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Alrajhi A, Alharbi S, Beecham S, Alotaibi F. Regulation of root growth and elongation in wheat. FRONTIERS IN PLANT SCIENCE 2024; 15:1397337. [PMID: 38835859 PMCID: PMC11148372 DOI: 10.3389/fpls.2024.1397337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Accepted: 05/06/2024] [Indexed: 06/06/2024]
Abstract
Currently, the control of rhizosphere selection on farms has been applied to achieve enhancements in phenotype, extending from improvements in single root characteristics to the dynamic nature of entire crop systems. Several specific signals, regulatory elements, and mechanisms that regulate the initiation, morphogenesis, and growth of new lateral or adventitious root species have been identified, but much more work remains. Today, phenotyping technology drives the development of root traits. Available models for simulation can support all phenotyping decisions (root trait improvement). The detection and use of markers for quantitative trait loci (QTLs) are effective for enhancing selection efficiency and increasing reproductive genetic gains. Furthermore, QTLs may help wheat breeders select the appropriate roots for efficient nutrient acquisition. Single-nucleotide polymorphisms (SNPs) or alignment of sequences can only be helpful when they are associated with phenotypic variation for root development and elongation. Here, we focus on major root development processes and detail important new insights recently generated regarding the wheat genome. The first part of this review paper discusses the root morphology, apical meristem, transcriptional control, auxin distribution, phenotyping of the root system, and simulation models. In the second part, the molecular genetics of the wheat root system, SNPs, TFs, and QTLs related to root development as well as genome editing (GE) techniques for the improvement of root traits in wheat are discussed. Finally, we address the effect of omics strategies on root biomass production and summarize existing knowledge of the main molecular mechanisms involved in wheat root development and elongation.
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Affiliation(s)
- Abdullah Alrajhi
- King Abdulaziz City for Science and Technology (KACST), Riyadh, Saudi Arabia
- Sustainable Infrastructure and Resource Management, University of South Australia, University of South Australia Science, Technology, Engineering, and Mathematics (UniSA STEM), Mawson Lakes, SA, Australia
| | - Saif Alharbi
- The National Research and Development Center for Sustainable Agriculture (Estidamah), Riyadh, Saudi Arabia
| | - Simon Beecham
- Sustainable Infrastructure and Resource Management, University of South Australia, University of South Australia Science, Technology, Engineering, and Mathematics (UniSA STEM), Mawson Lakes, SA, Australia
| | - Fahad Alotaibi
- King Abdulaziz City for Science and Technology (KACST), Riyadh, Saudi Arabia
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2
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Weihs BJ, Heuschele DJ, Tang Z, York LM, Zhang Z, Xu Z. The State of the Art in Root System Architecture Image Analysis Using Artificial Intelligence: A Review. PLANT PHENOMICS (WASHINGTON, D.C.) 2024; 6:0178. [PMID: 38711621 PMCID: PMC11070851 DOI: 10.34133/plantphenomics.0178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Accepted: 03/27/2024] [Indexed: 05/08/2024]
Abstract
Roots are essential for acquiring water and nutrients to sustain and support plant growth and anchorage. However, they have been studied less than the aboveground traits in phenotyping and plant breeding until recent decades. In modern times, root properties such as morphology and root system architecture (RSA) have been recognized as increasingly important traits for creating more and higher quality food in the "Second Green Revolution". To address the paucity in RSA and other root research, new technologies are being investigated to fill the increasing demand to improve plants via root traits and overcome currently stagnated genetic progress in stable yields. Artificial intelligence (AI) is now a cutting-edge technology proving to be highly successful in many applications, such as crop science and genetic research to improve crop traits. A burgeoning field in crop science is the application of AI to high-resolution imagery in analyses that aim to answer questions related to crops and to better and more speedily breed desired plant traits such as RSA into new cultivars. This review is a synopsis concerning the origins, applications, challenges, and future directions of RSA research regarding image analyses using AI.
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Affiliation(s)
- Brandon J. Weihs
- United States Department of Agriculture–Agricultural Research Service–Plant Science Research, St. Paul, MN 55108, USA
- Department of Agronomy and Plant Genetics,
University of Minnesota, St. Paul, MN, 55108, USA
| | - Deborah-Jo Heuschele
- United States Department of Agriculture–Agricultural Research Service–Plant Science Research, St. Paul, MN 55108, USA
- Department of Agronomy and Plant Genetics,
University of Minnesota, St. Paul, MN, 55108, USA
| | - Zhou Tang
- Department of Crop and Soil Sciences,
Washington State University, Pullman, WA 99164, USA
| | - Larry M. York
- Biosciences Division and Center for Bioenergy Innovation,
Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
| | - Zhiwu Zhang
- Department of Crop and Soil Sciences,
Washington State University, Pullman, WA 99164, USA
| | - Zhanyou Xu
- United States Department of Agriculture–Agricultural Research Service–Plant Science Research, St. Paul, MN 55108, USA
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3
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Lärm L, Bauer FM, Hermes N, van der Kruk J, Vereecken H, Vanderborght J, Nguyen TH, Lopez G, Seidel SJ, Ewert F, Schnepf A, Klotzsche A. Multi-year belowground data of minirhizotron facilities in Selhausen. Sci Data 2023; 10:672. [PMID: 37789016 PMCID: PMC10547842 DOI: 10.1038/s41597-023-02570-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 09/14/2023] [Indexed: 10/05/2023] Open
Abstract
The production of crops secure the human food supply, but climate change is bringing new challenges. Dynamic plant growth and corresponding environmental data are required to uncover phenotypic crop responses to the changing environment. There are many datasets on above-ground organs of crops, but roots and the surrounding soil are rarely the subject of longer term studies. Here, we present what we believe to be the first comprehensive collection of root and soil data, obtained at two minirhizotron facilities located close together that have the same local climate but differ in soil type. Both facilities have 7m-long horizontal tubes at several depths that were used for crosshole ground-penetrating radar and minirhizotron camera systems. Soil sensors provide observations at a high temporal and spatial resolution. The ongoing measurements cover five years of maize and wheat trials, including drought stress treatments and crop mixtures. We make the processed data available for use in investigating the processes within the soil-plant continuum and the root images to develop and compare image analysis methods.
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Affiliation(s)
- Lena Lärm
- Institute of Bio-and Geosciences, Agrosphere (IBG-3), Forschungszentrum Jülich GmbH, Jülich, 52425, Germany.
| | - Felix Maximilian Bauer
- Institute of Bio-and Geosciences, Agrosphere (IBG-3), Forschungszentrum Jülich GmbH, Jülich, 52425, Germany.
| | - Normen Hermes
- Institute of Bio-and Geosciences, Agrosphere (IBG-3), Forschungszentrum Jülich GmbH, Jülich, 52425, Germany
| | - Jan van der Kruk
- Institute of Bio-and Geosciences, Agrosphere (IBG-3), Forschungszentrum Jülich GmbH, Jülich, 52425, Germany
| | - Harry Vereecken
- Institute of Bio-and Geosciences, Agrosphere (IBG-3), Forschungszentrum Jülich GmbH, Jülich, 52425, Germany
| | - Jan Vanderborght
- Institute of Bio-and Geosciences, Agrosphere (IBG-3), Forschungszentrum Jülich GmbH, Jülich, 52425, Germany
| | - Thuy Huu Nguyen
- Crop Science Group, Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Bonn, 53115, Germany
| | - Gina Lopez
- Crop Science Group, Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Bonn, 53115, Germany
| | - Sabine Julia Seidel
- Crop Science Group, Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Bonn, 53115, Germany
| | - Frank Ewert
- Crop Science Group, Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Bonn, 53115, Germany
- Leibniz Centre for Agricultural Landscape Research (ZALF), Müncheberg, 15374, Germany
| | - Andrea Schnepf
- Institute of Bio-and Geosciences, Agrosphere (IBG-3), Forschungszentrum Jülich GmbH, Jülich, 52425, Germany
| | - Anja Klotzsche
- Institute of Bio-and Geosciences, Agrosphere (IBG-3), Forschungszentrum Jülich GmbH, Jülich, 52425, Germany.
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Huang L, Zhang Y, Guo J, Peng Q, Zhou Z, Duan X, Tanveer M, Guo Y. High-throughput root phenotyping of crop cultivars tolerant to low N in waterlogged soils. FRONTIERS IN PLANT SCIENCE 2023; 14:1271539. [PMID: 37780519 PMCID: PMC10533935 DOI: 10.3389/fpls.2023.1271539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 08/29/2023] [Indexed: 10/03/2023]
Affiliation(s)
- Liping Huang
- International Research Center for Environmental Membrane Biology, College of Food Science and Engineering, Foshan University, Foshan, China
- Foshan ZhiBao Ecological Technology Co. Ltd., Foshan, China
| | - Yujing Zhang
- International Research Center for Environmental Membrane Biology, College of Food Science and Engineering, Foshan University, Foshan, China
- Foshan ZhiBao Ecological Technology Co. Ltd., Foshan, China
| | - Jieru Guo
- International Research Center for Environmental Membrane Biology, College of Food Science and Engineering, Foshan University, Foshan, China
- Foshan ZhiBao Ecological Technology Co. Ltd., Foshan, China
| | - Qianlan Peng
- International Research Center for Environmental Membrane Biology, College of Food Science and Engineering, Foshan University, Foshan, China
| | - Zhaoyang Zhou
- International Research Center for Environmental Membrane Biology, College of Food Science and Engineering, Foshan University, Foshan, China
| | - Xiaosong Duan
- International Research Center for Environmental Membrane Biology, College of Food Science and Engineering, Foshan University, Foshan, China
| | - Mohsin Tanveer
- Tasmanian Institute of Agriculture, University of Tasmania, Hobart, TAS, Australia
| | - Yongjun Guo
- International Research Center for Environmental Membrane Biology, College of Food Science and Engineering, Foshan University, Foshan, China
- Foshan ZhiBao Ecological Technology Co. Ltd., Foshan, China
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Bacher H, Montagu A, Herrmann I, Walia H, Schwartz N, Peleg Z. Stress-induced deeper rooting introgression enhances wheat yield under terminal drought. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:4862-4874. [PMID: 36787201 DOI: 10.1093/jxb/erad059] [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: 10/06/2022] [Accepted: 02/10/2023] [Indexed: 06/18/2023]
Abstract
Water scarcity is the primary environmental constraint affecting wheat growth and production and is increasingly exacerbated due to climatic fluctuation, which jeopardizes future food security. Most breeding efforts to improve wheat yields under drought have focused on above-ground traits. Root traits are closely associated with various drought adaptability mechanisms, but the genetic variation underlying these traits remains untapped, even though it holds tremendous potential for improving crop resilience. Here, we examined this potential by re-introducing ancestral alleles from wild emmer wheat (Triticum turgidum ssp. dicoccoides) and studied their impact on root architecture diversity under terminal drought stress. We applied an active sensing electrical resistivity tomography approach to compare a wild emmer introgression line (IL20) and its drought-sensitive recurrent parent (Svevo) under field conditions. IL20 exhibited greater root elongation under drought, which resulted in higher root water uptake from deeper soil layers. This advantage initiated at the pseudo-stem stage and increased during the transition to the reproductive stage. The increased water uptake promoted higher gas exchange rates and enhanced grain yield under drought. Overall, we show that this presumably 'lost' drought-induced mechanism of deeper rooting profile can serve as a breeding target to improve wheat productiveness under changing climate.
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Affiliation(s)
- Harel Bacher
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot 7610001, Israel
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE 68583, USA
| | - Aviad Montagu
- The Institute of Environmental Sciences, The Hebrew University of Jerusalem, Rehovot 7610001, Israel
| | - Ittai Herrmann
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot 7610001, Israel
| | - Harkamal Walia
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE 68583, USA
| | - Nimrod Schwartz
- The Institute of Environmental Sciences, The Hebrew University of Jerusalem, Rehovot 7610001, Israel
| | - Zvi Peleg
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot 7610001, Israel
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6
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Zheng C, Bochmann H, Liu Z, Kant J, Schrey SD, Wojciechowski T, Postma JA. Plant root plasticity during drought and recovery: What do we know and where to go? FRONTIERS IN PLANT SCIENCE 2023; 14:1084355. [PMID: 37008469 PMCID: PMC10061088 DOI: 10.3389/fpls.2023.1084355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Accepted: 02/28/2023] [Indexed: 06/19/2023]
Abstract
AIMS Drought stress is one of the most limiting factors for agriculture and ecosystem productivity. Climate change exacerbates this threat by inducing increasingly intense and frequent drought events. Root plasticity during both drought and post-drought recovery is regarded as fundamental to understanding plant climate resilience and maximizing production. We mapped the different research areas and trends that focus on the role of roots in plant response to drought and rewatering and asked if important topics were overlooked. METHODS We performed a comprehensive bibliometric analysis based on journal articles indexed in the Web of Science platform from 1900-2022. We evaluated a) research areas and temporal evolution of keyword frequencies, b) temporal evolution and scientific mapping of the outputs over time, c) trends in the research topics analysis, d) marked journals and citation analysis, and e) competitive countries and dominant institutions to understand the temporal trends of root plasticity during both drought and recovery in the past 120 years. RESULTS Plant physiological factors, especially in the aboveground part (such as "photosynthesis", "gas-exchange", "abscisic-acid") in model plants Arabidopsis, crops such as wheat and maize, and trees were found to be the most popular study areas; they were also combined with other abiotic factors such as salinity, nitrogen, and climate change, while dynamic root growth and root system architecture responses received less attention. Co-occurrence network analysis showed that three clusters were classified for the keywords including 1) photosynthesis response; 2) physiological traits tolerance (e.g. abscisic acid); 3) root hydraulic transport. Thematically, themes evolved from classical agricultural and ecological research via molecular physiology to root plasticity during drought and recovery. The most productive (number of publications) and cited countries and institutions were situated on drylands in the USA, China, and Australia. In the past decades, scientists approached the topic mostly from a soil-plant hydraulic perspective and strongly focused on aboveground physiological regulation, whereas the actual belowground processes seemed to have been the elephant in the room. There is a strong need for better investigation into root and rhizosphere traits during drought and recovery using novel root phenotyping methods and mathematical modeling.
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Affiliation(s)
- Congcong Zheng
- Institute of Bio- and Geosciences – Plant Sciences (IBG-2), Forschungszentrum Jülich GmbH, Jülich, Germany
- Faculty of Agriculture, University of Bonn, Bonn, Germany
| | - Helena Bochmann
- Institute of Bio- and Geosciences – Plant Sciences (IBG-2), Forschungszentrum Jülich GmbH, Jülich, Germany
- Faculty of Agriculture, University of Bonn, Bonn, Germany
| | - Zhaogang Liu
- Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing, China
| | - Josefine Kant
- Institute of Bio- and Geosciences – Plant Sciences (IBG-2), Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Silvia D. Schrey
- Institute of Bio- and Geosciences – Plant Sciences (IBG-2), Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Tobias Wojciechowski
- Institute of Bio- and Geosciences – Plant Sciences (IBG-2), Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Johannes Auke Postma
- Institute of Bio- and Geosciences – Plant Sciences (IBG-2), Forschungszentrum Jülich GmbH, Jülich, Germany
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Üstüner S, Schäfer P, Eichmann R. Development specifies, diversifies and empowers root immunity. EMBO Rep 2022; 23:e55631. [PMID: 36330761 PMCID: PMC9724680 DOI: 10.15252/embr.202255631] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 10/10/2022] [Accepted: 10/13/2022] [Indexed: 08/04/2023] Open
Abstract
Roots are a highly organised plant tissue consisting of different cell types with distinct developmental functions defined by cell identity networks. Roots are the target of some of the most devastating diseases and possess a highly effective immune system. The recognition of microbe- or plant-derived molecules released in response to microbial attack is highly important in the activation of complex immunity gene networks. Development and immunity are intertwined, and immunity activation can result in growth inhibition. In turn, by connecting immunity and cell identity regulators, cell types are able to launch a cell type-specific immunity based on the developmental function of each cell type. By this strategy, fundamental developmental processes of each cell type contribute their most basic functions to drive cost-effective but highly diverse and, thus, efficient immune responses. This review highlights the interdependence of root development and immunity and how the developmental age of root cells contributes to positive and negative outcomes of development-immunity cross-talk.
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Affiliation(s)
- Sim Üstüner
- Institute of Phytopathology, Research Centre for BioSystems, Land Use and NutritionJustus Liebig UniversityGiessenGermany
| | - Patrick Schäfer
- Institute of Phytopathology, Research Centre for BioSystems, Land Use and NutritionJustus Liebig UniversityGiessenGermany
| | - Ruth Eichmann
- Institute of Phytopathology, Research Centre for BioSystems, Land Use and NutritionJustus Liebig UniversityGiessenGermany
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8
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Langan P, Bernád V, Walsh J, Henchy J, Khodaeiaminjan M, Mangina E, Negrão S. Phenotyping for waterlogging tolerance in crops: current trends and future prospects. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:5149-5169. [PMID: 35642593 PMCID: PMC9440438 DOI: 10.1093/jxb/erac243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Accepted: 05/30/2022] [Indexed: 06/15/2023]
Abstract
Yield losses to waterlogging are expected to become an increasingly costly and frequent issue in some regions of the world. Despite the extensive work that has been carried out examining the molecular and physiological responses to waterlogging, phenotyping for waterlogging tolerance has proven difficult. This difficulty is largely due to the high variability of waterlogging conditions such as duration, temperature, soil type, and growth stage of the crop. In this review, we highlight use of phenotyping to assess and improve waterlogging tolerance in temperate crop species. We start by outlining the experimental methods that have been utilized to impose waterlogging stress, ranging from highly controlled conditions of hydroponic systems to large-scale screenings in the field. We also describe the phenotyping traits used to assess tolerance ranging from survival rates and visual scoring to precise photosynthetic measurements. Finally, we present an overview of the challenges faced in attempting to improve waterlogging tolerance, the trade-offs associated with phenotyping in controlled conditions, limitations of classic phenotyping methods, and future trends using plant-imaging methods. If effectively utilized to increase crop resilience to changing climates, crop phenotyping has a major role to play in global food security.
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Affiliation(s)
- Patrick Langan
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
| | - Villő Bernád
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
| | - Jason Walsh
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
- School of Computer Science and UCD Energy Institute, University College Dublin, Dublin, Ireland
| | - Joey Henchy
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
| | | | - Eleni Mangina
- School of Computer Science and UCD Energy Institute, University College Dublin, Dublin, Ireland
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Shoaib M, Banerjee BP, Hayden M, Kant S. Roots’ Drought Adaptive Traits in Crop Improvement. PLANTS 2022; 11:plants11172256. [PMID: 36079644 PMCID: PMC9460784 DOI: 10.3390/plants11172256] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 08/26/2022] [Accepted: 08/26/2022] [Indexed: 11/16/2022]
Abstract
Drought is one of the biggest concerns in agriculture due to the projected reduction of global freshwater supply with a concurrent increase in global food demand. Roots can significantly contribute to improving drought adaptation and productivity. Plants increase water uptake by adjusting root architecture and cooperating with symbiotic soil microbes. Thus, emphasis has been given to root architectural responses and root–microbe relationships in drought-resilient crop development. However, root responses to drought adaptation are continuous and complex processes and involve additional root traits and interactions among themselves. This review comprehensively compiles and discusses several of these root traits such as structural, physiological, molecular, hydraulic, anatomical, and plasticity, which are important to consider together, with architectural changes, when developing drought resilient crop varieties. In addition, it describes the significance of root contribution in improving soil structure and water holding capacity and its implication on long-term resilience to drought. In addition, various drought adaptive root ideotypes of monocot and dicot crops are compared and proposed for given agroclimatic conditions. Overall, this review provides a broader perspective of understanding root structural, physiological, and molecular regulators, and describes the considerations for simultaneously integrating multiple traits for drought tolerance and crop improvement, under specific growing environments.
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Affiliation(s)
- Mirza Shoaib
- Agriculture Victoria, Grains Innovation Park, 110 Natimuk Road, Horsham, VIC 3400, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, Melbourne, VIC 3083, Australia
| | - Bikram P. Banerjee
- Agriculture Victoria, Grains Innovation Park, 110 Natimuk Road, Horsham, VIC 3400, Australia
| | - Matthew Hayden
- School of Applied Systems Biology, La Trobe University, Bundoora, Melbourne, VIC 3083, Australia
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, 5 Ring Road, Bundoora, Melbourne, VIC 3083, Australia
| | - Surya Kant
- Agriculture Victoria, Grains Innovation Park, 110 Natimuk Road, Horsham, VIC 3400, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, Melbourne, VIC 3083, Australia
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, 5 Ring Road, Bundoora, Melbourne, VIC 3083, Australia
- Correspondence:
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Pflugfelder D, Kochs J, Koller R, Jahnke S, Mohl C, Pariyar S, Fassbender H, Nagel KA, Watt M, van Dusschoten D. The root system architecture of wheat establishing in soil is associated with varying elongation rates of seminal roots: quantification using 4D magnetic resonance imaging. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:2050-2060. [PMID: 34918078 DOI: 10.1093/jxb/erab551] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Accepted: 12/14/2021] [Indexed: 06/14/2023]
Abstract
Seedling establishment is the first stage of crop productivity, and root phenotypes at seed emergence are critical to a successful start of shoot growth as well as for water and nutrient uptake. In this study, we investigate seedling establishment in winter wheat utilizing a newly developed workflow based on magnetic resonance imaging (MRI). Using the eight parents of the MAGIC (multi-parent advanced generation inter-cross) population we analysed the 4D root architecture of 288 individual seedlings grown in natural soils with plant neighbors over 3 d of development. Time of root and shoot emergence, total length, angle, and depth of the axile roots varied significantly among these genotypes. The temporal data resolved rates of elongation of primary roots and first and second seminal root pairs. Genotypes with slowly elongating primary roots had rapidly elongating first and second seminal root pairs and vice versa, resulting in variation in root system architecture mediated not only by root angle but also by initiation and relative elongation of axile roots. We demonstrated that our novel MRI workflow with a unique planting design and automated measurements allowed medium throughput phenotyping of wheat roots in 4D and could give new insights into regulation of root system architecture.
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Affiliation(s)
- Daniel Pflugfelder
- Forschungszentrum Jülich GmbH, IBG-2: Plant Sciences, 52425 Jülich, Germany
| | - Johannes Kochs
- Forschungszentrum Jülich GmbH, IBG-2: Plant Sciences, 52425 Jülich, Germany
| | - Robert Koller
- Forschungszentrum Jülich GmbH, IBG-2: Plant Sciences, 52425 Jülich, Germany
| | - Siegfried Jahnke
- Forschungszentrum Jülich GmbH, IBG-2: Plant Sciences, 52425 Jülich, Germany
- University of Duisburg-Essen, Biodiversity, Universitätsstr. 5, 45141 Essen, Germany
| | - Carola Mohl
- Forschungszentrum Jülich GmbH, IBG-2: Plant Sciences, 52425 Jülich, Germany
| | - Shree Pariyar
- Forschungszentrum Jülich GmbH, IBG-2: Plant Sciences, 52425 Jülich, Germany
| | - Heike Fassbender
- Forschungszentrum Jülich GmbH, IBG-2: Plant Sciences, 52425 Jülich, Germany
| | - Kerstin A Nagel
- Forschungszentrum Jülich GmbH, IBG-2: Plant Sciences, 52425 Jülich, Germany
| | - Michelle Watt
- Forschungszentrum Jülich GmbH, IBG-2: Plant Sciences, 52425 Jülich, Germany
- School of BioSciences, Faculty of Science, University of Melbourne, Parkville, Victoria, 3010Australia
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11
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Rajurkar AB, McCoy SM, Ruhter J, Mulcrone J, Freyfogle L, Leakey ADB. Installation and imaging of thousands of minirhizotrons to phenotype root systems of field-grown plants. PLANT METHODS 2022; 18:39. [PMID: 35346269 PMCID: PMC8958774 DOI: 10.1186/s13007-022-00874-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 03/10/2022] [Indexed: 05/27/2023]
Abstract
BACKGROUND Roots are vital to plant performance because they acquire resources from the soil and provide anchorage. However, it remains difficult to assess root system size and distribution because roots are inaccessible in the soil. Existing methods to phenotype entire root systems range from slow, often destructive, methods applied to relatively small numbers of plants in the field to rapid methods that can be applied to large numbers of plants in controlled environment conditions. Much has been learned recently by extensive sampling of the root crown portion of field-grown plants. But, information on large-scale genetic and environmental variation in the size and distribution of root systems in the field remains a key knowledge gap. Minirhizotrons are the only established, non-destructive technology that can address this need in a standard field trial. Prior experiments have used only modest numbers of minirhizotrons, which has limited testing to small numbers of genotypes or environmental conditions. This study addressed the need for methods to install and collect images from thousands of minirhizotrons and thereby help break the phenotyping bottleneck in the field. RESULTS Over three growing seasons, methods were developed and refined to install and collect images from up to 3038 minirhizotrons per experiment. Modifications were made to four tractors and hydraulic soil corers mounted to them. High quality installation was achieved at an average rate of up to 84.4 minirhizotron tubes per tractor per day. A set of four commercially available minirhizotron camera systems were each transported by wheelbarrow to allow collection of images of mature maize root systems at an average rate of up to 65.3 tubes per day per camera. This resulted in over 300,000 images being collected in as little as 11 days for a single experiment. CONCLUSION The scale of minirhizotron installation was increased by two orders of magnitude by simultaneously using four tractor-mounted, hydraulic soil corers with modifications to ensure high quality, rapid operation. Image collection can be achieved at the corresponding scale using commercially available minirhizotron camera systems. Along with recent advances in image analysis, these advances will allow use of minirhizotrons at unprecedented scale to address key knowledge gaps regarding genetic and environmental effects on root system size and distribution in the field.
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Affiliation(s)
- Ashish B. Rajurkar
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL USA
| | - Scott M. McCoy
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL USA
| | - Jeremy Ruhter
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL USA
| | - Jessica Mulcrone
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL USA
| | - Luke Freyfogle
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL USA
| | - Andrew D. B. Leakey
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL USA
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL USA
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL USA
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12
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Ultra-Wideband Microwave Imaging System for Root Phenotyping. SENSORS 2022; 22:s22052031. [PMID: 35271178 PMCID: PMC8914630 DOI: 10.3390/s22052031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 03/02/2022] [Accepted: 03/03/2022] [Indexed: 11/18/2022]
Abstract
The roots are a vital organ for plant growth and health. The opaque surrounding environment of the roots and the complicated growth process means that in situ and non-destructive root phenotyping face great challenges, which thus spur great research interests. The existing methods for root phenotyping are either unable to provide high-precision and high accuracy in situ detection, or they change the surrounding root environment and are destructive to root growth and health. Thus,we propose and develop an ultra-wideband microwave scanning method that uses time reversal to achieve in situ root phenotyping nondestructively. To verify the method’s feasibility, we studied an electromagnetic numerical model that simulates the transmission signal of two ultra-wideband microwave antennas. The simulated signal of roots with different shapes shows the proposed system’s capability to measure the root size in the soil. Experimental validations were conducted considering three sets of measurements with different sizes, numbers and locations, and the experimental results indicate that the developed imaging system was able to differentiate root sizes and numbers with high contrast. The reconstruction from both simulations and experimental measurements provided accurate size estimation of the carrots in the soil, which indicates the system’s potential for root imaging.
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13
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Sun D, Robbins K, Morales N, Shu Q, Cen H. Advances in optical phenotyping of cereal crops. TRENDS IN PLANT SCIENCE 2022; 27:191-208. [PMID: 34417079 DOI: 10.1016/j.tplants.2021.07.015] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 07/22/2021] [Accepted: 07/24/2021] [Indexed: 06/13/2023]
Abstract
Optical sensors and sensing-based phenotyping techniques have become mainstream approaches in high-throughput phenotyping for improving trait selection and genetic gains in crops. We review recent progress and contemporary applications of optical sensing-based phenotyping (OSP) techniques in cereal crops and highlight optical sensing principles for spectral response and sensor specifications. Further, we group phenotypic traits determined by OSP into four categories - morphological, biochemical, physiological, and performance traits - and illustrate appropriate sensors for each extraction. In addition to the current status, we discuss the challenges of OSP and provide possible solutions. We propose that optical sensing-based traits need to be explored further, and that standardization of the language of phenotyping and worldwide collaboration between phenotyping researchers and other fields need to be established.
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Affiliation(s)
- Dawei Sun
- College of Biosystems Engineering and Food Science, and State Key Laboratory of Modern Optical Instrumentation, Zhejiang University, Hangzhou 310058, PR China; Key Laboratory of Spectroscopy Sensing, Ministry of Agriculture and Rural Affairs, Hangzhou 310058, PR China
| | - Kelly Robbins
- Section of Plant Breeding and Genetics, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
| | - Nicolas Morales
- Section of Plant Breeding and Genetics, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
| | - Qingyao Shu
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Zhejiang University, Hangzhou, PR China; State Key Laboratory of Rice Biology, Zhejiang University, Hangzhou 310058, PR China
| | - Haiyan Cen
- College of Biosystems Engineering and Food Science, and State Key Laboratory of Modern Optical Instrumentation, Zhejiang University, Hangzhou 310058, PR China; Key Laboratory of Spectroscopy Sensing, Ministry of Agriculture and Rural Affairs, Hangzhou 310058, PR China.
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14
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Rambla C, Van Der Meer S, Voss-Fels KP, Makhoul M, Obermeier C, Snowdon R, Ober ES, Watt M, Alahmad S, Hickey LT. A toolkit to rapidly modify root systems through single plant selection. PLANT METHODS 2022; 18:2. [PMID: 35012581 PMCID: PMC8750989 DOI: 10.1186/s13007-021-00834-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 12/22/2021] [Indexed: 05/15/2023]
Abstract
BACKGROUND The incorporation of root traits into elite germplasm is typically a slow process. Thus, innovative approaches are required to accelerate research and pre-breeding programs targeting root traits to improve yield stability in different environments and soil types. Marker-assisted selection (MAS) can help to speed up the process by selecting key genes or quantitative trait loci (QTL) associated with root traits. However, this approach is limited due to the complex genetic control of root traits and the limited number of well-characterised large effect QTL. Coupling MAS with phenotyping could increase the reliability of selection. Here we present a useful framework to rapidly modify root traits in elite germplasm. In this wheat exemplar, a single plant selection (SPS) approach combined three main elements: phenotypic selection (in this case for seminal root angle); MAS using KASP markers (targeting a root biomass QTL); and speed breeding to accelerate each cycle. RESULTS To develop a SPS approach that integrates non-destructive screening for seminal root angle and root biomass, two initial experiments were conducted. Firstly, we demonstrated that transplanting wheat seedlings from clear pots (for seminal root angle assessment) into sand pots (for root biomass assessment) did not impact the ability to differentiate genotypes with high and low root biomass. Secondly, we demonstrated that visual scores for root biomass were correlated with root dry weight (r = 0.72), indicating that single plants could be evaluated for root biomass in a non-destructive manner. To highlight the potential of the approach, we applied SPS in a backcrossing program which integrated MAS and speed breeding for the purpose of rapidly modifying the root system of elite bread wheat line Borlaug100. Bi-directional selection for root angle in segregating generations successfully shifted the mean root angle by 30° in the subsequent generation (P ≤ 0.05). Within 18 months, BC2F4:F5 introgression lines were developed that displayed a full range of root configurations, while retaining similar above-ground traits to the recurrent parent. Notably, the seminal root angle displayed by introgression lines varied more than 30° compared to the recurrent parent, resulting in lines with both narrow and wide root angles, and high and low root biomass phenotypes. CONCLUSION The SPS approach enables researchers and plant breeders to rapidly manipulate root traits of future crop varieties, which could help improve productivity in the face of increasing environmental fluctuations. The newly developed elite wheat lines with modified root traits provide valuable materials to study the value of different root systems to support yield in different environments and soil types.
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Affiliation(s)
- Charlotte Rambla
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - Sarah Van Der Meer
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - Kai P Voss-Fels
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - Manar Makhoul
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Heinrich-Buff-Ring 26-32, 35392, Giessen, Germany
| | - Christian Obermeier
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Heinrich-Buff-Ring 26-32, 35392, Giessen, Germany
| | - Rod Snowdon
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, 4072, Australia
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Heinrich-Buff-Ring 26-32, 35392, Giessen, Germany
| | - Eric S Ober
- National Institute of Agricultural Botany (NIAB), 93 Lawrence Weaver Road, Cambridge, CB3 0LE, UK
| | - Michelle Watt
- School of BioSciences, Faculty of Science, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Samir Alahmad
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, 4072, Australia.
| | - Lee T Hickey
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, 4072, Australia.
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15
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Langstroff A, Heuermann MC, Stahl A, Junker A. Opportunities and limits of controlled-environment plant phenotyping for climate response traits. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:1-16. [PMID: 34302493 PMCID: PMC8741719 DOI: 10.1007/s00122-021-03892-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Accepted: 06/17/2021] [Indexed: 05/19/2023]
Abstract
Rising temperatures and changing precipitation patterns will affect agricultural production substantially, exposing crops to extended and more intense periods of stress. Therefore, breeding of varieties adapted to the constantly changing conditions is pivotal to enable a quantitatively and qualitatively adequate crop production despite the negative effects of climate change. As it is not yet possible to select for adaptation to future climate scenarios in the field, simulations of future conditions in controlled-environment (CE) phenotyping facilities contribute to the understanding of the plant response to special stress conditions and help breeders to select ideal genotypes which cope with future conditions. CE phenotyping facilities enable the collection of traits that are not easy to measure under field conditions and the assessment of a plant's phenotype under repeatable, clearly defined environmental conditions using automated, non-invasive, high-throughput methods. However, extrapolation and translation of results obtained under controlled environments to field environments is ambiguous. This review outlines the opportunities and challenges of phenotyping approaches under controlled environments complementary to conventional field trials. It gives an overview on general principles and introduces existing phenotyping facilities that take up the challenge of obtaining reliable and robust phenotypic data on climate response traits to support breeding of climate-adapted crops.
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Affiliation(s)
- Anna Langstroff
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University Giessen, Heinrich Buff-Ring 26, 35392, Giessen, Germany
| | - Marc C Heuermann
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstr. 3, OT Gatersleben, 06466, Seeland, Germany
| | - Andreas Stahl
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University Giessen, Heinrich Buff-Ring 26, 35392, Giessen, Germany
- Institute for Resistance Research and Stress Tolerance, Federal Research Centre for Cultivated Plants, Julius Kühn-Institut (JKI), Erwin-Baur-Strasse 27, 06484, Quedlinburg, Germany
| | - Astrid Junker
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstr. 3, OT Gatersleben, 06466, Seeland, Germany.
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16
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Bucciarelli B, Xu Z, Ao S, Cao Y, Monteros MJ, Topp CN, Samac DA. Phenotyping seedlings for selection of root system architecture in alfalfa (Medicago sativa L.). PLANT METHODS 2021; 17:125. [PMID: 34876178 PMCID: PMC8650460 DOI: 10.1186/s13007-021-00825-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 11/26/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND The root system architecture (RSA) of alfalfa (Medicago sativa L.) affects biomass production by influencing water and nutrient uptake, including nitrogen fixation. Further, roots are important for storing carbohydrates that are needed for regrowth in spring and after each harvest. Previous selection for a greater number of branched and fibrous roots significantly increased alfalfa biomass yield. However, phenotyping root systems of mature alfalfa plant is labor-intensive, time-consuming, and subject to environmental variability and human error. High-throughput and detailed phenotyping methods are needed to accelerate the development of alfalfa germplasm with distinct RSAs adapted to specific environmental conditions and for enhancing productivity in elite germplasm. In this study methods were developed for phenotyping 14-day-old alfalfa seedlings to identify measurable root traits that are highly heritable and can differentiate plants with either a branched or a tap rooted phenotype. Plants were grown in a soil-free mixture under controlled conditions, then the root systems were imaged with a flatbed scanner and measured using WinRhizo software. RESULTS The branched root plants had a significantly greater number of tertiary roots and significantly longer tertiary roots relative to the tap rooted plants. Additionally, the branch rooted population had significantly more secondary roots > 2.5 cm relative to the tap rooted population. These two parameters distinguishing phenotypes were confirmed using two machine learning algorithms, Random Forest and Gradient Boosting Machines. Plants selected as seedlings for the branch rooted or tap rooted phenotypes were used in crossing blocks that resulted in a genetic gain of 10%, consistent with the previous selection strategy that utilized manual root scoring to phenotype 22-week-old-plants. Heritability analysis of various root architecture parameters from selected seedlings showed tertiary root length and number are highly heritable with values of 0.74 and 0.79, respectively. CONCLUSIONS The results show that seedling root phenotyping is a reliable tool that can be used for alfalfa germplasm selection and breeding. Phenotypic selection of RSA in seedlings reduced time for selection by 20 weeks, significantly accelerating the breeding cycle.
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Affiliation(s)
- Bruna Bucciarelli
- Department of Agronomy and Plant Genetics, University of Minnesota, 1991 Upper Buford Circle, St. Paul, MN, 55108, USA
| | - Zhanyou Xu
- USDA-ARS, Plant Science Research Unit, 1991 Upper Buford Circle, St. Paul, MN, 55108, USA
| | - Samadangla Ao
- Department of Agronomy and Plant Genetics, University of Minnesota, 1991 Upper Buford Circle, St. Paul, MN, 55108, USA
- Kohima Science College, Jotsoma, 797002, Nagaland, India
| | - Yuanyuan Cao
- Department of Plant Pathology, University of Minnesota, 1991 Upper Buford Circle, 495 Borlaug Hall, St. Paul, MN, 55108, USA
- School of Life Sciences, Anhui Agricultural University, Hefei, 230036, Anhui, China
| | - Maria J Monteros
- Noble Research Institute, 2510 Sam Noble Parkway, Ardmore, OK, 73401, USA
- Bayer Crop Science, Chesterfield, MO, 63017, USA
| | - Christopher N Topp
- Donald Danforth Plant Science Center, 975 N Warson Road, Olivette, MO, 63132, USA
| | - Deborah A Samac
- USDA-ARS, Plant Science Research Unit, 1991 Upper Buford Circle, St. Paul, MN, 55108, USA.
- Department of Plant Pathology, University of Minnesota, 1991 Upper Buford Circle, 495 Borlaug Hall, St. Paul, MN, 55108, USA.
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17
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Aguilar JJ, Moore M, Johnson L, Greenhut RF, Rogers E, Walker D, O’Neil F, Edwards JL, Thystrup J, Farrow S, Windle JB, Benfey PN. Capturing in-field root system dynamics with RootTracker. PLANT PHYSIOLOGY 2021; 187:1117-1130. [PMID: 34618063 PMCID: PMC8566282 DOI: 10.1093/plphys/kiab352] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 06/30/2021] [Indexed: 06/13/2023]
Abstract
Optimizing root system architecture offers a promising approach to developing stress tolerant cultivars in the face of climate change, as root systems are critical for water and nutrient uptake as well as mechanical stability. However, breeding for optimal root system architecture has been hindered by the difficulty in measuring root growth in the field. Here, we describe the RootTracker, a technology that employs impedance touch sensors to monitor in-field root growth over time. Configured in a cylindrical, window shutter-like fashion around a planted seed, 264 electrodes are individually charged multiple times over the course of an experiment. Signature changes in the measured capacitance and resistance readings indicate when a root has touched or grown close to an electrode. Using the RootTracker, we have measured root system dynamics of commercial maize (Zea mays) hybrids growing in both typical Midwest field conditions and under different irrigation regimes. We observed rapid responses of root growth to water deficits and found evidence for a "priming response" in which an early water deficit causes more and deeper roots to grow at later time periods. Genotypic variation among hybrid maize lines in their root growth in response to drought indicated a potential to breed for root systems adapted for different environments. Thus, the RootTracker is able to capture changes in root growth over time in response to environmental perturbations.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - Philip N Benfey
- Hi Fidelity Genetics, Durham, NC USA
- Duke University, Department of Biology, Durham, NC, USA and Howard Hughes Medical Institute (HHMI)
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18
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Proline-Mediated Drought Tolerance in the Barley ( Hordeum vulgare L.) Isogenic Line Is Associated with Lateral Root Growth at the Early Seedling Stage. PLANTS 2021; 10:plants10102177. [PMID: 34685984 PMCID: PMC8538694 DOI: 10.3390/plants10102177] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 10/11/2021] [Accepted: 10/11/2021] [Indexed: 12/02/2022]
Abstract
A vigorous root system in barley promotes water uptake from the soil under water-limited conditions. We investigated three spring barley genotypes with varying water stress responses using rhizoboxes at the seedling stage. The genotypes comprised two elite German cultivars, Barke and Scarlett, and a near-isogenic line, NIL 143. The isogenic line harbors the wild allele pyrroline-5-carboxylate synthase1-P5cs1. Root growth in rhizoboxes under reduced water availability conditions caused a significant reduction in total root length, rooting depth, root maximum width, and root length density. On average, root growth was reduced by more than 20% due to water stress. Differences in organ proline concentrations were observed for all genotypes, with shoots grown under water stress exhibiting at least a 30% higher concentration than the roots. Drought induced higher leaf and root proline concentrations in NIL 143 compared with any of the other genotypes. Under reduced water availability conditions, NIL 143 showed less severe symptoms of drought, higher lateral root length, rooting depth, maximum root width, root length density, and convex hull area compared with Barke and Scarlett. Within the same comparison, under water stress, NIL 143 had a higher proportion of lateral roots (+30%), which were also placed at deeper substrate horizons. NIL 143 had a less negative plant water potential and higher relative leaf water content and stomatal conductance compared with the other genotypes under water stress. Under these conditions, this genotype also maintained an enhanced net photosynthetic rate and exhibited considerable fine root growth (diameter class 0.05–0.35 mm). These results show that water stress induces increased shoot and root proline accumulation in the NIL 143 barley genotype at the seedling stage and that this effect is associated with increased lateral root growth.
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19
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Ober ES, Alahmad S, Cockram J, Forestan C, Hickey LT, Kant J, Maccaferri M, Marr E, Milner M, Pinto F, Rambla C, Reynolds M, Salvi S, Sciara G, Snowdon RJ, Thomelin P, Tuberosa R, Uauy C, Voss-Fels KP, Wallington E, Watt M. Wheat root systems as a breeding target for climate resilience. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:1645-1662. [PMID: 33900415 PMCID: PMC8206059 DOI: 10.1007/s00122-021-03819-w] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 03/18/2021] [Indexed: 05/08/2023]
Abstract
In the coming decades, larger genetic gains in yield will be necessary to meet projected demand, and this must be achieved despite the destabilizing impacts of climate change on crop production. The root systems of crops capture the water and nutrients needed to support crop growth, and improved root systems tailored to the challenges of specific agricultural environments could improve climate resiliency. Each component of root initiation, growth and development is controlled genetically and responds to the environment, which translates to a complex quantitative system to navigate for the breeder, but also a world of opportunity given the right tools. In this review, we argue that it is important to know more about the 'hidden half' of crop plants and hypothesize that crop improvement could be further enhanced using approaches that directly target selection for root system architecture. To explore these issues, we focus predominantly on bread wheat (Triticum aestivum L.), a staple crop that plays a major role in underpinning global food security. We review the tools available for root phenotyping under controlled and field conditions and the use of these platforms alongside modern genetics and genomics resources to dissect the genetic architecture controlling the wheat root system. To contextualize these advances for applied wheat breeding, we explore questions surrounding which root system architectures should be selected for, which agricultural environments and genetic trait configurations of breeding populations are these best suited to, and how might direct selection for these root ideotypes be implemented in practice.
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Affiliation(s)
- Eric S Ober
- NIAB, 93 Lawrence Weaver Road, Cambridge, CB3 0LE, UK.
| | - Samir Alahmad
- Centre for Crop Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - James Cockram
- NIAB, 93 Lawrence Weaver Road, Cambridge, CB3 0LE, UK
| | - Cristian Forestan
- Department of Agricultural and Food Sciences, University of Bologna, Viale G Fanin 44, 40127, Bologna, Italy
| | - Lee T Hickey
- Centre for Crop Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Josefine Kant
- Forschungszentrum Jülich, IBG-2, Wilhelm-Johnen-Straße, 52428, Jülich, Germany
| | - Marco Maccaferri
- Department of Agricultural and Food Sciences, University of Bologna, Viale G Fanin 44, 40127, Bologna, Italy
| | - Emily Marr
- NIAB, 93 Lawrence Weaver Road, Cambridge, CB3 0LE, UK
| | | | - Francisco Pinto
- Global Wheat Program, International Maize and Wheat Improvement Center (CIMMYT), 56237, Texcoco, Estado de Mexico, Mexico
| | - Charlotte Rambla
- Centre for Crop Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Matthew Reynolds
- Global Wheat Program, International Maize and Wheat Improvement Center (CIMMYT), 56237, Texcoco, Estado de Mexico, Mexico
| | - Silvio Salvi
- Department of Agricultural and Food Sciences, University of Bologna, Viale G Fanin 44, 40127, Bologna, Italy
| | - Giuseppe Sciara
- Department of Agricultural and Food Sciences, University of Bologna, Viale G Fanin 44, 40127, Bologna, Italy
| | - Rod J Snowdon
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Heinrich-Buff-Ring 26-32, 35392, Giessen, Germany
| | | | - Roberto Tuberosa
- Department of Agricultural and Food Sciences, University of Bologna, Viale G Fanin 44, 40127, Bologna, Italy
| | - Cristobal Uauy
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, NR4 7UH, UK
| | - Kai P Voss-Fels
- Centre for Animal Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD, 4072, Australia
| | | | - Michelle Watt
- School of BioSciences, University of Melbourne, Parkville, VIC, 3010, Australia
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20
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Kumar J, Sen Gupta D, Djalovic I, Kumar S, Siddique KHM. Root-omics for drought tolerance in cool-season grain legumes. PHYSIOLOGIA PLANTARUM 2021; 172:629-644. [PMID: 33314181 DOI: 10.1111/ppl.13313] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Accepted: 12/02/2020] [Indexed: 06/12/2023]
Abstract
Root traits can be exploited to increase the physiological efficiency of crop water use under drought. Root length, root hairs, root branching, root diameter, and root proliferation rate are genetically defined traits that can help to improve the water productivity potential of crops. Recently, high-throughput phenotyping techniques/platforms have been used to screen the germplasm of major cool-season grain legumes for root traits and their impact on different physiological processes, including nutrient uptake and yield potential. Advances in omics approaches have led to the dissection of genomic, proteomic, and metabolomic structures of these traits. This knowledge facilitates breeders to improve the water productivity and nutrient uptake of cultivars under limited soil moisture conditions in major cool-season grain legumes that usually face terminal drought. This review discusses the advances in root traits and their potential for developing drought-tolerant cultivars in cool-season grain legumes.
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Affiliation(s)
- Jitendra Kumar
- Division of Crop Improvement, ICAR-Indian Institute of Pulses Research, Kanpur, India
| | - Debjyoti Sen Gupta
- Division of Crop Improvement, ICAR-Indian Institute of Pulses Research, Kanpur, India
| | - Ivica Djalovic
- Maize Department, Institute of Field and Vegetable Crops, Novi Sad, Serbia
| | - Shiv Kumar
- Biodiversity and Crop Improvement Program, International Centre for Agricultural Research in the Dry Areas (ICARDA), Rabat, Morocco
| | - Kadambot H M Siddique
- The UWA Institute of Agriculture and School of Agriculture and Environment, The University of Western Australia, Perth, Western Australia, Australia
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21
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Zhang X, Man Y, Zhuang X, Shen J, Zhang Y, Cui Y, Yu M, Xing J, Wang G, Lian N, Hu Z, Ma L, Shen W, Yang S, Xu H, Bian J, Jing Y, Li X, Li R, Mao T, Jiao Y, Sodmergen, Ren H, Lin J. Plant multiscale networks: charting plant connectivity by multi-level analysis and imaging techniques. SCIENCE CHINA-LIFE SCIENCES 2021; 64:1392-1422. [PMID: 33974222 DOI: 10.1007/s11427-020-1910-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 03/04/2021] [Indexed: 12/21/2022]
Abstract
In multicellular and even single-celled organisms, individual components are interconnected at multiscale levels to produce enormously complex biological networks that help these systems maintain homeostasis for development and environmental adaptation. Systems biology studies initially adopted network analysis to explore how relationships between individual components give rise to complex biological processes. Network analysis has been applied to dissect the complex connectivity of mammalian brains across different scales in time and space in The Human Brain Project. In plant science, network analysis has similarly been applied to study the connectivity of plant components at the molecular, subcellular, cellular, organic, and organism levels. Analysis of these multiscale networks contributes to our understanding of how genotype determines phenotype. In this review, we summarized the theoretical framework of plant multiscale networks and introduced studies investigating plant networks by various experimental and computational modalities. We next discussed the currently available analytic methodologies and multi-level imaging techniques used to map multiscale networks in plants. Finally, we highlighted some of the technical challenges and key questions remaining to be addressed in this emerging field.
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Affiliation(s)
- Xi Zhang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, 100083, China.,College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Yi Man
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, 100083, China.,College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Xiaohong Zhuang
- School of Life Sciences, Centre for Cell & Developmental Biology and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, 999077, China
| | - Jinbo Shen
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, 311300, China
| | - Yi Zhang
- Key Laboratory of Cell Proliferation and Regulation Biology, Ministry of Education, College of Life Science, Beijing Normal University, Beijing, 100875, China
| | - Yaning Cui
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, 100083, China.,College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Meng Yu
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, 100083, China.,College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Jingjing Xing
- Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, Kaifeng, 457004, China
| | - Guangchao Wang
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Na Lian
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, 100083, China.,College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Zijian Hu
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Lingyu Ma
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Weiwei Shen
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Shunyao Yang
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Huimin Xu
- College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Jiahui Bian
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Yanping Jing
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Xiaojuan Li
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, 100083, China.,College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Ruili Li
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, 100083, China.,College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Tonglin Mao
- State Key Laboratory of Plant Physiology and Biochemistry, Department of Plant Sciences, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Yuling Jiao
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, and National Center for Plant Gene Research, Beijing, 100101, China
| | - Sodmergen
- Key Laboratory of Ministry of Education for Cell Proliferation and Differentiation, College of Life Sciences, Peking University, Beijing, 100871, China
| | - Haiyun Ren
- Key Laboratory of Cell Proliferation and Regulation Biology, Ministry of Education, College of Life Science, Beijing Normal University, Beijing, 100875, China
| | - Jinxing Lin
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, 100083, China. .,College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China.
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22
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Burridge JD, Black CK, Nord EA, Postma JA, Sidhu JS, York LM, Lynch JP. An Analysis of Soil Coring Strategies to Estimate Root Depth in Maize ( Zea mays) and Common Bean ( Phaseolus vulgaris). PLANT PHENOMICS (WASHINGTON, D.C.) 2020; 2020:3252703. [PMID: 33313549 PMCID: PMC7706327 DOI: 10.34133/2020/3252703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 09/05/2020] [Indexed: 06/12/2023]
Abstract
A soil coring protocol was developed to cooptimize the estimation of root length distribution (RLD) by depth and detection of functionally important variation in root system architecture (RSA) of maize and bean. The functional-structural model OpenSimRoot was used to perform in silico soil coring at six locations on three different maize and bean RSA phenotypes. Results were compared to two seasons of field soil coring and one trench. Two one-sided T-test (TOST) analysis of in silico data suggests a between-row location 5 cm from plant base (location 3), best estimates whole-plot RLD/D of deep, intermediate, and shallow RSA phenotypes, for both maize and bean. Quadratic discriminant analysis indicates location 3 has ~70% categorization accuracy for bean, while an in-row location next to the plant base (location 6) has ~85% categorization accuracy in maize. Analysis of field data suggests the more representative sampling locations vary by year and species. In silico and field studies suggest location 3 is most robust, although variation is significant among seasons, among replications within a field season, and among field soil coring, trench, and simulations. We propose that the characterization of the RLD profile as a dynamic rhizo canopy effectively describes how the RLD profile arises from interactions among an individual plant, its neighbors, and the pedosphere.
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Affiliation(s)
- James D. Burridge
- The Pennsylvania State University, Department of Plant Science, Tyson Building, University Park, PA 16802, USA
| | - Christopher K. Black
- The Pennsylvania State University, Department of Plant Science, Tyson Building, University Park, PA 16802, USA
| | - Eric A. Nord
- The Pennsylvania State University, Department of Plant Science, Tyson Building, University Park, PA 16802, USA
- Department of Biology, Greenville University, 315 E. College Ave, Greenville, IL 62246, USA
| | - Johannes A. Postma
- Forschungszentrum Jülich GmbH, Institute of Bio-and Geosciences-Plant Sciences (IBG-2), 52425 Jülich, Germany
| | - Jagdeep S. Sidhu
- The Pennsylvania State University, Department of Plant Science, Tyson Building, University Park, PA 16802, USA
| | - Larry M. York
- The Pennsylvania State University, Department of Plant Science, Tyson Building, University Park, PA 16802, USA
- Noble Research Institute, LLC, 2510 Sam Noble Parkway, Ardmore, OK 73401, USA
| | - Jonathan P. Lynch
- The Pennsylvania State University, Department of Plant Science, Tyson Building, University Park, PA 16802, USA
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23
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Li Z, Guo R, Li M, Chen Y, Li G. A review of computer vision technologies for plant phenotyping. COMPUTERS AND ELECTRONICS IN AGRICULTURE 2020; 176:105672. [PMID: 0 DOI: 10.1016/j.compag.2020.105672] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
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24
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Korwin Krukowski P, Ellenberger J, Röhlen-Schmittgen S, Schubert A, Cardinale F. Phenotyping in Arabidopsis and Crops-Are We Addressing the Same Traits? A Case Study in Tomato. Genes (Basel) 2020; 11:E1011. [PMID: 32867311 PMCID: PMC7564427 DOI: 10.3390/genes11091011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 08/21/2020] [Accepted: 08/24/2020] [Indexed: 11/18/2022] Open
Abstract
The convenient model Arabidopsis thaliana has allowed tremendous advances in plant genetics and physiology, in spite of only being a weed. It has also unveiled the main molecular networks governing, among others, abiotic stress responses. Through the use of the latest genomic tools, Arabidopsis research is nowadays being translated to agronomically interesting crop models such as tomato, but at a lagging pace. Knowledge transfer has been hindered by invariable differences in plant architecture and behaviour, as well as the divergent direct objectives of research in Arabidopsis versus crops compromise transferability. In this sense, phenotype translation is still a very complex matter. Here, we point out the challenges of "translational phenotyping" in the case study of drought stress phenotyping in Arabidopsis and tomato. After briefly defining and describing drought stress and survival strategies, we compare drought stress protocols and phenotyping techniques most commonly used in the two species, and discuss their potential to gain insights, which are truly transferable between species. This review is intended to be a starting point for discussion about translational phenotyping approaches among plant scientists, and provides a useful compendium of methods and techniques used in modern phenotyping for this specific plant pair as a case study.
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Affiliation(s)
- Paolo Korwin Krukowski
- Plant Stress Lab, Department of Agriculture, Forestry and Food Sciences DISAFA-Turin University, 10095 Grugliasco, Italy; (A.S.); (F.C.)
| | - Jan Ellenberger
- INRES Horticultural Sciences, University of Bonn, 53121 Bonn, Germany;
| | | | - Andrea Schubert
- Plant Stress Lab, Department of Agriculture, Forestry and Food Sciences DISAFA-Turin University, 10095 Grugliasco, Italy; (A.S.); (F.C.)
| | - Francesca Cardinale
- Plant Stress Lab, Department of Agriculture, Forestry and Food Sciences DISAFA-Turin University, 10095 Grugliasco, Italy; (A.S.); (F.C.)
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25
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Mochida K, Nishii R, Hirayama T. Decoding Plant-Environment Interactions That Influence Crop Agronomic Traits. PLANT & CELL PHYSIOLOGY 2020; 61:1408-1418. [PMID: 32392328 PMCID: PMC7434589 DOI: 10.1093/pcp/pcaa064] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 04/26/2020] [Indexed: 05/16/2023]
Abstract
To ensure food security in the face of increasing global demand due to population growth and progressive urbanization, it will be crucial to integrate emerging technologies in multiple disciplines to accelerate overall throughput of gene discovery and crop breeding. Plant agronomic traits often appear during the plants' later growth stages due to the cumulative effects of their lifetime interactions with the environment. Therefore, decoding plant-environment interactions by elucidating plants' temporal physiological responses to environmental changes throughout their lifespans will facilitate the identification of genetic and environmental factors, timing and pathways that influence complex end-point agronomic traits, such as yield. Here, we discuss the expected role of the life-course approach to monitoring plant and crop health status in improving crop productivity by enhancing the understanding of plant-environment interactions. We review recent advances in analytical technologies for monitoring health status in plants based on multi-omics analyses and strategies for integrating heterogeneous datasets from multiple omics areas to identify informative factors associated with traits of interest. In addition, we showcase emerging phenomics techniques that enable the noninvasive and continuous monitoring of plant growth by various means, including three-dimensional phenotyping, plant root phenotyping, implantable/injectable sensors and affordable phenotyping devices. Finally, we present an integrated review of analytical technologies and applications for monitoring plant growth, developed across disciplines, such as plant science, data science and sensors and Internet-of-things technologies, to improve plant productivity.
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Affiliation(s)
- Keiichi Mochida
- RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama, Japan
- Kihara Institute for Biological Research, Yokohama City University, Totsuka-ku, Yokohama, Japan
- Graduate School of Nanobioscience, Yokohama City University, Kanazawa-ku, Yokohama, Japan
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Japan
- Corresponding author: E-mail, ; Fax, +81-45-503-9609
| | - Ryuei Nishii
- School of Information and Data Sciences, Nagasaki University, Nagasaki, Japan
| | - Takashi Hirayama
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Japan
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26
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Watt M, Fiorani F, Usadel B, Rascher U, Muller O, Schurr U. Phenotyping: New Windows into the Plant for Breeders. ANNUAL REVIEW OF PLANT BIOLOGY 2020; 71:689-712. [PMID: 32097567 DOI: 10.1146/annurev-arplant-042916-041124] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Plant phenotyping enables noninvasive quantification of plant structure and function and interactions with environments. High-capacity phenotyping reaches hitherto inaccessible phenotypic characteristics. Diverse, challenging, and valuable applications of phenotyping have originated among scientists, prebreeders, and breeders as they study the phenotypic diversity of genetic resources and apply increasingly complex traits to crop improvement. Noninvasive technologies are used to analyze experimental and breeding populations. We cover the most recent research in controlled-environment and field phenotyping for seed, shoot, and root traits. Select field phenotyping technologies have become state of the art and show promise for speeding up the breeding process in early generations. We highlight the technologies behind the rapid advances in proximal and remote sensing of plants in fields. We conclude by discussing the new disciplines working with the phenotyping community: data science, to address the challenge of generating FAIR (findable, accessible, interoperable, and reusable) data, and robotics, to apply phenotyping directly on farms.
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Affiliation(s)
- Michelle Watt
- IBG-2: Plant Sciences, Institute of Bio- and Geosciences, Forschungszentrum Jülich, 52425 Jülich, Germany; ,
| | - Fabio Fiorani
- IBG-2: Plant Sciences, Institute of Bio- and Geosciences, Forschungszentrum Jülich, 52425 Jülich, Germany; ,
| | - Björn Usadel
- IBG-2: Plant Sciences, Institute of Bio- and Geosciences, Forschungszentrum Jülich, 52425 Jülich, Germany; ,
- Institute for Botany and Molecular Genetics, BioSC, RWTH Aachen University, 52074 Aachen, Germany
| | - Uwe Rascher
- IBG-2: Plant Sciences, Institute of Bio- and Geosciences, Forschungszentrum Jülich, 52425 Jülich, Germany; ,
| | - Onno Muller
- IBG-2: Plant Sciences, Institute of Bio- and Geosciences, Forschungszentrum Jülich, 52425 Jülich, Germany; ,
| | - Ulrich Schurr
- IBG-2: Plant Sciences, Institute of Bio- and Geosciences, Forschungszentrum Jülich, 52425 Jülich, Germany; ,
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27
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Han E, Dresbøll DB, Thorup-Kristensen K. Core-labelling technique (CLT): a novel combination of the ingrowth-core method and tracer technique for deep root study. PLANT METHODS 2020; 16:84. [PMID: 32528551 PMCID: PMC7285440 DOI: 10.1186/s13007-020-00622-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Accepted: 05/26/2020] [Indexed: 05/11/2023]
Abstract
BACKGROUND Ingrowth-core method is a useful tool to determine fine root growth of standing crops by inserting root-free soil in mesh-bags for certain period of time. However, the root density observed by the method does not directly explain the nutrient uptake potential of crop plants as it varies over soil depth and incubation time. We have inserted an access-tube up to 4.2 m of soil depth with openings directly under crop plants, through which ingrowth-cores containing labelled soil with nutrient tracers were installed, called core-labelling technique (CLT). The main advantage of CLT would be its capacity to determine both root density and root activity from the same crop plants in deep soil layers. We tested the validity of the new method using a model crop species, alfalfa (Medicago sativa) against three depth-levels (1.0, 2.5 and 4.2 m), three sampling spots with varying distance (0-0.36, 0.36-0.72 and > 5 m from core-labelled spot), two sampling times (week 4 and 8), and two plant parts (young and old leaves) under two field experiments (spring and autumn). RESULTS Using CLT, we were able to observe both deep root growth and root activity up to 4.2 m of soil depth. Tracer concentrations revealed that there was no sign of tracer-leakage to adjacent areas which is considered to be advantageous over the generic tracer-injection. Root activity increased with longer incubation period and tracer concentrations were higher in younger leaves only for anionic tracers. CONCLUSIONS Our results indicate that CLT can lead to a comprehensive deep root study aiming at measuring both deep root growth and root activity from the same plants. Once produced and installed, the access-tubes and ingrowth-cores can be used for a long-term period, which reduces the workload and cost for the research. Therefore, CLT has a wide range of potential applications to the research involving roots in deep soil layers, which requires further confirmation by future experiments.
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Affiliation(s)
- Eusun Han
- Department of Plant and Environmental Sciences, University of Copenhagen, Højbakkegård Allé 13, 2630 Taastrup, Denmark
| | - Dorte Bodin Dresbøll
- Department of Plant and Environmental Sciences, University of Copenhagen, Højbakkegård Allé 13, 2630 Taastrup, Denmark
| | - Kristian Thorup-Kristensen
- Department of Plant and Environmental Sciences, University of Copenhagen, Højbakkegård Allé 13, 2630 Taastrup, Denmark
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