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Tao H, Xu S, Tian Y, Li Z, Ge Y, Zhang J, Wang Y, Zhou G, Deng X, Zhang Z, Ding Y, Jiang D, Guo Q, Jin S. Proximal and remote sensing in plant phenomics: 20 years of progress, challenges, and perspectives. PLANT COMMUNICATIONS 2022; 3:100344. [PMID: 35655429 PMCID: PMC9700174 DOI: 10.1016/j.xplc.2022.100344] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 05/08/2022] [Accepted: 05/27/2022] [Indexed: 06/01/2023]
Abstract
Plant phenomics (PP) has been recognized as a bottleneck in studying the interactions of genomics and environment on plants, limiting the progress of smart breeding and precise cultivation. High-throughput plant phenotyping is challenging owing to the spatio-temporal dynamics of traits. Proximal and remote sensing (PRS) techniques are increasingly used for plant phenotyping because of their advantages in multi-dimensional data acquisition and analysis. Substantial progress of PRS applications in PP has been observed over the last two decades and is analyzed here from an interdisciplinary perspective based on 2972 publications. This progress covers most aspects of PRS application in PP, including patterns of global spatial distribution and temporal dynamics, specific PRS technologies, phenotypic research fields, working environments, species, and traits. Subsequently, we demonstrate how to link PRS to multi-omics studies, including how to achieve multi-dimensional PRS data acquisition and processing, how to systematically integrate all kinds of phenotypic information and derive phenotypic knowledge with biological significance, and how to link PP to multi-omics association analysis. Finally, we identify three future perspectives for PRS-based PP: (1) strengthening the spatial and temporal consistency of PRS data, (2) exploring novel phenotypic traits, and (3) facilitating multi-omics communication.
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Affiliation(s)
- Haiyu Tao
- Plant Phenomics Research Centre, Academy for Advanced Interdisciplinary Studies, National Engineering and Technology Center for Information Agriculture, Collaborative Innovation Centre for Modern Crop Production co-sponsored by Province and Ministry, Nanjing Agricultural University, Address: No. 1 Weigang, Xuanwu District, Nanjing 210095, China
| | - Shan Xu
- Plant Phenomics Research Centre, Academy for Advanced Interdisciplinary Studies, National Engineering and Technology Center for Information Agriculture, Collaborative Innovation Centre for Modern Crop Production co-sponsored by Province and Ministry, Nanjing Agricultural University, Address: No. 1 Weigang, Xuanwu District, Nanjing 210095, China
| | - Yongchao Tian
- Plant Phenomics Research Centre, Academy for Advanced Interdisciplinary Studies, National Engineering and Technology Center for Information Agriculture, Collaborative Innovation Centre for Modern Crop Production co-sponsored by Province and Ministry, Nanjing Agricultural University, Address: No. 1 Weigang, Xuanwu District, Nanjing 210095, China
| | - Zhaofeng Li
- The Key Laboratory of Oasis Eco-agriculture, Xinjiang Production and Construction Corps, Agriculture College, Shihezi University, Shihezi 832003, China
| | - Yan Ge
- Plant Phenomics Research Centre, Academy for Advanced Interdisciplinary Studies, National Engineering and Technology Center for Information Agriculture, Collaborative Innovation Centre for Modern Crop Production co-sponsored by Province and Ministry, Nanjing Agricultural University, Address: No. 1 Weigang, Xuanwu District, Nanjing 210095, China
| | - Jiaoping Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Key Laboratory for Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), Nanjing Agricultural University, Nanjing 210095, China
| | - Yu Wang
- Plant Phenomics Research Centre, Academy for Advanced Interdisciplinary Studies, National Engineering and Technology Center for Information Agriculture, Collaborative Innovation Centre for Modern Crop Production co-sponsored by Province and Ministry, Nanjing Agricultural University, Address: No. 1 Weigang, Xuanwu District, Nanjing 210095, China
| | - Guodong Zhou
- Sanya Research Institute of Nanjing Agriculture University, Sanya 572024, China
| | - Xiong Deng
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Ze Zhang
- The Key Laboratory of Oasis Eco-agriculture, Xinjiang Production and Construction Corps, Agriculture College, Shihezi University, Shihezi 832003, China
| | - Yanfeng Ding
- Plant Phenomics Research Centre, Academy for Advanced Interdisciplinary Studies, National Engineering and Technology Center for Information Agriculture, Collaborative Innovation Centre for Modern Crop Production co-sponsored by Province and Ministry, Nanjing Agricultural University, Address: No. 1 Weigang, Xuanwu District, Nanjing 210095, China; Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China; Sanya Research Institute of Nanjing Agriculture University, Sanya 572024, China
| | - Dong Jiang
- Plant Phenomics Research Centre, Academy for Advanced Interdisciplinary Studies, National Engineering and Technology Center for Information Agriculture, Collaborative Innovation Centre for Modern Crop Production co-sponsored by Province and Ministry, Nanjing Agricultural University, Address: No. 1 Weigang, Xuanwu District, Nanjing 210095, China; Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China; Sanya Research Institute of Nanjing Agriculture University, Sanya 572024, China
| | - Qinghua Guo
- Institute of Ecology, College of Urban and Environmental Science, Peking University, Beijing 100871, China
| | - Shichao Jin
- Plant Phenomics Research Centre, Academy for Advanced Interdisciplinary Studies, National Engineering and Technology Center for Information Agriculture, Collaborative Innovation Centre for Modern Crop Production co-sponsored by Province and Ministry, Nanjing Agricultural University, Address: No. 1 Weigang, Xuanwu District, Nanjing 210095, China; Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China; Sanya Research Institute of Nanjing Agriculture University, Sanya 572024, China; Jiangsu Provincial Key Laboratory of Geographic Information Science and Technology, International Institute for Earth System Sciences, Nanjing University, Nanjing, Jiangsu 210023, China.
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2
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Vello E, Aguirre J, Shao Y, Bureau T. Camelina sativa High-Throughput Phenotyping Under Normal and Salt Conditions Using a Plant Phenomics Platform. Methods Mol Biol 2022; 2539:25-36. [PMID: 35895193 DOI: 10.1007/978-1-0716-2537-8_4] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Climate change and environmental pollution will have a great impact on food security worldwide. More than 30% of the world's irrigated areas are estimated to be perturbed by high salinity affecting the productivity of crops. Camelina sativa, also known as false flax, is a flowering plant that is mainly cultivated as an oilseed crop that has many potential economic benefits; it can be used in food products, in industrial applications, and in animal feed and converted into biofuel. However, natural disasters due to climate events have led to significant crop losses. In this work, we developed a high-throughput phenotyping protocol to analyze the effects of different concentrations of salt on C. sativa using the McGill Plant Phenomics Platform (MP3). We present an adapted protocol to be applied with phenomics facilities in a greenhouse environment and the most effective way for high-throughput phenotyping.
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Affiliation(s)
- Emilio Vello
- Department of Biology, McGill University, Montreal, QC, Canada.
| | - John Aguirre
- Department of Biology, McGill University, Montreal, QC, Canada
| | - Yang Shao
- Department of Biology, McGill University, Montreal, QC, Canada
| | - Thomas Bureau
- Department of Biology, McGill University, Montreal, QC, Canada.
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3
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Amini S, Arsova B, Gobert S, Carnol M, Bosman B, Motte P, Watt M, Hanikenne M. Transcriptional regulation of ZIP genes is independent of local zinc status in Brachypodium shoots upon zinc deficiency and resupply. PLANT, CELL & ENVIRONMENT 2021; 44:3376-3397. [PMID: 34263935 DOI: 10.1111/pce.14151] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 07/05/2021] [Accepted: 07/10/2021] [Indexed: 06/13/2023]
Abstract
The biological processes underlying zinc homeostasis are targets for genetic improvement of crops to counter human malnutrition. Detailed phenotyping, ionomic, RNA-Seq analyses and flux measurements with 67 Zn isotope revealed whole-plant molecular events underlying zinc homeostasis upon varying zinc supply and during zinc resupply to starved Brachypodium distachyon (Brachypodium) plants. Although both zinc deficiency and excess hindered Brachypodium growth, accumulation of biomass and micronutrients into roots and shoots differed depending on zinc supply. The zinc resupply dynamics involved 1,893 zinc-responsive genes. Multiple zinc-regulated transporter and iron-regulated transporter (IRT)-like protein (ZIP) transporter genes and dozens of other genes were rapidly and transiently down-regulated in early stages of zinc resupply, suggesting a transient zinc shock, sensed locally in roots. Notably, genes with identical regulation were observed in shoots without zinc accumulation, pointing to root-to-shoot signals mediating whole-plant responses to zinc resupply. Molecular events uncovered in the grass model Brachypodium are useful for the improvement of staple monocots.
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Affiliation(s)
- Sahand Amini
- InBioS - PhytoSystems, Functional Genomics and Plant Molecular Imaging, University of Liège, Liège, Belgium
| | - Borjana Arsova
- Root Dynamics Group, IBG-2 - Plant Sciences, Institut für Bio- und Geowissenschaften (IBG), Forschungszentrum Jülich, Jülich, Germany
| | - Sylvie Gobert
- Laboratory of Oceanology, MARE Center, FOCUS, University of Liège, Liège, Belgium
- Station de Recherches Sous-Marines et Océanographiques (STARESO), Pointe de la Revellata, Calvi, France
| | - Monique Carnol
- InBioS - PhytoSystems, Laboratory of Plant and Microbial Ecology, Department of Biology, Ecology, Evolution, University of Liège, Liège, Belgium
| | - Bernard Bosman
- InBioS - PhytoSystems, Laboratory of Plant and Microbial Ecology, Department of Biology, Ecology, Evolution, University of Liège, Liège, Belgium
| | - Patrick Motte
- InBioS - PhytoSystems, Functional Genomics and Plant Molecular Imaging, University of Liège, Liège, Belgium
| | - Michelle Watt
- Root Dynamics Group, IBG-2 - Plant Sciences, Institut für Bio- und Geowissenschaften (IBG), Forschungszentrum Jülich, Jülich, Germany
| | - Marc Hanikenne
- InBioS - PhytoSystems, Functional Genomics and Plant Molecular Imaging, University of Liège, Liège, Belgium
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Verbyla AP, De Faveri J, Deery DM, Rebetzke GJ. Modelling temporal genetic and spatio‐temporal residual effects for high‐throughput phenotyping data*. AUST NZ J STAT 2021. [DOI: 10.1111/anzs.12336] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- A. P. Verbyla
- Data61 CSIRO 47 Maunds Rd. Atherton QLD4883Australia
| | - J. De Faveri
- Data61 CSIRO 47 Maunds Rd. Atherton QLD4883Australia
| | - D. M. Deery
- Agriculture and Food CSIRO 2 ‐ 40 Clunies Ross Street Acton ACT2601Australia
| | - G. J. Rebetzke
- Agriculture and Food CSIRO 2 ‐ 40 Clunies Ross Street Acton ACT2601Australia
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Baudson C, Delory BM, Spaepen S, du Jardin P, Delaplace P. Developmental plasticity of Brachypodium distachyon in response to P deficiency: Modulation by inoculation with phosphate-solubilizing bacteria. PLANT DIRECT 2021; 5:e00296. [PMID: 33532689 PMCID: PMC7833465 DOI: 10.1002/pld3.296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 06/17/2020] [Accepted: 11/14/2020] [Indexed: 06/12/2023]
Abstract
BACKGROUND Mineral phosphorus (P) fertilizers must be used wisely in order to preserve rock phosphate, a limited and non-renewable resource. The use of bio-inoculants to improve soil nutrient availability and trigger an efficient plant response to nutrient deficiency is one potential strategy in the attempt to decrease P inputs in agriculture. METHOD An in vitro co-cultivation system was used to study the response of Brachypodium distachyon to contrasted P supplies (soluble and poorly soluble forms of P) and inoculation with P solubilizing bacteria. Brachypodium's responses to P conditions and inoculation with bacteria were studied in terms of developmental plasticity and P use efficiency. RESULTS Brachypodium showed plasticity in its biomass allocation pattern in response to variable P conditions, specifically by prioritizing root development over shoot productivity under poorly soluble P conditions. Despite the ability of the bacteria to solubilize P, shoot productivity was depressed in plants inoculated with bacteria, although the root system development was maintained. The negative impact of bacteria on biomass production in Brachypodium might be attributed to inadequate C supply to bacteria, an increased competition for P between both organisms under P-limiting conditions, or an accumulation of toxic bacterial metabolites in our cultivation system. Both P and inoculation treatments impacted root system morphology. The modulation of Brachypodium's developmental response to P supplies by P solubilizing bacteria did not lead to improved P use efficiency. CONCLUSION Our results support the hypothesis that plastic responses of Brachypodium cultivated under P-limited conditions are modulated by P solubilizing bacteria. The considered experimental context impacts plant-bacteria interactions. Choosing experimental conditions as close as possible to real ones is important in the selection of P solubilizing bacteria. Both persistent homology and allometric analyses proved to be useful tools that should be considered when studying the impact of bio-inoculants on plant development in response to varying nutritional context.
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Affiliation(s)
- Caroline Baudson
- Plant SciencesGembloux Agro‐Bio TechUniversity of LiègeLiègeBelgium
| | | | - Stijn Spaepen
- Leuven Institute for Beer ResearchUniversity of LeuvenLeuvenBelgium
| | | | - Pierre Delaplace
- Plant SciencesGembloux Agro‐Bio TechUniversity of LiègeLiègeBelgium
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Wang J, Dimech AM, Spangenberg G, Smith K, Badenhorst P. Rapid Screening of Nitrogen Use Efficiency in Perennial Ryegrass ( Lolium perenne L.) Using Automated Image-Based Phenotyping. FRONTIERS IN PLANT SCIENCE 2020; 11:565361. [PMID: 32973856 PMCID: PMC7481514 DOI: 10.3389/fpls.2020.565361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 08/12/2020] [Indexed: 06/11/2023]
Abstract
Perennial ryegrass (Lolium perenne L.) is a dominant species in temperate Australian pastures. Currently, nitrogenous fertilizers are used to support herbage production for pasture and fodder. Increasing the nitrogen use efficiency (NUE) of pasture grasses could decrease the amount of fertilizer application and reduce nitrogen (N) leaching into the environment. NUE, defined as units of dry matter production per unit of supplied nitrogen, is a complex trait in which genomic selection may provide a promising strategy in breeding. Our objective was to develop a rapid, high-throughput screening method to enable genomic selection for y -60NUE in perennial ryegrass. NUE of 76 genotypes of perennial ryegrass from a breeding population were screened in a greenhouse using an automated image-based phenomics platform under low (0.5 mM) and moderate (5 mM) N levels over 3 consecutive harvests. Significant (p < 0.05) genotype, treatment, and genotype by treatment interactions for dry matter yield and NUE were observed. NUE under low and moderate N treatments was significantly correlated. Of the seven plant architecture features directly extracted from image analysis and four secondarily derived measures, mean projected plant area (MPPA) from the two side view images had the highest correlation with dry matter yield (r = 0.94). Automated digital image-based phenotyping enables temporal plant growth responses to N to be measured efficiently and non-destructively. The method developed in this study would be suitable for screening large populations of perennial ryegrass growth in response to N for genomic selection purposes.
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Affiliation(s)
- Junping Wang
- Agriculture Victoria Research, Hamilton, VIC, Australia
| | - Adam M. Dimech
- AgriBio Centre for AgriBioscience, Agriculture Victoria Research, Bundoora, VIC, Australia
| | - German Spangenberg
- AgriBio Centre for AgriBioscience, Agriculture Victoria Research, Bundoora, VIC, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, Australia
| | - Kevin Smith
- Agriculture Victoria Research, Hamilton, VIC, Australia
- The Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC, Australia
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Banerjee BP, Joshi S, Thoday-Kennedy E, Pasam RK, Tibbits J, Hayden M, Spangenberg G, Kant S. High-throughput phenotyping using digital and hyperspectral imaging-derived biomarkers for genotypic nitrogen response. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:4604-4615. [PMID: 32185382 PMCID: PMC7382386 DOI: 10.1093/jxb/eraa143] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Accepted: 03/17/2020] [Indexed: 05/18/2023]
Abstract
The development of crop varieties with higher nitrogen use efficiency is crucial for sustainable crop production. Combining high-throughput genotyping and phenotyping will expedite the discovery of novel alleles for breeding crop varieties with higher nitrogen use efficiency. Digital and hyperspectral imaging techniques can efficiently evaluate the growth, biophysical, and biochemical performance of plant populations by quantifying canopy reflectance response. Here, these techniques were used to derive automated phenotyping of indicator biomarkers, biomass and chlorophyll levels, corresponding to different nitrogen levels. A detailed description of digital and hyperspectral imaging and the associated challenges and required considerations are provided, with application to delineate the nitrogen response in wheat. Computational approaches for spectrum calibration and rectification, plant area detection, and derivation of vegetation index analysis are presented. We developed a novel vegetation index with higher precision to estimate chlorophyll levels, underpinned by an image-processing algorithm that effectively removed background spectra. Digital shoot biomass and growth parameters were derived, enabling the efficient phenotyping of wheat plants at the vegetative stage, obviating the need for phenotyping until maturity. Overall, our results suggest value in the integration of high-throughput digital and spectral phenomics for rapid screening of large wheat populations for nitrogen response.
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Affiliation(s)
- Bikram P Banerjee
- Agriculture Victoria, Grains Innovation Park, Horsham, VIC, Australia
| | - Sameer Joshi
- Agriculture Victoria, Grains Innovation Park, Horsham, VIC, Australia
| | | | - Raj K Pasam
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, Australia
| | - Josquin Tibbits
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, Australia
| | - Matthew Hayden
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, Australia
| | - German Spangenberg
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, Australia
| | - Surya Kant
- Agriculture Victoria, Grains Innovation Park, Horsham, VIC, Australia
- Centre for Agricultural Innovation, School of Agriculture and Food, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Victoria, Australia
- Correspondence:
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Nam BE, Park YJ, Gil KE, Kim JH, Kim JG, Park CM. Auxin mediates the touch-induced mechanical stimulation of adventitious root formation under windy conditions in Brachypodium distachyon. BMC PLANT BIOLOGY 2020; 20:335. [PMID: 32678030 PMCID: PMC7364541 DOI: 10.1186/s12870-020-02544-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Accepted: 07/07/2020] [Indexed: 05/20/2023]
Abstract
BACKGROUND It is widely perceived that mechanical or thigmomorphogenic stimuli, such as rubbing and bending by passing animals, wind, raindrop, and flooding, broadly influence plant growth and developmental patterning. In particular, wind-driven mechanical stimulation is known to induce the incidence of radial expansion and shorter and stockier statue. Wind stimulation also affects the adaptive propagation of the root system in various plant species. However, it is unknown how plants sense and transmit the wind-derived mechanical signals to launch appropriate responses, leading to the wind-adaptive root growth. RESULTS Here, we found that Brachypodium distachyon, a model grass widely used for studies on bioenergy crops and cereals, efficiently adapts to wind-mediated lodging stress by forming adventitious roots (ARs) from nonroot tissues. Experimental dissection of wind stimuli revealed that not bending of the mesocotyls but physical contact of the leaf nodes with soil particles triggers the transcriptional induction of a group of potential auxin-responsive genes encoding WUSCHEL RELATED HOMEOBOX and LATERAL ORGAN BOUNDARIES DOMAIN transcription factors, which are likely to be involved in the induction of AR formation. CONCLUSIONS Our findings would contribute to further understanding molecular mechanisms governing the initiation and development of ARs, which will be applicable to crop agriculture in extreme wind climates.
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Affiliation(s)
- Bo Eun Nam
- Department of Chemistry, Seoul National University, Seoul, 08826, South Korea
- Department of Biology Education, Seoul National University, Seoul, 08826, South Korea
| | - Young-Joon Park
- Department of Chemistry, Seoul National University, Seoul, 08826, South Korea
| | - Kyung-Eun Gil
- Department of Chemistry, Seoul National University, Seoul, 08826, South Korea
| | - Ju-Heon Kim
- Department of Chemistry, Seoul National University, Seoul, 08826, South Korea
| | - Jae Geun Kim
- Department of Biology Education, Seoul National University, Seoul, 08826, South Korea
| | - Chung-Mo Park
- Department of Chemistry, Seoul National University, Seoul, 08826, South Korea.
- Plant Genomics and Breeding Institute, Seoul National University, Seoul, 08826, South Korea.
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Nguyen GN, Maharjan P, Maphosa L, Vakani J, Thoday-Kennedy E, Kant S. A Robust Automated Image-Based Phenotyping Method for Rapid Vegetative Screening of Wheat Germplasm for Nitrogen Use Efficiency. FRONTIERS IN PLANT SCIENCE 2019; 10:1372. [PMID: 31772563 PMCID: PMC6849468 DOI: 10.3389/fpls.2019.01372] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Accepted: 10/04/2019] [Indexed: 05/29/2023]
Abstract
Nitrogen use efficiency (NUE) in crops is generally low, with more than 60% of applied nitrogen (N) being lost to the environment, which increases production costs and affects ecosystems and human habitats. To overcome these issues, the breeding of crop varieties with improved NUE is needed, requiring efficient phenotyping methods along with molecular and genetic approaches. To develop an effective phenotypic screening method, experiments on wheat varieties under various N levels were conducted in the automated phenotyping platform at Plant Phenomics Victoria, Horsham. The results from the initial experiment showed that two relative N levels-5 mM and 20 mM, designated as low and optimum N, respectively-were ideal to screen a diverse range of wheat germplasm for NUE on the automated imaging phenotyping platform. In the second experiment, estimated plant parameters such as shoot biomass and top-view area, derived from digital images, showed high correlations with phenotypic traits such as shoot biomass and leaf area seven weeks after sowing, indicating that they could be used as surrogate measures of the latter. Plant growth analysis confirmed that the estimated plant parameters from the vegetative linear growth phase determined by the "broken-stick" model could effectively differentiate the performance of wheat varieties for NUE. Based on this study, vegetative phenotypic screens should focus on selecting wheat varieties under low N conditions, which were highly correlated with biomass and grain yield at harvest. Analysis indicated a relationship between controlled and field conditions for the same varieties, suggesting that greenhouse screens could be used to prioritise a higher value germplasm for subsequent field studies. Overall, our results showed that this phenotypic screening method is highly applicable and can be applied for the identification of N-efficient wheat germplasm at the vegetative growth phase.
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Affiliation(s)
- Giao N. Nguyen
- Agriculture Victoria, Grains Innovation Park, Horsham, VIC, Australia
| | - Pankaj Maharjan
- Agriculture Victoria, Grains Innovation Park, Horsham, VIC, Australia
| | - Lance Maphosa
- Agriculture Victoria, Grains Innovation Park, Horsham, VIC, Australia
| | - Jignesh Vakani
- Agriculture Victoria, Grains Innovation Park, Horsham, VIC, Australia
| | | | - Surya Kant
- Agriculture Victoria, Grains Innovation Park, Horsham, VIC, Australia
- Centre for Agricultural Innovation, The University of Melbourne, Melbourne, VIC, Australia
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Neji M, Kouas S, Gandour M, Aydi S, Abdelly C. Genetic variability of morpho-physiological response to phosphorus deficiency in Tunisian populations of Brachypodium hybridum. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2019; 143:246-256. [PMID: 31525602 DOI: 10.1016/j.plaphy.2019.09.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 09/03/2019] [Accepted: 09/04/2019] [Indexed: 06/10/2023]
Abstract
Brachypodium hybridum (Poaceae) is widely distributed in the dry environments in Mediterranean basin, due to its high tolerance to drought. Investigating the natural variation of B. hybridum in response to environmental stresses is crucial for unraveling the genetic network of its stress tolerance. 79 B. hybridum lines from eight Tunisian populations were screened for their performance to low P availability using morpho-physiological parameters. ANOVA showed that treatment and population*treatment factors were the most contributors in the explained variance for the majority of parameters. A considerable population differentiation was detected in control and under P level (Qst = 0.77 vs Qst = 0.62). This suggests that B. hybridum exhibit an adaptive differential response to P deficiency related environmental conditions. Results revealed that Raouad and Sejnen lines were the most tolerant to P deficiency followed by Haouaria and Enfidha lines. The remaining populations were classified as sensitive. This pattern suggests that coastal populations were more tolerant to P deficiency than the inland ones. A slightly higher heritability was evidenced under low P level for most of traits, indicating that the direct selection under P deficiency is more reliable than an indirect one under optimal P supply.
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Affiliation(s)
- Mohamed Neji
- Laboratory of Extremophile Plants, Centre of Biotechnology of Borj Cedria, BP 901 Hammam Lif 2050, Tunisia; Department of Life Sciences, Faculty of Sciences of Gabès, University of Gabès, Cité Erriadh 6072 Zrig, Gabès, Tunisia; Unit of Evolutionary Biology & Ecology, Faculté des Sciences, Université Libre de Bruxelles, Av. F.D. Roosevelt, 50, CP 160/12, B-1050, Brussels, Belgium.
| | - Saber Kouas
- Laboratory of Extremophile Plants, Centre of Biotechnology of Borj Cedria, BP 901 Hammam Lif 2050, Tunisia; Department of Life Sciences, Faculty of Sciences of Gabès, University of Gabès, Cité Erriadh 6072 Zrig, Gabès, Tunisia; Plant Physiology and Functional Genomics Research Unit, Institute of Biotechnology, University of Sfax, BP 1175, 3038 Sfax, Tunisia
| | - Mhemmed Gandour
- Laboratory of Extremophile Plants, Centre of Biotechnology of Borj Cedria, BP 901 Hammam Lif 2050, Tunisia; Faculty of Sciences and Technology of Sidi Bouzid, 9100, Sidi Bouzid, Tunisia
| | - Samir Aydi
- Department of Life Sciences, Faculty of Sciences of Gabès, University of Gabès, Cité Erriadh 6072 Zrig, Gabès, Tunisia
| | - Chedly Abdelly
- Laboratory of Extremophile Plants, Centre of Biotechnology of Borj Cedria, BP 901 Hammam Lif 2050, Tunisia
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de la Peña M, González-Moro MB, Marino D. Providing carbon skeletons to sustain amide synthesis in roots underlines the suitability of Brachypodium distachyon for the study of ammonium stress in cereals. AOB PLANTS 2019; 11:plz029. [PMID: 31139336 PMCID: PMC6534281 DOI: 10.1093/aobpla/plz029] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Revised: 03/04/2019] [Accepted: 05/09/2019] [Indexed: 05/24/2023]
Abstract
Plants mainly acquire N from the soil in the form of nitrate (NO3 -) or ammonium (NH4 +). Ammonium-based nutrition is gaining interest because it helps to avoid the environmental pollution associated with nitrate fertilization. However, in general, plants prefer NO3 - and indeed, when growing only with NH4 + they can encounter so-called ammonium stress. Since Brachypodium distachyon is a useful model species for the study of monocot physiology and genetics, we chose it to characterize performance under ammonium nutrition. Brachypodium distachyon Bd21 plants were grown hydroponically in 1 or 2.5 mM NO3 - or NH4 +. Nitrogen and carbon metabolism associated with NH4 + assimilation was evaluated in terms of tissue contents of NO3 -, NH4 +, K, Mg, Ca, amino acids and organic acids together with tricarboxylic acid (TCA) cycle and NH4 +-assimilating enzyme activities and RNA transcript levels. The roots behaved as a physiological barrier preventing NH4 + translocation to aerial parts, as indicated by a sizeable accumulation of NH4 +, Asn and Gln in the roots. A continuing high NH4 + assimilation rate was made possible by a tuning of the TCA cycle and its associated anaplerotic pathways to match 2-oxoglutarate and oxaloacetate demand for Gln and Asn synthesis. These results show B. distachyon to be a highly suitable tool for the study of the physiological, molecular and genetic basis of ammonium nutrition in cereals.
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Affiliation(s)
- Marlon de la Peña
- Department of Plant Biology and Ecology, University of the Basque Country (UPV/EHU), Leioa, Spain
| | | | - Daniel Marino
- Department of Plant Biology and Ecology, University of the Basque Country (UPV/EHU), Leioa, Spain
- Ikerbasque, Basque Foundation for Science, Bilbao, Spain
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12
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Non-Invasive Sensing of Nitrogen in Plant Using Digital Images and Machine Learning for Brassica Campestris ssp. Chinensis L. SENSORS 2019; 19:s19112448. [PMID: 31146350 PMCID: PMC6603544 DOI: 10.3390/s19112448] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Revised: 05/24/2019] [Accepted: 05/24/2019] [Indexed: 11/25/2022]
Abstract
Monitoring plant nitrogen (N) in a timely way and accurately is critical for precision fertilization. The imaging technology based on visible light is relatively inexpensive and ubiquitous, and open-source analysis tools have proliferated. In this study, texture- and geometry-related phenotyping combined with color properties were investigated for their potential use in evaluating N in pakchoi (Brassica campestris ssp. chinensis L.). Potted pakchoi treated with four levels of N were cultivated in a greenhouse. Their top-view images were acquired using a camera at six growth stages. The corresponding plant N concentration was determined destructively. The quantitative relationships between the nitrogen nutrition index (NNI) and the image-based phenotyping features were established using the following algorithms: random forest (RF), support vector regression (SVR), and neural network (NN). The results showed the full model based on the color, texture, and geometry-related features outperforms the model based on only the color-related feature in predicting the NNI. The RF full model exhibited the most robust performance in both the seedling and harvest stages, reaching prediction accuracies of 0.823 and 0.943, respectively. The high prediction accuracy of the model allows for a low-cost, non-destructive monitoring of N in the field of precision crop management.
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13
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David LC, Girin T, Fleurisson E, Phommabouth E, Mahfoudhi A, Citerne S, Berquin P, Daniel-Vedele F, Krapp A, Ferrario-Méry S. Developmental and physiological responses of Brachypodium distachyon to fluctuating nitrogen availability. Sci Rep 2019; 9:3824. [PMID: 30846873 PMCID: PMC6405861 DOI: 10.1038/s41598-019-40569-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Accepted: 02/12/2019] [Indexed: 02/03/2023] Open
Abstract
The Nitrogen Use Efficiency (NUE) of grain cereals depends on nitrate (NO3-) uptake from the soil, translocation to the aerial parts, nitrogen (N) assimilation and remobilization to the grains. Brachypodium distachyon has been proposed as a model species to identify the molecular players and mechanisms that affects these processes, for the improvement of temperate C3 cereals. We report on the developmental, physiological and grain-characteristic responses of the Bd21-3 accession of Brachypodium to variations in NO3- availability. As previously described in wheat and barley, we show that vegetative growth, shoot/root ratio, tiller formation, spike development, tissue NO3- and N contents, grain number per plant, grain yield and grain N content are sensitive to pre- and/or post-anthesis NO3- supply. We subsequently described constitutive and NO3--inducible components of both High and Low Affinity Transport Systems (HATS and LATS) for root NO3- uptake, and BdNRT2/3 candidate genes potentially involved in the HATS. Taken together, our data validate Brachypodium Bd21-3 as a model to decipher cereal N nutrition. Apparent specificities such as high grain N content, strong post-anthesis NO3- uptake and efficient constitutive HATS, further identify Brachypodium as a direct source of knowledge for crop improvement.
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Affiliation(s)
- L C David
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, 78000, Versailles, France
| | - T Girin
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, 78000, Versailles, France.
| | - E Fleurisson
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, 78000, Versailles, France
| | - E Phommabouth
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, 78000, Versailles, France
| | - A Mahfoudhi
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, 78000, Versailles, France
| | - S Citerne
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, 78000, Versailles, France
| | - P Berquin
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, 78000, Versailles, France
| | - F Daniel-Vedele
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, 78000, Versailles, France
| | - A Krapp
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, 78000, Versailles, France
| | - S Ferrario-Méry
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, 78000, Versailles, France
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14
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Danzi D, Briglia N, Petrozza A, Summerer S, Povero G, Stivaletta A, Cellini F, Pignone D, De Paola D, Janni M. Can High Throughput Phenotyping Help Food Security in the Mediterranean Area? FRONTIERS IN PLANT SCIENCE 2019; 10:15. [PMID: 30740116 PMCID: PMC6355677 DOI: 10.3389/fpls.2019.00015] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 01/07/2019] [Indexed: 05/21/2023]
Abstract
According to the IPCC 2014 report the Mediterranean region will be affected by strong climatic changes, both in terms of average temperature and of precipitations regime. This area hosts some half a billion people and the impact on food production will be severe. To implement a climate smart agriculture paradigm and a sustainable increase of agricultural productivity different approaches can be deployed. Agriculture alone consumes 70% of the entire water available on the planet, thus the observed reduction of useful rainfall and growing costs for irrigation water may severely constrain food security. In our work we focused on two typical Mediterranean crops: durum wheat, a rainfed crop, and tomato, an irrigated one. In wheat we explored the possibility of identifying genotypes resilient to water stress for future breeding aims, while in tomato we explored the possibility of using biostimulants to increase the plant capacity of using water. In order to achieve these targets, we used high throughput phenotyping (HTP). Two traits were considered: digital biovolume, a measure based on imaging techniques in the RGB domain, and Water Use Efficiency index as calculated semi-automatically on the basis of evaporation measurements resulting in a high throughput, non-destructive, non-invasive approach, as opposed to destructive and time consuming traditional methods. Our results clearly indicate that HTP is able to discriminate genotypes and biostimulant treatments that allow plants to use soil water more efficiently. In addition, these methods based on RGB quality images can easily be scaled to field phenotyping structure USVs or UAVs.
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Affiliation(s)
- Donatella Danzi
- Institute of Biosciences and Bioresources, National Research Council, Bari, Italy
| | - Nunzio Briglia
- Dipartimento delle Culture Europee e del Mediterraneo: Architettura, Ambiente, Patrimoni Culturali, Università degli Studi della Basilicata, Matera, Italy
| | | | | | | | | | | | - Domenico Pignone
- Institute of Biosciences and Bioresources, National Research Council, Bari, Italy
- Institute for Veterinary and AgriFood Bioethics, Fiumicino, Italy
| | - Domenico De Paola
- Institute of Biosciences and Bioresources, National Research Council, Bari, Italy
| | - Michela Janni
- Institute of Biosciences and Bioresources, National Research Council, Bari, Italy
- Institute of Materials for Electronics and Magnetism, National Research Council, Parma, Italy
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15
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Chen S, Guo Y, Sirault X, Stefanova K, Saradadevi R, Turner NC, Nelson MN, Furbank RT, Siddique KHM, Cowling WA. Nondestructive Phenomic Tools for the Prediction of Heat and Drought Tolerance at Anthesis in Brassica Species. PLANT PHENOMICS (WASHINGTON, D.C.) 2019; 2019:3264872. [PMID: 33313525 PMCID: PMC7718632 DOI: 10.34133/2019/3264872] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Accepted: 04/21/2019] [Indexed: 05/08/2023]
Abstract
Oilseed Brassica species are vulnerable to heat and drought stress, especially in the early reproductive stage. We evaluated plant imaging of whole plant and flower tissue, leaf stomatal conductance, leaf and bud temperature, photochemical reflectance index, quantum yield of photosynthesis, and leaf gas exchange for their suitability to detect tolerance to heat (H) and/or drought (D) stress treatments in 12 Brassica genotypes (G). A replicated factorial experiment was set up with 7 d of stress treatment from the beginning of anthesis with various levels of three factors H, D, and G. Most phenomics tools detected plant stress as indicated by significant main effects of H, D, and H×D. Whole plant volume was highly correlated with fresh weight changes, suggesting that whole plant imaging may be a useful surrogate for fresh weight in future studies. Vcmax, the maximum carboxylation rate of photosynthesis, increased rapidly on day 1 in H and H+D treatments, and there were significant interactions of G×H and G×D. Vcmax of genotypes on day 1 in H and H+D treatments was positively correlated with their harvested seed yield. Vcmax on day 1 and day 3 were clustered with seed yield in H and H+D treatments as shown in the heatmaps of genotypic correlations. TPU, the rate of triose phosphate use, also showed significant positive genotypic correlations with seed yield in H+D treatments. Flower volume showed significant interactions of G×H and G×D on day 7, and flower volume of genotypes on day 7 in H was positively correlated with their harvested seed yield. There were few interactions of G×H or G×D for leaf stomatal conductance, leaf and bud temperature, photochemical reflectance index, and quantum yield of photosynthesis. Vcmax, TPU, and volume of flowers are potential nondestructive phenomic traits for heat or combined heat and drought stress tolerance screening in Brassica germplasm.
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Affiliation(s)
- Sheng Chen
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA 6001, Australia
- UWA School of Agriculture and Environment, The University of Western Australia, Perth, WA 6001, Australia
| | - Yiming Guo
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA 6001, Australia
| | - Xavier Sirault
- High Resolution Plant Phenomics Centre, Australian Plant Phenomics Facility, CSIRO Agriculture and Food, Canberra, ACT 2601, Australia
| | - Katia Stefanova
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA 6001, Australia
| | - Renu Saradadevi
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA 6001, Australia
| | - Neil C. Turner
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA 6001, Australia
| | - Matthew N. Nelson
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA 6001, Australia
| | - Robert T. Furbank
- High Resolution Plant Phenomics Centre, Australian Plant Phenomics Facility, CSIRO Agriculture and Food, Canberra, ACT 2601, Australia
- ARC Centre of Excellence for Translational Photosynthesis, Australian National University, Canberra, ACT 2601, Australia
| | - Kadambot H. M. Siddique
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA 6001, Australia
| | - Wallace A. Cowling
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA 6001, Australia
- UWA School of Agriculture and Environment, The University of Western Australia, Perth, WA 6001, Australia
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16
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Czedik‐Eysenberg A, Seitner S, Güldener U, Koemeda S, Jez J, Colombini M, Djamei A. The 'PhenoBox', a flexible, automated, open-source plant phenotyping solution. THE NEW PHYTOLOGIST 2018; 219:808-823. [PMID: 29621393 PMCID: PMC6485332 DOI: 10.1111/nph.15129] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 02/22/2018] [Indexed: 05/11/2023]
Abstract
There is a need for flexible and affordable plant phenotyping solutions for basic research and plant breeding. We demonstrate our open source plant imaging and processing solution ('PhenoBox'/'PhenoPipe') and provide construction plans, source code and documentation to rebuild the system. Use of the PhenoBox is exemplified by studying infection of the model grass Brachypodium distachyon by the head smut fungus Ustilago bromivora, comparing phenotypic responses of maize to infection with a solopathogenic Ustilago maydis (corn smut) strain and effector deletion strains, and studying salt stress response in Nicotiana benthamiana. In U. bromivora-infected grass, phenotypic differences between infected and uninfected plants were detectable weeks before qualitative head smut symptoms. Based on this, we could predict the infection outcome for individual plants with high accuracy. Using a PhenoPipe module for calculation of multi-dimensional distances from phenotyping data, we observe a time after infection-dependent impact of U. maydis effector deletion strains on phenotypic response in maize. The PhenoBox/PhenoPipe system is able to detect established salt stress responses in N. benthamiana. We have developed an affordable, automated, open source imaging and data processing solution that can be adapted to various phenotyping applications in plant biology and beyond.
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Affiliation(s)
- Angelika Czedik‐Eysenberg
- Gregor Mendel Institute (GMI)Austrian Academy of SciencesVienna BioCenter (VBC)Dr. Bohr‐Gasse 31030ViennaAustria
| | - Sebastian Seitner
- Gregor Mendel Institute (GMI)Austrian Academy of SciencesVienna BioCenter (VBC)Dr. Bohr‐Gasse 31030ViennaAustria
| | - Ulrich Güldener
- Department of Genome‐oriented BioinformaticsTechnische Universität MünchenWissenschaftszentrum WeihenstephanFreisingGermany
| | - Stefanie Koemeda
- Vienna Biocenter Core Facilities (VBCF)Dr. Bohr‐Gasse 31030ViennaAustria
| | - Jakub Jez
- Vienna Biocenter Core Facilities (VBCF)Dr. Bohr‐Gasse 31030ViennaAustria
| | - Martin Colombini
- Workshop, Research Institute of Molecular Pathology (IMP)Vienna BioCenter (VBC)Campus‐Vienna‐Biocenter 11030ViennaAustria
| | - Armin Djamei
- Gregor Mendel Institute (GMI)Austrian Academy of SciencesVienna BioCenter (VBC)Dr. Bohr‐Gasse 31030ViennaAustria
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17
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Nguyen GN, Kant S. Improving nitrogen use efficiency in plants: effective phenotyping in conjunction with agronomic and genetic approaches. FUNCTIONAL PLANT BIOLOGY : FPB 2018; 45:606-619. [PMID: 32290963 DOI: 10.1071/fp17266] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 01/04/2018] [Indexed: 05/03/2023]
Abstract
For global sustainable food production and environmental benefits, there is an urgent need to improve N use efficiency (NUE) in crop plants. Excessive and inefficient use of N fertiliser results in increased crop production costs and environmental pollution. Therefore, cost-effective strategies such as proper management of the timing and quantity of N fertiliser application, and breeding for better varieties are needed to improve NUE in crops. However, for these efforts to be feasible, high-throughput and reliable phenotyping techniques would be very useful for monitoring N status in planta, as well as to facilitate faster decisions during breeding and selection processes. This review provides an insight into contemporary approaches to phenotyping NUE-related traits and associated challenges. We discuss recent and advanced, sensor- and image-based phenotyping techniques that use a variety of equipment, tools and platforms. The review also elaborates on how high-throughput phenotyping will accelerate efforts for screening large populations of diverse genotypes in controlled environment and field conditions to identify novel genotypes with improved NUE.
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Affiliation(s)
- Giao N Nguyen
- Agriculture Victoria, Grains Innovation Park, 110 Natimuk Road, Horsham, Vic. 3400, Australia
| | - Surya Kant
- Agriculture Victoria, Grains Innovation Park, 110 Natimuk Road, Horsham, Vic. 3400, Australia
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18
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Tiwari JK, Plett D, Garnett T, Chakrabarti SK, Singh RK. Integrated genomics, physiology and breeding approaches for improving nitrogen use efficiency in potato: translating knowledge from other crops. FUNCTIONAL PLANT BIOLOGY : FPB 2018; 45:587-605. [PMID: 32290962 DOI: 10.1071/fp17303] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Accepted: 12/06/2017] [Indexed: 05/22/2023]
Abstract
Potato plays a key role in global food and nutritional security. Potato is an N fertiliser-responsive crop, producing high tuber yields. However, excessive use of N can result in environmental damage and high production costs, hence improving nitrogen use efficiency (NUE) of potato plants is one of the sustainable options to address these issues and increase yield. Advanced efforts have been undertaken to improve NUE in other plants like Arabidopsis, rice, wheat and maize through molecular and physiological approaches. Conversely, in potato, NUE studies have predominantly focussed on agronomy or soil management, except for a few researchers who have measured gene expression and proteins relevant to N uptake or metabolism. The focus of this review is to adapt knowledge gained from other plants to inform investigation of N metabolism and associated traits in potato with the aim of improving potato NUE using integrated genomics, physiology and breeding methods.
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Affiliation(s)
- Jagesh K Tiwari
- ICAR-Central Potato Research Institute, Shimla - 171001, Himachal Pradesh, India
| | - Darren Plett
- School of Agriculture, Food and Wine, Waite Research Institute, University of Adelaide, Adelaide, SA 5064, Australia
| | - Trevor Garnett
- School of Agriculture, Food and Wine, Waite Research Institute, University of Adelaide, Adelaide, SA 5064, Australia
| | - Swarup K Chakrabarti
- ICAR-Central Potato Research Institute, Shimla - 171001, Himachal Pradesh, India
| | - Rajesh K Singh
- ICAR-Central Potato Research Institute, Shimla - 171001, Himachal Pradesh, India
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19
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Sun Y, Zhu S, Yang X, Weston MV, Wang K, Shen Z, Xu H, Chen L. Nitrogen diagnosis based on dynamic characteristics of rice leaf image. PLoS One 2018; 13:e0196298. [PMID: 29689107 PMCID: PMC5916860 DOI: 10.1371/journal.pone.0196298] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Accepted: 04/10/2018] [Indexed: 11/29/2022] Open
Abstract
Digital image processing is widely used in the non-destructive diagnosis of plant nutrition. Previous plant nitrogen diagnostic studies have mostly focused on characteristics of the rice canopy or leaves at some specific points in time, with the long sampling intervals unable to provide detailed and specific “dynamic features.” According to plant growth mechanisms, the dynamic changing rate in leaf shape and color differ between different nitrogen supplements. Therefore, the objective of this study was to diagnose nitrogen stress levels by analyzing the dynamic characteristics of rice leaves. Scanning technology was implemented to collect rice leaf images every 3 days, with the characteristics of the leaves from different leaf positions extracted utilizing MATLAB. Newly developed shape characteristics such as etiolation area (EA) and etiolation degree (ED), in addition to shape (area, perimeter) and color characteristics (green, normalized red index, etc.), were used to quantify the process of leaf change. These characteristics allowed sensitive indices to be established for further model validation. Our results indicate that the changing rates in dynamic characteristics, in particular the shape characteristics of the first incomplete leaf (FIL) and the characteristics of the 3rd leaf (leaf color and etiolation indices), expressed obvious distinctions among different nitrogen treatments. Consequently, we achieved acceptable diagnostic accuracy (training accuracy 77.3%, validation accuracy 64.4%) by using the FIL at six days after leaf emergence, and the new shape characteristics developed in this article (ED and EA) also showed good performance in nitrogen diagnosis. Based on the aforementioned results, dynamic analysis is valuable not only in further studies but also in practice.
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Affiliation(s)
- Yuanyuan Sun
- Institute of Applied Remote Sensing and Information Technology, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, Zhejiang Province, China
| | - Shaochun Zhu
- Institute of Applied Remote Sensing and Information Technology, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, Zhejiang Province, China
| | - Xuan Yang
- Institute of Applied Remote Sensing and Information Technology, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, Zhejiang Province, China
| | - Melanie Valerie Weston
- Institute of Applied Remote Sensing and Information Technology, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, Zhejiang Province, China
| | - Ke Wang
- Institute of Applied Remote Sensing and Information Technology, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, Zhejiang Province, China
- * E-mail: (KW); (LSC)
| | - Zhangquan Shen
- Institute of Applied Remote Sensing and Information Technology, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, Zhejiang Province, China
| | - Hongwei Xu
- Institute of Applied Remote Sensing and Information Technology, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, Zhejiang Province, China
| | - Lisu Chen
- Institute of Applied Remote Sensing and Information Technology, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, Zhejiang Province, China
- College of Ocean Science and Engineering, Shanghai Maritime University, Shanghai, China
- * E-mail: (KW); (LSC)
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20
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Identification of Nitrogen, Phosphorus, and Potassium Deficiencies Based on Temporal Dynamics of Leaf Morphology and Color. SUSTAINABILITY 2018. [DOI: 10.3390/su10030762] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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21
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Zhao P, Wang L, Yin H. Transcriptional responses to phosphate starvation in Brachypodium distachyon roots. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2018; 122:113-120. [PMID: 29216498 DOI: 10.1016/j.plaphy.2017.11.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Revised: 11/16/2017] [Accepted: 11/16/2017] [Indexed: 06/07/2023]
Abstract
Brachypodium distachyon is a model plant that has recently emerged in grass research. Although the growth and photochemical efficiency of this species respond strongly to phosphate (Pi) availability, its Pi starvation response mechanism, which controls the Pi homeostasis, remains largely unknown. This study presents the transcriptomic response profiles of Pi-deficient roots at growth stages during which the plants were starved but obvious growth defects were absent. The results identify several phosphate transporters (i.e., PHO1), purple acid phosphatases, and SYG1/PHO81/XPR1 (SPX) domain-containing proteins out of a total of 1740 differentially expressed genes (DEGs). In particular, the transcription factor ethylene response factor (ERF), basic helix-loop-helix (bHLH), and WRKY family genes were the three most abundant DEG groups and the latter was significantly enriched. Comparative transcriptome analysis of Brachypodium versus Arabidopsis and rice revealed the presence of several common components in response to Pi fluctuations. Most significantly, jasmonic acid (JA) signaling-related genes were overrepresented in gene ontology (GO) enrichment tests. The presence of a possible link between low Pi response, inositol polyphosphates, and JA signaling is therefore discussed.
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Affiliation(s)
- Pengshan Zhao
- Key Laboratory of Stress Physiology and Ecology in Cold and Arid Regions, Gansu Province, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, China; Shapotou Desert Research & Experiment Station, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, China.
| | - Lirong Wang
- Key Laboratory of Stress Physiology and Ecology in Cold and Arid Regions, Gansu Province, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, China.
| | - Hengxia Yin
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, 810016, China.
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22
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Joly-Lopez Z, Forczek E, Vello E, Hoen DR, Tomita A, Bureau TE. Abiotic Stress Phenotypes Are Associated with Conserved Genes Derived from Transposable Elements. FRONTIERS IN PLANT SCIENCE 2017; 8:2027. [PMID: 29250089 PMCID: PMC5715367 DOI: 10.3389/fpls.2017.02027] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Accepted: 11/14/2017] [Indexed: 05/08/2023]
Abstract
Plant phenomics offers unique opportunities to accelerate our understanding of gene function and plant response to different environments, and may be particularly useful for studying previously uncharacterized genes. One important type of poorly characterized genes is those derived from transposable elements (TEs), which have departed from a mobility-driven lifestyle to attain new adaptive roles for the host (exapted TEs). We used phenomics approaches, coupled with reverse genetics, to analyze T-DNA insertion mutants of both previously reported and novel protein-coding exapted TEs in the model plant Arabidopsis thaliana. We show that mutations in most of these exapted TEs result in phenotypes, particularly when challenged by abiotic stress. We built statistical multi-dimensional phenotypic profiles and compared them to wild-type and known stress responsive mutant lines for each particular stress condition. We found that these exapted TEs may play roles in responses to phosphate limitation, tolerance to high salt concentration, freezing temperatures, and arsenic toxicity. These results not only experimentally validate a large set of putative functional exapted TEs recently discovered through computational analysis, but also uncover additional novel phenotypes for previously well-characterized exapted TEs in A. thaliana.
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23
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Brozynska M, Furtado A, Henry RJ. Genomics of crop wild relatives: expanding the gene pool for crop improvement. PLANT BIOTECHNOLOGY JOURNAL 2016; 14:1070-85. [PMID: 26311018 DOI: 10.1111/pbi.12454] [Citation(s) in RCA: 177] [Impact Index Per Article: 22.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2015] [Revised: 06/26/2015] [Accepted: 07/16/2015] [Indexed: 05/20/2023]
Abstract
Plant breeders require access to new genetic diversity to satisfy the demands of a growing human population for more food that can be produced in a variable or changing climate and to deliver the high-quality food with nutritional and health benefits demanded by consumers. The close relatives of domesticated plants, crop wild relatives (CWRs), represent a practical gene pool for use by plant breeders. Genomics of CWR generates data that support the use of CWR to expand the genetic diversity of crop plants. Advances in DNA sequencing technology are enabling the efficient sequencing of CWR and their increased use in crop improvement. As the sequencing of genomes of major crop species is completed, attention has shifted to analysis of the wider gene pool of major crops including CWR. A combination of de novo sequencing and resequencing is required to efficiently explore useful genetic variation in CWR. Analysis of the nuclear genome, transcriptome and maternal (chloroplast and mitochondrial) genome of CWR is facilitating their use in crop improvement. Genome analysis results in discovery of useful alleles in CWR and identification of regions of the genome in which diversity has been lost in domestication bottlenecks. Targeting of high priority CWR for sequencing will maximize the contribution of genome sequencing of CWR. Coordination of global efforts to apply genomics has the potential to accelerate access to and conservation of the biodiversity essential to the sustainability of agriculture and food production.
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Affiliation(s)
- Marta Brozynska
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, Qld, Australia
| | - Agnelo Furtado
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, Qld, Australia
| | - Robert J Henry
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, Qld, Australia
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24
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Neumann K, Klukas C, Friedel S, Rischbeck P, Chen D, Entzian A, Stein N, Graner A, Kilian B. Dissecting spatiotemporal biomass accumulation in barley under different water regimes using high-throughput image analysis. PLANT, CELL & ENVIRONMENT 2015; 38:1980-96. [PMID: 25689277 DOI: 10.1111/pce.12516] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2014] [Revised: 01/29/2015] [Accepted: 01/30/2015] [Indexed: 05/18/2023]
Abstract
Phenotyping large numbers of genotypes still represents the rate-limiting step in many plant genetic experiments and in breeding. To address this issue, novel automated phenotyping technologies have been developed. We investigated for a core set of barley cultivars if high-throughput image analysis can help to dissect vegetative biomass accumulation in response to two different watering regimes under semi-controlled greenhouse conditions. We found that experiments, treatments, genotypes and genotype by environment interaction (G × E) can be characterized at any time point by certain digital traits. Biomass accumulation under control and stress conditions was highly heritable. Growth model-derived maximum vegetative biomass (K max), inflection point (I) and regrowth rate (k) were identified as promising candidate traits for genome-wide association studies. Drought stress symptoms can be visualized, dissected and modelled. Especially the highly heritable regrowth rate, which had the biggest influence on biomass accumulation in stress treatment, seems promising for future studies to improve drought tolerance in different crop species. A proof of concept study revealed potential correlations between digital traits obtained from pot experiments under greenhouse conditions and agronomic traits from field experiments. Overall, non-invasive, imaging-based phenotyping platforms under greenhouse conditions offer excellent possibilities for trait discovery, trait development and industrial applications.
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Affiliation(s)
- Kerstin Neumann
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Christian Klukas
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Swetlana Friedel
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
- BASF SE, Limburgerhof, Germany
| | - Pablo Rischbeck
- Technische Universität München (TUM), Freising-Weihenstephan, Germany
| | - Dijun Chen
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Alexander Entzian
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Andreas Graner
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Benjamin Kilian
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
- Innovation Center, BCS R&D, Bayer CropScience NV, Gent, Belgium
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Kjaer KH, Ottosen CO. 3D Laser Triangulation for Plant Phenotyping in Challenging Environments. SENSORS 2015; 15:13533-47. [PMID: 26066990 PMCID: PMC4507705 DOI: 10.3390/s150613533] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Accepted: 06/05/2015] [Indexed: 11/16/2022]
Abstract
To increase the understanding of how the plant phenotype is formed by genotype and environmental interactions, simple and robust high-throughput plant phenotyping methods should be developed and considered. This would not only broaden the application range of phenotyping in the plant research community, but also increase the ability for researchers to study plants in their natural environments. By studying plants in their natural environment in high temporal resolution, more knowledge on how multiple stresses interact in defining the plant phenotype could lead to a better understanding of the interaction between plant responses and epigenetic regulation. In the present paper, we evaluate a commercial 3D NIR-laser scanner (PlantEye, Phenospex B.V., Herleen, The Netherlands) to track daily changes in plant growth with high precision in challenging environments. Firstly, we demonstrate that the NIR laser beam of the scanner does not affect plant photosynthetic performance. Secondly, we demonstrate that it is possible to estimate phenotypic variation amongst the growth pattern of ten genotypes of Brassica napus L. (rapeseed), using a simple linear correlation between scanned parameters and destructive growth measurements. Our results demonstrate the high potential of 3D laser triangulation for simple measurements of phenotypic variation in challenging environments and in a high temporal resolution.
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Affiliation(s)
- Katrine Heinsvig Kjaer
- Department of Food Science, Aarhus University, Kirstinebjergvej 10, 5792 Aarslev, Denmark.
| | - Carl-Otto Ottosen
- Department of Food Science, Aarhus University, Kirstinebjergvej 10, 5792 Aarslev, Denmark.
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Humplík JF, Lazár D, Husičková A, Spíchal L. Automated phenotyping of plant shoots using imaging methods for analysis of plant stress responses - a review. PLANT METHODS 2015; 11:29. [PMID: 25904970 PMCID: PMC4406171 DOI: 10.1186/s13007-015-0072-8] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Accepted: 04/09/2015] [Indexed: 05/18/2023]
Abstract
Current methods of in-house plant phenotyping are providing a powerful new tool for plant biology studies. The self-constructed and commercial platforms established in the last few years, employ non-destructive methods and measurements on a large and high-throughput scale. The platforms offer to certain extent, automated measurements, using either simple single sensor analysis, or advanced integrative simultaneous analysis by multiple sensors. However, due to the complexity of the approaches used, it is not always clear what such forms of plant phenotyping can offer the potential end-user, i.e. plant biologist. This review focuses on imaging methods used in the phenotyping of plant shoots including a brief survey of the sensors used. To open up this topic to a broader audience, we provide here a simple introduction to the principles of automated non-destructive analysis, namely RGB, chlorophyll fluorescence, thermal and hyperspectral imaging. We further on present an overview on how and to which extent, the automated integrative in-house phenotyping platforms have been used recently to study the responses of plants to various changing environments.
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Affiliation(s)
- Jan F Humplík
- />Department of Chemical Biology and Genetics, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Šlechtitelů 11, Olomouc, CZ-78371 Czech Republic
| | - Dušan Lazár
- />Department of Biophysics, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Šlechtitelů 11, Olomouc, CZ-78371 Czech Republic
| | - Alexandra Husičková
- />Department of Biophysics, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Šlechtitelů 11, Olomouc, CZ-78371 Czech Republic
| | - Lukáš Spíchal
- />Department of Chemical Biology and Genetics, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Šlechtitelů 11, Olomouc, CZ-78371 Czech Republic
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Girin T, David LC, Chardin C, Sibout R, Krapp A, Ferrario-Méry S, Daniel-Vedele F. Brachypodium: a promising hub between model species and cereals. JOURNAL OF EXPERIMENTAL BOTANY 2014; 65:5683-96. [PMID: 25262566 DOI: 10.1093/jxb/eru376] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Brachypodium distachyon was proposed as a model species for genetics and molecular genomics in cereals less than 10 years ago. It is now established as a standard for research on C3 cereals on a variety of topics, due to its close phylogenetic relationship with Triticeae crops such as wheat and barley, and to its simple genome, its minimal growth requirement, and its short life cycle. In this review, we first highlight the tools and resources for Brachypodium that are currently being developed and made available by the international community. We subsequently describe how this species has been used for comparative genomic studies together with cereal crops, before illustrating major research fields in which Brachypodium has been successfully used as a model: cell wall synthesis, plant-pathogen interactions, root architecture, and seed development. Finally, we discuss the usefulness of research on Brachypodium in order to improve nitrogen use efficiency in cereals, with the aim of reducing the amount of applied fertilizer while increasing the grain yield. Several paths are considered, namely an improvement of either nitrogen remobilization from the vegetative organs, nitrate uptake from the soil, or nitrate assimilation by the plant. Altogether, these examples position the research on Brachypodium as at an intermediate stage between basic research, carried out mainly in Arabidopsis, and applied research carried out on wheat and barley, enabling a complementarity of the studies and reciprocal benefits.
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Affiliation(s)
- Thomas Girin
- Institut National de la Recherche Agronomique (INRA), UMR1318, Institut Jean-Pierre Bourgin, Saclay Plant Sciences, RD10, F-78000 Versailles, France AgroParisTech, Institut Jean-Pierre Bourgin, RD10, F-78000 Versailles, France
| | - Laure C David
- Institut National de la Recherche Agronomique (INRA), UMR1318, Institut Jean-Pierre Bourgin, Saclay Plant Sciences, RD10, F-78000 Versailles, France AgroParisTech, Institut Jean-Pierre Bourgin, RD10, F-78000 Versailles, France
| | - Camille Chardin
- Institut National de la Recherche Agronomique (INRA), UMR1318, Institut Jean-Pierre Bourgin, Saclay Plant Sciences, RD10, F-78000 Versailles, France AgroParisTech, Institut Jean-Pierre Bourgin, RD10, F-78000 Versailles, France
| | - Richard Sibout
- Institut National de la Recherche Agronomique (INRA), UMR1318, Institut Jean-Pierre Bourgin, Saclay Plant Sciences, RD10, F-78000 Versailles, France AgroParisTech, Institut Jean-Pierre Bourgin, RD10, F-78000 Versailles, France
| | - Anne Krapp
- Institut National de la Recherche Agronomique (INRA), UMR1318, Institut Jean-Pierre Bourgin, Saclay Plant Sciences, RD10, F-78000 Versailles, France AgroParisTech, Institut Jean-Pierre Bourgin, RD10, F-78000 Versailles, France
| | - Sylvie Ferrario-Méry
- Institut National de la Recherche Agronomique (INRA), UMR1318, Institut Jean-Pierre Bourgin, Saclay Plant Sciences, RD10, F-78000 Versailles, France AgroParisTech, Institut Jean-Pierre Bourgin, RD10, F-78000 Versailles, France
| | - Françoise Daniel-Vedele
- Institut National de la Recherche Agronomique (INRA), UMR1318, Institut Jean-Pierre Bourgin, Saclay Plant Sciences, RD10, F-78000 Versailles, France AgroParisTech, Institut Jean-Pierre Bourgin, RD10, F-78000 Versailles, France
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