacht
- Institute for Agricultural and Fisheries Research (ILVO), Plant Burgemeester Van Gansberghelaan 109, BE-9820 Merelbeke, Belgium
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Devacht S, Lootens P, Carlier L, Baert J, Van Waes J, Van Bockstaele E. Effect of cold stress on early vigour, photosynthesis, chlorophyll A fluorescence and pigment content of industrial chicory. Commun Agric Appl Biol Sci 2007; 72:165-9. [PMID: 18018880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Affiliation(s)
- S Devacht
- Institute for Agricultural and Fisheries Research (ILVO), Plant Burg. Van Gansberghelaan 109 box 1, BE-9820 Merelbeke, Belgium
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Coart E, Lamote V, De Loose M, Van Bockstaele E, Lootens P, Roldán-Ruiz I. AFLP markers demonstrate local genetic differentiation between two indigenous oak species [ Quercus robur L. and Quercus petraea (Matt.) Liebl.] in Flemish populations. Theor Appl Genet 2002; 105:431-439. [PMID: 12582548 DOI: 10.1007/s00122-002-0920-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2001] [Accepted: 11/26/2001] [Indexed: 05/24/2023]
Abstract
The nuclear genetic variation within and between four sessile ( Q. petraea) and six pedunculate ( Q. robur) autochthonous Flemish oak populations was investigated with AFLP markers. One sessile and one pedunculate oak population were additionally screened for detailed leaf characteristics using an image analysis system. Principal coordinate analysis on the AFLP data classified the oaks in two main groups, according to their taxonomic status. No species-specific AFLP markers were found using four primer combinations, but marker frequency differences up to 71% were recorded between both species. Analysis of the genetic structure showed that the divergence between species, as observed by ordination, was significant. Both species revealed similar diversity levels. A smaller though significant differentiation was also revealed for both species among populations within species. Molecular and morphology based approaches showed a high degree of consistency. Screening of 60 AFLP primer combinations using a bulking strategy did not allow identifying species-specific markers, which supports the conclusions reached in previous studies. The distribution of genetic variability at the species and at the population level is discussed.
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Affiliation(s)
- E. Coart
- Department for Plant Genetics and Breeding, Agricultural Research Centre, Caritasstraat 21, 9090 Melle, Belgium,
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Hulsen K, Minne V, Lootens P, Vandecasteele P, Höfte M. A chlorophyll a fluorescence-based Lemna minor bioassay to monitor microbial degradation of nanomolar to micromolar concentrations of linuron. Environ Microbiol 2002; 4:327-37. [PMID: 12071978 DOI: 10.1046/j.1462-2920.2002.00309.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
A plant-microbial bioassay, based on the aquatic macrophyte Lemna minor L. (duckweed), was used to monitor biodegradation of nano- and micromolar concentrations of the phenylurea herbicide linuron. After 7 days of exposure to linuron, log-logistic-based dose-response analysis revealed significant growth inhibition on the total frond area of L. minor when linuron concentrations > or = 80 nM were added to the bioassay. A plant-protective effect was obtained for all concentrations > 80 nM by inoculation with either a bacterial consortium or Variovorax paradoxus WDL1, which is probably the main actor in this consortium. The outcome of the plant-microbe-toxicant interaction was also assessed using pulse amplitude-modulated chlorophyll a fluorescence and chlorophyll a fluorescence imaging. Linuron toxicity to L. minor became apparent as a significant decrease in the effective quantum yield (Delta F/Fm') within 90 min after exposure of the plants to linuron concentrations > or = 160 nM. Inoculation of the bioassay with the linuron-degrading bacteria neutralized the effect on the effective quantum yield at concentrations > or = 160 nM, indicating microbial degradation of these concentrations. The chlorophyll a fluorescence-based Lemna bioassay described here offers a sensitive, fast and cost-effective approach to study the potential of biodegrading microorganisms to break down minute concentrations of photosynthesis-inhibiting xenobiotics.
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Affiliation(s)
- Kris Hulsen
- Laboratory of Phytopathology, Department of Crop Protection, Faculty of Agricultural and Applied Biological Sciences, Ghent University, Coupure Links 653, B-9000 Gent, Belgium
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