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Liu Z, Qin T, Atienza M, Zhao Y, Nguyen H, Sheng H, Olukayode T, Song H, Panjvani K, Magalhaes J, Lucas WJ, Kochian LV. Constitutive basis of root system architecture: uncovering a promising trait for breeding nutrient- and drought-resilient crops. ABIOTECH 2023; 4:315-331. [PMID: 38106432 PMCID: PMC10721591 DOI: 10.1007/s42994-023-00112-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Accepted: 07/20/2023] [Indexed: 12/19/2023]
Abstract
Root system architecture (RSA) plays a pivotal role in efficient uptake of essential nutrients, such as phosphorous (P), nitrogen (N), and water. In soils with heterogeneous nutrient distribution, root plasticity can optimize acquisition and plant growth. Here, we present evidence that a constitutive RSA can confer benefits for sorghum grown under both sufficient and limiting growth conditions. Our studies, using P efficient SC103 and inefficient BTx635 sorghum cultivars, identified significant differences in root traits, with SC103 developing a larger root system with more and longer lateral roots, and enhanced shoot biomass, under both nutrient sufficient and deficient conditions. In addition to this constitutive attribute, under P deficiency, both cultivars exhibited an initial increase in lateral root development; however, SC103 still maintained the larger root biomass. Although N deficiency and drought stress inhibited both root and shoot growth, for both sorghum cultivars, SC103 again maintained the better performance. These findings reveal that SC103, a P efficient sorghum cultivar, also exhibited enhanced growth performance under N deficiency and drought. Our results provide evidence that this constitutive nature of RSA can provide an avenue for breeding nutrient- and drought-resilient crops. Supplementary Information The online version contains supplementary material available at 10.1007/s42994-023-00112-w.
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Affiliation(s)
- Zhigang Liu
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, SK S7N 4L8 Canada
| | - Tongfei Qin
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, SK S7N 4L8 Canada
| | - Michaella Atienza
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, SK S7N 4L8 Canada
| | - Yang Zhao
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, SK S7N 4L8 Canada
| | - Hanh Nguyen
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, SK S7N 4L8 Canada
| | - Huajin Sheng
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, SK S7N 4L8 Canada
| | - Toluwase Olukayode
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, SK S7N 4L8 Canada
| | - Hao Song
- Department of Computer Science, University of Saskatchewan, Saskatoon, SK S7N 5C9 Canada
| | - Karim Panjvani
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, SK S7N 4L8 Canada
| | - Jurandir Magalhaes
- Embrapa Maize and Sorghum, Brazilian Agricultural Research Corporation, Sete Lagoas, MG 35701-970 Brazil
| | - William J. Lucas
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, SK S7N 4L8 Canada
- Department of Plant Biology, College of Biological Sciences, University of California, Davis, CA 95616 USA
| | - Leon V. Kochian
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, SK S7N 4L8 Canada
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Rishmawi L, Bauget F, Protto V, Bauland C, Nacry P, Maurel C. Natural variation of maize root hydraulic architecture underlies highly diverse water uptake capacities. PLANT PHYSIOLOGY 2023; 192:2404-2418. [PMID: 37052178 PMCID: PMC10315320 DOI: 10.1093/plphys/kiad213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 02/21/2023] [Accepted: 03/16/2023] [Indexed: 06/19/2023]
Abstract
Plant water uptake is determined by the root system architecture and its hydraulic capacity, which together define the root hydraulic architecture. The current research aims at understanding the water uptake capacities of maize (Zea mays), a model organism and major crop. We explored the genetic variations within a collection of 224 maize inbred Dent lines and successively defined core genotype subsets to access multiple architectural, anatomical, and hydraulic parameters in the primary root (PR) and seminal roots (SR) of hydroponically grown seedlings. We found 9-, 3.5-, and 12.4-fold genotypic differences for root hydraulics (Lpr), PR size, and lateral root size, respectively, that shaped wide and independent variations of root structure and function. Within genotypes, PR and SR showed similarities in hydraulics and, to a lesser extent, in anatomy. They had comparable aquaporin activity profiles that, however, could not be explained by aquaporin expression levels. Genotypic variations in the size and number of late meta xylem vessels were positively correlated with Lpr. Inverse modeling further revealed dramatic genotypic differences in the xylem conductance profile. Thus, tremendous natural variation of maize root hydraulic architecture underlies a high diversity of water uptake strategies and paves the way to quantitative genetic dissection of its elementary traits.
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Affiliation(s)
- Louai Rishmawi
- IPSiM, Univ Montpellier, CNRS, INRAE, Institut Agro, 34060 Montpellier, France
| | - Fabrice Bauget
- IPSiM, Univ Montpellier, CNRS, INRAE, Institut Agro, 34060 Montpellier, France
| | - Virginia Protto
- IPSiM, Univ Montpellier, CNRS, INRAE, Institut Agro, 34060 Montpellier, France
| | - Cyril Bauland
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE—Le Moulon, Gif-sur-Yvette, France
| | - Philippe Nacry
- IPSiM, Univ Montpellier, CNRS, INRAE, Institut Agro, 34060 Montpellier, France
| | - Christophe Maurel
- IPSiM, Univ Montpellier, CNRS, INRAE, Institut Agro, 34060 Montpellier, France
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Hudzik C, Maguire S, Guan S, Held J, Axtell MJ. Trans-species microRNA loci in the parasitic plant Cuscuta campestris have a U6-like snRNA promoter. THE PLANT CELL 2023; 35:1834-1847. [PMID: 36896651 PMCID: PMC10226579 DOI: 10.1093/plcell/koad076] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 01/09/2023] [Accepted: 02/12/2023] [Indexed: 05/30/2023]
Abstract
Small regulatory RNAs can move between organisms and regulate gene expression in the recipient. Whether the trans-species small RNAs being exported are distinguished from the normal endogenous small RNAs of the source organism is not known. The parasitic plant Cuscuta campestris (dodder) produces many microRNAs that specifically accumulate at the host-parasite interface, several of which have trans-species activity. We found that induction of C. campestris interface-induced microRNAs is similar regardless of host species and occurs in C. campestris haustoria produced in the absence of any host. The loci-encoding C. campestris interface-induced microRNAs are distinguished by a common cis-regulatory element. This element is identical to a conserved upstream sequence element (USE) used by plant small nuclear RNA loci. The properties of the interface-induced microRNA primary transcripts strongly suggest that they are produced via U6-like transcription by RNA polymerase III. The USE promotes accumulation of interface-induced miRNAs (IIMs) in a heterologous system. This promoter element distinguishes C. campestris IIM loci from other plant small RNAs. Our data suggest that C. campestris IIMs are produced in a manner distinct from canonical miRNAs. All confirmed C. campestris microRNAs with documented trans-species activity are interface-induced and possess these features. We speculate that RNA polymerase III transcription of IIMs may allow these miRNAs to be exported to hosts.
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Affiliation(s)
- Collin Hudzik
- Department of Biology, The Pennsylvania State University, University Park, PA 16802, USA
- Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA
| | - Sean Maguire
- New England Biolabs, Inc., 240 County Road, Ipswich, MA 01938, USA
| | - Shengxi Guan
- New England Biolabs, Inc., 240 County Road, Ipswich, MA 01938, USA
| | - Jeremy Held
- Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA
- Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Michael J Axtell
- Department of Biology, The Pennsylvania State University, University Park, PA 16802, USA
- Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA
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4
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Thomas DJ, Rainbow J, Bartley LE. The rapid-tome, a 3D-printed microtome, and an updated hand-sectioning method for high-quality plant sectioning. PLANT METHODS 2023; 19:12. [PMID: 36739429 PMCID: PMC9898918 DOI: 10.1186/s13007-023-00986-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 01/21/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND Microscopic analysis of plant anatomy is a common procedure in biology to study structure and function that requires high-quality sections for accurate measurements. Hand sectioning of specimens is typically limited to moderately soft tissue while harder samples prohibit sectioning by hand and/or result in inconsistent thicknesses. RESULTS Here we present both a clearly described hand-sectioning method and a novel microtome design that together provide the means to section a variety of plant sample types. The described hand-sectioning method for herbaceous stems works well for softer subjects but is less suitable for samples with secondary growth (e.g., wood production). Instead, the "Rapid-Tome" is a novel tool for sectioning both soft and tougher high-aspect-ratio samples, such as stems and roots, with excellent sample control. The Rapid-Tome can be 3D-printed in approximately 18 h on a mid-quality printer common at university maker spaces. After printing and trimming, Rapid-Tome assembly takes a few minutes with five metal parts common at hardware stores. Users sectioned a variety of plant samples including the hollow internodes of switchgrass (Panicum virgatum), fibrous switchgrass roots containing aerenchyma, and woody branches of eastern red cedar (Juniperus virginiana) and American sycamore (Platanus occidentalis). A comparative analyses with Rapid-Tome-produced sections readily revealed a significant difference in seasonal growth of sycamore xylem vessel area in spring (49%) vs. summer (23%). Additionally, high school students with no prior experience produced sections with the Rapid-Tome adequate for comparative analyses of various plant samples in less than an hour. CONCLUSIONS The described hand-sectioning method is suitable for softer tissues, including hollow-stemmed grasses and similar samples. In addition, the Rapid-Tome provides capacity to safely produce high-quality sections of tougher plant materials at a fraction of the cost of traditional microtomes combined with excellent sample control. The Rapid-Tome features rapid sectioning, sample advancement, blade changes, and sample changes; it is highly portable and can be used easily with minimal training making production of thin sections accessible for classroom and outreach use, in addition to research.
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Affiliation(s)
- David J Thomas
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, 73019, USA
- Institute of Biological Chemistry, Washington State University, Pullman, WA, 99164, USA
| | - Jordan Rainbow
- Institute of Biological Chemistry, Washington State University, Pullman, WA, 99164, USA
| | - Laura E Bartley
- Institute of Biological Chemistry, Washington State University, Pullman, WA, 99164, USA.
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5
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Hériché M, Arnould C, Wipf D, Courty PE. Imaging plant tissues: advances and promising clearing practices. TRENDS IN PLANT SCIENCE 2022; 27:601-615. [PMID: 35339361 DOI: 10.1016/j.tplants.2021.12.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 12/03/2021] [Accepted: 12/09/2021] [Indexed: 06/14/2023]
Abstract
The study of the organ structure of plants and understanding their physiological complexity requires 3D imaging with subcellular resolution. Most plant organs are highly opaque to light, and their study under optical sectioning microscopes is therefore difficult. In animals, many protocols have been developed to make organs transparent to light using clearing protocols (CPs). By contrast, clearing plant tissues is challenging because of the presence of fibers and pigments. We describe progress in the development of plant CPs over the past 20 years through a modified taxonomy of CPs based on their physical and optical parameters that affect tissue properties. We also discuss successful approaches that combine CPs with new microscopy methods and their future applications in plant science research.
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Affiliation(s)
- Mathilde Hériché
- Agroécologie, AgroSup Dijon, Centre National de la Recherche Scientifique (CNRS), Université de Bourgogne, Institut National de Recherche pour l'Agriculture, l'Alimentation, et l'Environnement (INRAE), Université Bourgogne Franche-Comté, Dijon, France
| | - Christine Arnould
- Agroécologie, AgroSup Dijon, Centre National de la Recherche Scientifique (CNRS), Université de Bourgogne, Institut National de Recherche pour l'Agriculture, l'Alimentation, et l'Environnement (INRAE), Université Bourgogne Franche-Comté, Dijon, France
| | - Daniel Wipf
- Agroécologie, AgroSup Dijon, Centre National de la Recherche Scientifique (CNRS), Université de Bourgogne, Institut National de Recherche pour l'Agriculture, l'Alimentation, et l'Environnement (INRAE), Université Bourgogne Franche-Comté, Dijon, France
| | - Pierre-Emmanuel Courty
- Agroécologie, AgroSup Dijon, Centre National de la Recherche Scientifique (CNRS), Université de Bourgogne, Institut National de Recherche pour l'Agriculture, l'Alimentation, et l'Environnement (INRAE), Université Bourgogne Franche-Comté, Dijon, France.
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6
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Strock CF, Schneider HM, Lynch JP. Anatomics: High-throughput phenotyping of plant anatomy. TRENDS IN PLANT SCIENCE 2022; 27:520-523. [PMID: 35307268 DOI: 10.1016/j.tplants.2022.02.009] [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: 12/07/2021] [Revised: 02/20/2022] [Accepted: 02/22/2022] [Indexed: 06/14/2023]
Abstract
Anatomics is a novel phenotyping strategy focused on high-throughput imaging and quantification of plant anatomy from field-grown plants. Here we highlight its potential applications for genetic and physiological analysis of plant anatomical phenotypes.
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Affiliation(s)
| | - Hannah M Schneider
- Centre for Crop Systems Analysis, Wageningen University & Research, Wageningen, The Netherlands
| | - Jonathan P Lynch
- Department of Plant Sciences, The Pennsylvania State University, State College, PA, USA.
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7
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Falcioni R, Moriwaki T, Furlanetto RH, Nanni MR, Antunes WC. Simple, Fast and Efficient Methods for Analysing the Structural, Ultrastructural and Cellular Components of the Cell Wall. PLANTS 2022; 11:plants11070995. [PMID: 35406975 PMCID: PMC9003262 DOI: 10.3390/plants11070995] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 10/30/2021] [Accepted: 11/13/2021] [Indexed: 12/17/2022]
Abstract
Plant cell walls are a fundamental component of plant biology and play an essential role in plant growth and development. The metabolic components of the cell wall can be investigated in a fast, simple, and highly efficient manner using various and distinct microscopy techniques. Here, we report implementing a flowchart to analyse tobacco plants’ structural, ultrastructural, and metabolic components supplemented with far-red light. In addition, biochemical components, such as lignin, cellulose, phenolic compounds, and reducing sugars, present in the plant cell walls were quantified using light, fluorescence, and electron microscopy. Our data were generated from samples prepared via tissue fixation, incorporation in resins, and slicing using microtomes. Moreover, we have used routine staining and contrast techniques to characterise plant cell walls. Here, we describe several protocols that use classic and modern techniques as well as qualitative and quantitative analytical methods to study cell walls, enabling the plant research community to understand and select the most suitable methods for the microscopic analysis of metabolic components. Finally, we discuss specific ideas aimed at new students of plant anatomy and microscopy. This research not only described the structural, ultrastructural, and metabolic components of the plant cell wall, but also explained the strategies for understanding cellular development.
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Affiliation(s)
- Renan Falcioni
- Department of Agronomy, State University of Maringá, Av. Colombo, 5790, Maringá 87020-900, PR, Brazil or (T.M.); (R.H.F.); (M.R.N.); (W.C.A.)
- Department of Biology, Paraná Federal Institute of Education, Science and Technology, Avenida Bento Munhoz da Rocha, PRT 280, s/n°, Trevo Codapar, Palmas 85555-000, PR, Brazil
- Correspondence: or ; Tel.: +55-463-262-1274
| | - Thaise Moriwaki
- Department of Agronomy, State University of Maringá, Av. Colombo, 5790, Maringá 87020-900, PR, Brazil or (T.M.); (R.H.F.); (M.R.N.); (W.C.A.)
| | - Renato Herrig Furlanetto
- Department of Agronomy, State University of Maringá, Av. Colombo, 5790, Maringá 87020-900, PR, Brazil or (T.M.); (R.H.F.); (M.R.N.); (W.C.A.)
| | - Marcos Rafael Nanni
- Department of Agronomy, State University of Maringá, Av. Colombo, 5790, Maringá 87020-900, PR, Brazil or (T.M.); (R.H.F.); (M.R.N.); (W.C.A.)
| | - Werner Camargos Antunes
- Department of Agronomy, State University of Maringá, Av. Colombo, 5790, Maringá 87020-900, PR, Brazil or (T.M.); (R.H.F.); (M.R.N.); (W.C.A.)
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8
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Vanhees DJ, Schneider HM, Sidhu JS, Loades KW, Bengough AG, Bennett MJ, Pandey BK, Brown KM, Mooney SJ, Lynch JP. Soil penetration by maize roots is negatively related to ethylene-induced thickening. PLANT, CELL & ENVIRONMENT 2022; 45:789-804. [PMID: 34453329 PMCID: PMC9291135 DOI: 10.1111/pce.14175] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Revised: 08/20/2021] [Accepted: 08/22/2021] [Indexed: 05/22/2023]
Abstract
Radial expansion is a classic response of roots to a mechanical impedance that has generally been assumed to aid penetration. We analysed the response of maize nodal roots to impedance to test the hypothesis that radial expansion is not related to the ability of roots to cross a compacted soil layer. Genotypes varied in their ability to cross the compacted layer, and those with a steeper approach to the compacted layer or less radial expansion in the compacted layer were more likely to cross the layer and achieve greater depth. Root radial expansion was due to cortical cell size expansion, while cortical cell file number remained constant. Genotypes and nodal root classes that exhibited radial expansion in the compacted soil layer generally also thickened in response to exogenous ethylene in hydroponic culture, that is, radial expansion in response to ethylene was correlated with the thickening response to impedance in soil. We propose that ethylene insensitive roots, that is, those that do not thicken and can overcome impedance, have a competitive advantage under mechanically impeded conditions as they can maintain their elongation rates. We suggest that prolonged exposure to ethylene could function as a stop signal for axial root growth.
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Affiliation(s)
- Dorien J. Vanhees
- School of BiosciencesUniversity of Nottingham, Sutton Bonington CampusLeicestershireUK
- The James Hutton InstituteInvergowrieUK
| | - Hannah M. Schneider
- Department of Plant ScienceThe Pennsylvania State UniversityUniversity ParkPennsylvaniaUSA
- Centre for Crop Systems AnalysisWageningen University & ResearchWageningenThe Netherlands
| | - Jagdeep Singh Sidhu
- Department of Plant ScienceThe Pennsylvania State UniversityUniversity ParkPennsylvaniaUSA
| | | | - A. Glyn Bengough
- The James Hutton InstituteInvergowrieUK
- School of Science and EngineeringThe University of DundeeDundeeUK
| | - Malcolm J. Bennett
- School of BiosciencesUniversity of Nottingham, Sutton Bonington CampusLeicestershireUK
| | - Bipin K. Pandey
- School of BiosciencesUniversity of Nottingham, Sutton Bonington CampusLeicestershireUK
| | - Kathleen M. Brown
- Department of Plant ScienceThe Pennsylvania State UniversityUniversity ParkPennsylvaniaUSA
| | - Sacha J. Mooney
- School of BiosciencesUniversity of Nottingham, Sutton Bonington CampusLeicestershireUK
| | - Jonathan P. Lynch
- School of BiosciencesUniversity of Nottingham, Sutton Bonington CampusLeicestershireUK
- Department of Plant ScienceThe Pennsylvania State UniversityUniversity ParkPennsylvaniaUSA
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Pandey BK, Atkinson JA, Sturrock CJ. Non-invasive Imaging of Rice Roots in Non-compacted and Compacted Soil. Bio Protoc 2021; 11:e4252. [PMID: 35087914 DOI: 10.21769/bioprotoc.4252] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 09/09/2021] [Accepted: 10/06/2021] [Indexed: 11/02/2022] Open
Abstract
Roots are the prime organ for nutrient and water uptake and are therefore fundamental to the growth and development of plants. However, physical challenges of a heterogeneous environment and diverse edaphic stresses affect root growth in soil. Compacted soil is a serious global problem, causing inhibition of root elongation, which reduces surface area and impacts resource foraging. Visualisation and quantification of roots in soil is difficult due to this growth substrate's opaque nature; however, non-destructive imaging technologies are now becoming more widely available to plant and soil scientists working to address this challenge. We have recently developed an integrated approach, combining X-ray Computed Tomography (X-ray CT) and confocal microscopy to image roots grown in compacted soil conditions from a plant to a cellular scale. The method is suited to visualize cellular responses of root tips grown in both non-compacted and compacted soils. This protocol presents a fully integrated workflow, including soil column preparation, creation of compaction conditions, plant growth, imaging, and quantification of root adaptive responses at a cellular scale.
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Affiliation(s)
- Bipin K Pandey
- Division of Plant and Crop Science, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, UK
| | - Jonathan A Atkinson
- Division of Plant and Crop Science, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, UK
| | - Craig J Sturrock
- The Hounsfield Facility, Division of Agricultural and Environmental Sciences, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, UK
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10
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Jones DH, Atkinson BS, Ware A, Sturrock CJ, Bishopp A, Wells DM. Preparation, Scanning and Analysis of Duckweed Using X-Ray Computed Microtomography. FRONTIERS IN PLANT SCIENCE 2021; 11:617830. [PMID: 33488660 PMCID: PMC7820725 DOI: 10.3389/fpls.2020.617830] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 12/07/2020] [Indexed: 05/05/2023]
Abstract
Quantification of anatomical and compositional features underpins both fundamental and applied studies of plant structure and function. Relatively few non-invasive techniques are available for aquatic plants. Traditional methods such as sectioning are low-throughput and provide 2-dimensional information. X-ray Computed Microtomography (μCT) offers a non-destructive method of three dimensional (3D) imaging in planta, but has not been widely used for aquatic species, due to the difficulties in sample preparation and handling. We present a novel sample handling protocol for aquatic plant material developed for μCT imaging, using duckweed plants and turions as exemplars, and compare the method against existing approaches. This technique allows for previously unseen 3D volume analysis of gaseous filled spaces, cell material, and sub-cellular features. The described embedding method, utilizing petrolatum gel for sample mounting, was shown to preserve sample quality during scanning, and to display sufficiently different X-ray attenuation to the plant material to be easily differentiated by image analysis pipelines. We present this technique as an improved method for anatomical structural analysis that provides novel cellular and developmental information.
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Affiliation(s)
- Dylan H. Jones
- Integrated Phenomics Group, School of Biosciences, University of Nottingham, Nottingham, United Kingdom
| | - Brian S. Atkinson
- Hounsfield Facility, School of Biosciences, University of Nottingham, Nottingham, United Kingdom
| | - Alexander Ware
- Division of Plant and Crop Sciences, School of Biosciences, University of Nottingham, Nottingham, United Kingdom
| | - Craig J. Sturrock
- Hounsfield Facility, School of Biosciences, University of Nottingham, Nottingham, United Kingdom
| | - Anthony Bishopp
- Division of Plant and Crop Sciences, School of Biosciences, University of Nottingham, Nottingham, United Kingdom
| | - Darren M. Wells
- Integrated Phenomics Group, School of Biosciences, University of Nottingham, Nottingham, United Kingdom
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11
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Nakhforoosh A, Nagel KA, Fiorani F, Bodner G. Deep soil exploration vs. topsoil exploitation: distinctive rooting strategies between wheat landraces and wild relatives. PLANT AND SOIL 2020; 459:397-421. [PMID: 33603255 PMCID: PMC7870630 DOI: 10.1007/s11104-020-04794-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Accepted: 12/03/2020] [Indexed: 05/27/2023]
Abstract
AIMS Diversity of root systems among genetic resources can contribute to optimize water and nutrient uptake. Topsoil exploitation vs. deep soil exploration represent two contrasting ideotypes in relation to resource use. Our study reveals how rooting patterns changed between wheat wild progenitors and landraces in regard to these ideotypes. METHODS Root (partitioning, morphology, distribution, elongation, anatomy) and shoot traits (dry-matter, leaf area, assimilation) of durum landraces, wild emmer and wild einkorn from Iran, Syria, Turkey and Lebanon were phenotyped using the GrowScreen-Rhizo platform. Distinctive rooting patterns were identified via principal component analysis and relations with collection site characteristics analyzed. RESULTS Shoot trait differentiation was strongly driven by seed weight, leading to superior early vigor of landraces. Wild progenitors formed superficial root systems with a higher contribution of lateral and early-emerging nodal axes to total root length. Durum landraces had a root system dominated by seminal axes allocated evenly over depth. Xylem anatomy was the trait most affected by the environmental influence of the collection site. CONCLUSIONS The durum landrace root system approximated a deep soil exploration ideotype which would optimize subsoil water uptake, while monococcum-type wild einkorn was most similar to a topsoil exploiting strategy with potential competitive advantages for subsistence in natural vegetation. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s11104-020-04794-9.
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Affiliation(s)
- Alireza Nakhforoosh
- Division of Agronomy, Department of Crop Sciences, University of Natural Resources and Life Sciences, Vienna (BOKU), Konrad Lorenz-Straße 24, A-3430 Tulln an der Donau, Austria
- Global Institute of Food Security, University of Saskatchewan, Saskatoon, SK S7N 0W9 Canada
| | - Kerstin A. Nagel
- IBG-2: Plant Sciences, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Fabio Fiorani
- IBG-2: Plant Sciences, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Gernot Bodner
- Division of Agronomy, Department of Crop Sciences, University of Natural Resources and Life Sciences, Vienna (BOKU), Konrad Lorenz-Straße 24, A-3430 Tulln an der Donau, Austria
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12
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Burr CA, Sun J, Yamburenko MV, Willoughby A, Hodgens C, Boeshore SL, Elmore A, Atkinson J, Nimchuk ZL, Bishopp A, Schaller GE, Kieber JJ. The HK5 and HK6 cytokinin receptors mediate diverse developmental pathways in rice. Development 2020; 147:dev191734. [PMID: 33028608 PMCID: PMC7648598 DOI: 10.1242/dev.191734] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 09/23/2020] [Indexed: 12/22/2022]
Abstract
The phytohormone cytokinin regulates diverse aspects of plant growth and development. Our understanding of the metabolism and perception of cytokinin has made great strides in recent years, mostly from studies of the model dicot Arabidopsis Here, we employed a CRISPR/Cas9-based approach to disrupt a subset of cytokinin histidine kinase (HK) receptors in rice (Oryza sativa) in order to explore the role of cytokinin in a monocot species. In hk5 and hk6 single mutants, the root growth, leaf width, inflorescence architecture and/or floral development were affected. The double hk5 hk6 mutant showed more substantial defects, including severely reduced root and shoot growth, a smaller shoot apical meristem, and an enlarged root cap. Flowering was delayed in the hk5 hk6 mutant and the panicle was significantly reduced in size and infertile due to multiple defects in floral development. The hk5 hk6 mutant also exhibited a severely reduced cytokinin response, consistent with the developmental phenotypes arising from a defect in cytokinin signaling. These results indicate that HK5 and HK6 act as cytokinin receptors, with overlapping functions to regulate diverse aspects of rice growth and development.
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Affiliation(s)
- Christian A Burr
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Jinjing Sun
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599, USA
| | | | - Andrew Willoughby
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Charles Hodgens
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599, USA
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC 27599, USA
| | | | - Agustus Elmore
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Jonathan Atkinson
- School of Bioscience, University of Nottingham, Nottingham LE12 5RD, UK
| | - Zachary L Nimchuk
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Anthony Bishopp
- School of Bioscience, University of Nottingham, Nottingham LE12 5RD, UK
| | - G Eric Schaller
- Department of Biological Sciences, Dartmouth College, Hanover, NH 03755
| | - Joseph J Kieber
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599, USA
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC 27599, USA
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13
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Kim KW. Methanol fixation for scanning electron microscopy of plants. Appl Microsc 2020; 50:10. [PMID: 33580311 PMCID: PMC7818355 DOI: 10.1186/s42649-020-00028-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Accepted: 04/06/2020] [Indexed: 11/24/2022] Open
Abstract
Plant specimens for scanning electron microscopy (SEM) are commonly treated using standard protocols. Conventional fixatives consist of toxic chemicals such as glutaraldehyde, paraformaldehyde, and osmium tetroxide. In 1996, methanol fixation was reported as a rapid alternative to the standard protocols. If specimens are immersed in methanol for 30 s or longer and critical-point dried, they appear to be comparable in preservation quality to those treated with the chemical fixatives. A modified version that consists of methanol fixation and ethanol dehydration was effective at preserving the tissue morphology and dimensions. These solvent-based fixation and dehydration protocols are regarded as rapid and simple alternatives to standard protocols for SEM of plants.
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Affiliation(s)
- Ki Woo Kim
- School of Ecology and Environmental System, Kyungpook National University, Sangju, 37224, Republic of Korea. .,Tree Diagnostic Center, Kyungpook National University, Sangju, 37224, South Korea.
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14
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Heymans A, Couvreur V, LaRue T, Paez-Garcia A, Lobet G. GRANAR, a Computational Tool to Better Understand the Functional Importance of Monocotyledon Root Anatomy. PLANT PHYSIOLOGY 2020; 182:707-720. [PMID: 31744934 PMCID: PMC6997708 DOI: 10.1104/pp.19.00617] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Accepted: 11/10/2019] [Indexed: 05/05/2023]
Abstract
Root hydraulic conductivity is a limiting factor along the water pathways between the soil and the leaf, and root radial conductivity is itself defined by cell-scale hydraulic properties and anatomical features. However, quantifying the influence of anatomical features on the radial conductivity remains challenging due to complex time-consuming experimental procedures. We present an open-source computational tool, the Generator of Root Anatomy in R (GRANAR; http://granar.github.io), that can be used to rapidly generate digital versions of contrasted monocotyledon root anatomical networks. GRANAR uses a limited set of root anatomical parameters, easily acquired with existing image analysis tools. The generated anatomical network can then be used in combination with hydraulic models to estimate the corresponding hydraulic properties. We used GRANAR to reanalyze large maize (Zea mays) anatomical datasets from the literature. Our model was successful at creating virtual anatomies for each experimental observation. We also used GRANAR to generate anatomies not observed experimentally over wider ranges of anatomical parameters. The generated anatomies were then used to estimate the corresponding radial conductivities with the hydraulic model MECHA (model of explicit cross-section hydraulic architecture). Our simulations highlight the large importance of the width of the stele and the cortex. GRANAR is a computational tool that generates root anatomical networks from experimental data. It enables the quantification of the effect of individual anatomical features on the root radial conductivity.
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Affiliation(s)
- Adrien Heymans
- Earth and Life Institute, UCLouvain, 1348 Louvain-la-Neuve, Belgium
| | | | - Therese LaRue
- Department of Biology, Stanford University, Stanford, California 94305
| | | | - Guillaume Lobet
- Earth and Life Institute, UCLouvain, 1348 Louvain-la-Neuve, Belgium
- Agrosphere IBG3, Forschungszentrum Jülich, 52428 Jülich, Germany
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15
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Lentini Z, Tabares E, Buitrago ME. Vibratome Sectioning and Clearing for Easing Studies of Cassava Embryo Formation. FRONTIERS IN PLANT SCIENCE 2020; 11:1180. [PMID: 32849730 PMCID: PMC7417605 DOI: 10.3389/fpls.2020.01180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 07/21/2020] [Indexed: 05/09/2023]
Abstract
This work describes the application of clearing on vibratome sections to study the embryo formation in cassava. This procedure provides high-resolution images and reduces significantly the number of sections that need to be analyzed per ovule. This methodology was instrumental for the development of the protocol for embryo rescue in cassava. It has been also applied to monitor the embryo formation response when optimizing seed setting from regular and broad crosses for cassava breeding. Broad crosses between cassava and castor bean (incompatible-euphorbiaceae species) were made aiming to induce doubled haploids through the elimination of the incompatible-male parent genome as done in cereals. Castor bean is widely available and provides continues supply of pollen. Our results suggest that this methodology is easy and effective to assess the response of hundreds of cassava ovules pollinated with castor bean pollen, allowing the identification of multicellular structures in the embryo sac without apparent formation of endosperm. The protocol is also useful when developing and optimizing a methodology to induce doubled haploids in cassava via gynogenesis or from ovules pollinated with irradiated cassava pollen.
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16
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Griffiths M. A 3D Print Repository for Plant Phenomics. PLANT PHENOMICS (WASHINGTON, D.C.) 2020; 2020:8640215. [PMID: 33575669 PMCID: PMC7870102 DOI: 10.34133/2020/8640215] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Accepted: 10/10/2020] [Indexed: 05/19/2023]
Affiliation(s)
- M. Griffiths
- Noble Research Institute, LLC, 2510 Sam Noble Parkway, Ardmore, OK 73401, USA
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17
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Anupama A, Bhugra S, Lall B, Chaudhury S, Chugh A. Morphological, transcriptomic and proteomic responses of contrasting rice genotypes towards drought stress. ENVIRONMENTAL AND EXPERIMENTAL BOTANY 2019; 166:103795. [DOI: 10.1016/j.envexpbot.2019.06.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/19/2023]
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18
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Colombi T, Herrmann AM, Vallenback P, Keller T. Cortical Cell Diameter Is Key To Energy Costs of Root Growth in Wheat. PLANT PHYSIOLOGY 2019; 180:2049-2060. [PMID: 31123094 PMCID: PMC6670075 DOI: 10.1104/pp.19.00262] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Accepted: 05/08/2019] [Indexed: 05/22/2023]
Abstract
Root growth requires substantial amounts of energy and thus carbohydrates. The energy costs of root growth are particularly high in both dry and compacted soil, due to high soil penetration resistance. Consequently, more carbon must be allocated from aboveground plant tissue to roots, which limits crop productivity. In this study, we tested the utility of root cortical cell diameter as a potential selection target to reduce the energy costs of root growth. Isothermal calorimetry was adopted for in situ quantification of the energy costs of root growth of 16 wheat (Triticum aestivum) genotypes under three levels of penetration resistance. We show that cortical cell diameter is a pivotal and heritable trait, which is strongly related to the energy costs of root growth. Genotypic diversity was found for cortical cell diameter and the energy costs of root growth. A large root cortical cell diameter correlated with reduced energy costs of root growth, particularly under high soil penetration resistance. Moreover, significant correlations were found between the ability to radially enlarge cortical cells upon greater penetration resistance (i.e. phenotypic plasticity) and the responsiveness in the energy costs of root growth. A higher degree of phenotypic plasticity in cortical cell diameter was associated with reduced energy costs of root growth as soil penetration resistance increased. We therefore suggest that genotypic diversity and phenotypic plasticity in cortical cell diameter should be harnessed to adapt crops to dry and compacted soils.
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Affiliation(s)
- Tino Colombi
- Department of Soil and Environment, Swedish University of Agricultural Sciences, 750 07 Uppsala, Sweden
| | - Anke Marianne Herrmann
- Department of Soil and Environment, Swedish University of Agricultural Sciences, 750 07 Uppsala, Sweden
| | | | - Thomas Keller
- Department of Soil and Environment, Swedish University of Agricultural Sciences, 750 07 Uppsala, Sweden
- Department of Agroecology and Environment, Agroscope, 8046 Zürich, Switzerland
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19
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Mohammed U, Caine RS, Atkinson JA, Harrison EL, Wells D, Chater CC, Gray JE, Swarup R, Murchie EH. Rice plants overexpressing OsEPF1 show reduced stomatal density and increased root cortical aerenchyma formation. Sci Rep 2019; 9:5584. [PMID: 30944383 PMCID: PMC6447545 DOI: 10.1038/s41598-019-41922-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Accepted: 03/19/2019] [Indexed: 01/07/2023] Open
Abstract
Stomata are adjustable pores in the aerial epidermis of plants. The role of stomata is usually described in terms of the trade-off between CO2 uptake and water loss. Little consideration has been given to their interaction with below-ground development or diffusion of other gases. We overexpressed the rice EPIDERMAL PATTERNING FACTOR1 (OsEPF1) to produce rice plants with reduced stomatal densities, resulting in lowered leaf stomatal conductance and enhanced water use efficiency. Surprisingly, we found that root cortical aerenchyma (RCA) is formed constitutively in OsEPF1OE lines regardless of tissue age and position. Aerenchyma is tissue containing air-spaces that can develop in the plant root during stressful conditions, e.g. oxygen deficiency when it functions to increase O2 diffusion from shoot to root. The relationship with stomata is unknown. We conclude that RCA development and stomatal development are linked by two possible mechanisms: first that reduced stomatal conductance inhibits the diffusion of oxygen to the root, creating an oxygen deficit and stimulating the formation of RCA, second that an unknown EPF signalling pathway may be involved. Our observations have fundamental implications for the understanding of whole plant gas diffusion and root-to-shoot signalling events.
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Affiliation(s)
- U. Mohammed
- 0000 0004 1936 8868grid.4563.4Division of Plant and Crop Science, School of Biosciences, University of Nottingham, Sutton Bonington campus, LE12 5RD Nottingham, UK
| | - R. S. Caine
- 0000 0004 1936 9262grid.11835.3eDepartment of Molecular Biology and Biotechnology, University of Sheffield, Western Bank, S10 2TN Sheffield, UK
| | - J. A. Atkinson
- 0000 0004 1936 8868grid.4563.4Division of Plant and Crop Science, School of Biosciences, University of Nottingham, Sutton Bonington campus, LE12 5RD Nottingham, UK
| | - E. L. Harrison
- 0000 0004 1936 9262grid.11835.3eDepartment of Molecular Biology and Biotechnology, University of Sheffield, Western Bank, S10 2TN Sheffield, UK
| | - D. Wells
- 0000 0004 1936 8868grid.4563.4Division of Plant and Crop Science, School of Biosciences, University of Nottingham, Sutton Bonington campus, LE12 5RD Nottingham, UK
| | - C. C. Chater
- 0000 0004 1936 9262grid.11835.3eDepartment of Molecular Biology and Biotechnology, University of Sheffield, Western Bank, S10 2TN Sheffield, UK
| | - J. E. Gray
- 0000 0004 1936 9262grid.11835.3eDepartment of Molecular Biology and Biotechnology, University of Sheffield, Western Bank, S10 2TN Sheffield, UK
| | - R. Swarup
- 0000 0004 1936 8868grid.4563.4Division of Plant and Crop Science, School of Biosciences, University of Nottingham, Sutton Bonington campus, LE12 5RD Nottingham, UK
| | - E. H. Murchie
- 0000 0004 1936 8868grid.4563.4Division of Plant and Crop Science, School of Biosciences, University of Nottingham, Sutton Bonington campus, LE12 5RD Nottingham, UK
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20
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Atkinson JA, Pound MP, Bennett MJ, Wells DM. Uncovering the hidden half of plants using new advances in root phenotyping. Curr Opin Biotechnol 2019; 55:1-8. [PMID: 30031961 PMCID: PMC6378649 DOI: 10.1016/j.copbio.2018.06.002] [Citation(s) in RCA: 150] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Revised: 06/06/2018] [Accepted: 06/15/2018] [Indexed: 11/08/2022]
Abstract
Major increases in crop yield are required to keep pace with population growth and climate change. Improvements to the architecture of crop roots promise to deliver increases in water and nutrient use efficiency but profiling the root phenome (i.e. its structure and function) represents a major bottleneck. We describe how advances in imaging and sensor technologies are making root phenomic studies possible. However, methodological advances in acquisition, handling and processing of the resulting 'big-data' is becoming increasingly important. Advances in automated image analysis approaches such as Deep Learning promise to transform the root phenotyping landscape. Collectively, these innovations are helping drive the selection of the next-generation of crops to deliver real world impact for ongoing global food security efforts.
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Affiliation(s)
| | - Michael P Pound
- School of Biosciences, University of Nottingham, Sutton Bonington, UK; School of Computer Science, University of Nottingham, Nottingham, UK
| | - Malcolm J Bennett
- School of Biosciences, University of Nottingham, Sutton Bonington, UK.
| | - Darren M Wells
- School of Biosciences, University of Nottingham, Sutton Bonington, UK.
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21
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Mandoreba TY, Cloete KJ, Minnis-Ndimba R, Kupika OL. A Novel Application of a Cryosectioning Technique to Aid Scat Hair Microanalysis. J Forensic Sci 2018; 64:1181-1186. [PMID: 30513553 DOI: 10.1111/1556-4029.13976] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Revised: 11/19/2018] [Accepted: 11/19/2018] [Indexed: 11/29/2022]
Abstract
Scat hair presents a diverse profile of hairs for morphological assessment that may find versatile applications in wildlife forensic investigations. Successful morphological assessment of scat hair microstructure, however, depends on a robust sectioning methodology. We assessed the feasibility and efficacy of a cryosectioning technique compared to that of a gold standard hand-sectioning technique. Scat hairs were embedded in paraffin wax and hand-sectioned, while cryopreserved scat hairs were sectioned with a cryostat. The results showed that cryosectioning preserved the pristine morphology of the scat hair and provided cross sections more amenable to high-resolution imaging of hair internal microstructure than hand-sectioning. The cryosectioning technique may find novel applications as a more reliable and robust technique to aid (i) scat hair internal microstructure analysis for cross-referencing with species identification keys in wildlife forensic studies and (ii) downstream toxicological analysis in wildlife forensic studies as hair biochemistry is not altered during cryopreservation.
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Affiliation(s)
- Talia Y Mandoreba
- Department of Wildlife Ecology and Conservation, School of Wildlife, Ecology and Conservation, Chinhoyi University of Technology, Private Bag 7724, Chinhoyi, Zimbabwe.,Cheetah Outreach Project, PO Box 1009, Somerset West, 7137, South Africa
| | - Karen J Cloete
- Materials Research Department, iThemba Laboratory for Accelerator Based Sciences, National Research Foundation, PO Box 722, Somerset West, 7129, South Africa
| | - Roya Minnis-Ndimba
- Materials Research Department, iThemba Laboratory for Accelerator Based Sciences, National Research Foundation, PO Box 722, Somerset West, 7129, South Africa
| | - Olga L Kupika
- Department of Wildlife Ecology and Conservation, School of Wildlife, Ecology and Conservation, Chinhoyi University of Technology, Private Bag 7724, Chinhoyi, Zimbabwe
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