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Lemiere L, Jaeger M, Gosme M, Subsol G. Combinatorial Maps, a New Framework to Model Agroforestry Systems. PLANT PHENOMICS (WASHINGTON, D.C.) 2023; 5:0120. [PMID: 38107769 PMCID: PMC10723776 DOI: 10.34133/plantphenomics.0120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 11/04/2023] [Indexed: 12/19/2023]
Abstract
Agroforestry systems are complex due to the diverse interactions between their elements, and they develop over several decades. Existing numerical models focus either on the structure or on the functions of agroforestry systems. However, both of these aspects are necessary, as function influences structure and vice versa. Here, we present a representation of agroforestry systems based on combinatorial maps (which are a type of multidimensional graphs), that allows conceptualizing the structure-function relationship at the agroecosystem scale. We show that such a model can represent the structure of agroforestry systems at multiple scales and its evolution through time. We propose an implementation of this framework, coded in Python, which is available on GitHub. In the future, this framework could be coupled with knowledge based or with biophysical simulation models to predict the production of ecosystem services. The code can also be integrated into visualization tools. Combinatorial maps seem promising to provide a unifying and generic description of agroforestry systems, including their structure, functions, and dynamics, with the possibility to translate to and from other representations.
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Affiliation(s)
- Laëtitia Lemiere
- ABSys, Univ Montpellier, CIHEAM-IAMM, CIRAD, INRAE, Institut Agro, Montpellier, France
- CIRAD, UMR AMAP, F-34398 Montpellier, France
- AMAP, Univ Montpellier, CIRAD, CNRS, INRAE, IRD, Montpellier, France
| | - Marc Jaeger
- CIRAD, UMR AMAP, F-34398 Montpellier, France
- AMAP, Univ Montpellier, CIRAD, CNRS, INRAE, IRD, Montpellier, France
| | - Marie Gosme
- ABSys, Univ Montpellier, CIHEAM-IAMM, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Gérard Subsol
- Research-Team ICAR, LIRMM, Univ Montpellier, CNRS, Montpellier, France
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Blanc E, Enjalbert J, Flutre T, Barbillon P. Efficient Bayesian automatic calibration of a functional-structural wheat model using an adaptive design and a metamodelling approach. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:6722-6734. [PMID: 37632355 DOI: 10.1093/jxb/erad339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 08/25/2023] [Indexed: 08/28/2023]
Abstract
Functional-structural plant models are increasingly being used by plant scientists to address a wide variety of questions. However, the calibration of these complex models is often challenging, mainly because of their high computational cost, and, as a result, error propagation is usually ignored. Here we applied an automatic method to the calibration of WALTer: a functional-structural wheat model that simulates the plasticity of tillering in response to competition for light. We used a Bayesian calibration method to jointly estimate the values of five parameters and quantify their uncertainty by fitting the model outputs to tillering dynamics data. We made recourse to Gaussian process metamodels in order to alleviate the computational cost of WALTer. These metamodels are built from an adaptive design that consists of successive runs of WALTer chosen by an efficient global optimization algorithm specifically adapted to this particular calibration task. The method presented here performed well on both synthetic and experimental data. It is an efficient approach for the calibration of WALTer and should be of interest for the calibration of other functional-structural plant models.
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Affiliation(s)
- Emmanuelle Blanc
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE-Le Moulon, 91190, Gif-sur-Yvette, France
| | - Jérôme Enjalbert
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE-Le Moulon, 91190, Gif-sur-Yvette, France
| | - Timothée Flutre
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE-Le Moulon, 91190, Gif-sur-Yvette, France
| | - Pierre Barbillon
- Université Paris-Saclay, AgroParisTech, INRAE, UMR MIA-Paris, 75005, Paris, France
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3
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Levionnois S, Pradal C, Fournier C, Sanner J, Robert C. Modeling the Impact of Proportion, Sowing Date, and Architectural Traits of a Companion Crop on Foliar Fungal Pathogens of Wheat in Crop Mixtures. PHYTOPATHOLOGY 2023; 113:1876-1889. [PMID: 37097642 DOI: 10.1094/phyto-06-22-0197-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Diversification of cropping systems is a lever for the management of epidemics. However, most research to date has focused on cultivar mixtures, especially for cereals, even though crop mixtures can also improve disease management. To investigate the benefits of crop mixtures, we studied the effect of different crop mixture characteristics (i.e., companion proportion, sowing date, and traits) on the protective effect of the mixture. We developed a SEIR (Susceptible, Exposed, Infectious, Removed) model of two damaging wheat diseases (Zymoseptoria tritici and Puccinia triticina), which were applied to different canopy components, ascribable to wheat and a theoretical companion crop. We used the model to study the sensitivity of disease intensity to the following parameters: wheat-versus-companion proportion, companion sowing date and growth, and architectural traits. For both pathogens, the companion proportion had the strongest effect, with 25% of companion reducing disease severity by 50%. However, changing companion growth and architectural traits also significantly improved the protective effect. The effect of companion characteristics was consistent across different weather conditions. After decomposing the dilution and barrier effects, the model suggested that the barrier effect is maximized for an intermediate proportion of companion crop. Our study thus supports crop mixtures as a promising strategy to improve disease management. Future studies should identify real species and determine the combination of host and companion traits to maximize the protective effect of the mixture. [Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Sébastien Levionnois
- UMR EcoSys, INRAE, AgroParisTech, Campus Agro Paris-Saclay, 91120 Palaiseau, France
- UMR AGAP Institut, Univ. Montpellier, CIRAD, INRAE, Institut Agro, 34398 Montpellier, France
| | - Christophe Pradal
- CIRAD, UMR AGAP Institut, 34398 Montpellier, France
- INRIA & LIRMM, Univ. Montpellier, CNRS, 34090 Montpellier, France
| | - Christian Fournier
- UMR LEPSE, Université de Montpellier, INRAE, Montpellier SupAgro, 34000 Montpellier, France
| | - Jonathan Sanner
- UMR EcoSys, INRAE, AgroParisTech, Campus Agro Paris-Saclay, 91120 Palaiseau, France
| | - Corinne Robert
- UMR EcoSys, INRAE, AgroParisTech, Campus Agro Paris-Saclay, 91120 Palaiseau, France
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Zhang P, Huang J, Ma Y, Wang X, Kang M, Song Y. Crop/Plant Modeling Supports Plant Breeding: II. Guidance of Functional Plant Phenotyping for Trait Discovery. PLANT PHENOMICS (WASHINGTON, D.C.) 2023; 5:0091. [PMID: 37780969 PMCID: PMC10538623 DOI: 10.34133/plantphenomics.0091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 08/26/2023] [Indexed: 10/03/2023]
Abstract
Observable morphological traits are widely employed in plant phenotyping for breeding use, which are often the external phenotypes driven by a chain of functional actions in plants. Identifying and phenotyping inherently functional traits for crop improvement toward high yields or adaptation to harsh environments remains a major challenge. Prediction of whole-plant performance in functional-structural plant models (FSPMs) is driven by plant growth algorithms based on organ scale wrapped up with micro-environments. In particular, the models are flexible for scaling down or up through specific functions at the organ nexus, allowing the prediction of crop system behaviors from the genome to the field. As such, by virtue of FSPMs, model parameters that determine organogenesis, development, biomass production, allocation, and morphogenesis from a molecular to the whole plant level can be profiled systematically and made readily available for phenotyping. FSPMs can provide rich functional traits representing biological regulatory mechanisms at various scales in a dynamic system, e.g., Rubisco carboxylation rate, mesophyll conductance, specific leaf nitrogen, radiation use efficiency, and source-sink ratio apart from morphological traits. High-throughput phenotyping such traits is also discussed, which provides an unprecedented opportunity to evolve FSPMs. This will accelerate the co-evolution of FSPMs and plant phenomics, and thus improving breeding efficiency. To expand the great promise of FSPMs in crop science, FSPMs still need more effort in multiscale, mechanistic, reproductive organ, and root system modeling. In summary, this study demonstrates that FSPMs are invaluable tools in guiding functional trait phenotyping at various scales and can thus provide abundant functional targets for phenotyping toward crop improvement.
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Affiliation(s)
- Pengpeng Zhang
- School of Agronomy, Anhui Agricultural University, Hefei, Anhui Province 230036, China
| | - Jingyao Huang
- School of Agronomy, Anhui Agricultural University, Hefei, Anhui Province 230036, China
| | - Yuntao Ma
- College of Land Science and Technology, China Agricultural University, Beijing 100094, China
| | - Xiujuan Wang
- The State Key Laboratory for Management and Control of Complex Systems, Institute of Automation, Chinese Academy of Sciences, Beijing 100190, China
| | - Mengzhen Kang
- The State Key Laboratory for Management and Control of Complex Systems, Institute of Automation, Chinese Academy of Sciences, Beijing 100190, China
| | - Youhong Song
- School of Agronomy, Anhui Agricultural University, Hefei, Anhui Province 230036, China
- Centre for Crop Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD 4350, Australia
- Centre for Crop Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD 4350, Australia
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Pelech EA, Evers JB, Pederson TL, Drag DW, Fu P, Bernacchi CJ. Leaf, plant, to canopy: A mechanistic study on aboveground plasticity and plant density within a maize-soybean intercrop system for the Midwest, USA. PLANT, CELL & ENVIRONMENT 2023; 46:405-421. [PMID: 36358006 PMCID: PMC10100491 DOI: 10.1111/pce.14487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 11/04/2022] [Accepted: 11/06/2022] [Indexed: 06/16/2023]
Abstract
Plants have evolved to adapt to their neighbours through plastic trait responses. In intercrop systems, plant growth occurs at different spatial and temporal dimensions, creating a competitive light environment where aboveground plasticity may support complementarity in light-use efficiency, realizing yield gains per unit area compared with monoculture systems. Physiological and architectural plasticity including the consequences for light-use efficiency and yield in a maize-soybean solar corridor intercrop system was compared, empirically, with the standard monoculture systems of the Midwest, USA. The impact of reducing maize plant density on yield was investigated in the following year. Intercropped maize favoured physiological plasticity over architectural plasticity, which maintained harvest index (HI) but reduced light interception efficiency (ɛi ) and conversion efficiency (ɛc ). Intercropped soybean invested in both plasticity responses, which maintained ɛi , but HI and ɛc decreased. Reducing maize plant density within the solar corridor rows did not improve yields under monoculture and intercrop systems. Overall, the intercrop decreased land-use efficiency by 9%-19% and uncoordinated investment in aboveground plasticity by each crop under high maize plant density does not support complementarity in light-use efficiency. Nonetheless, the mechanistic understanding gained from this study may improve crop cultivars and intercrop designs for the Midwest to increase yield.
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Affiliation(s)
- Elena A. Pelech
- The Carl R. Woese Institute for Genomic BiologyUniversity of Illinois at Urbana‐ChampaignUrbanaIllinois
| | - Jochem B. Evers
- Department of Plant Sciences, Centre for Crop Systems AnalysisWageningen UniversityWageningenThe Netherlands
| | - Taylor L. Pederson
- The Carl R. Woese Institute for Genomic BiologyUniversity of Illinois at Urbana‐ChampaignUrbanaIllinois
| | - David W. Drag
- The Carl R. Woese Institute for Genomic BiologyUniversity of Illinois at Urbana‐ChampaignUrbanaIllinois
| | - Peng Fu
- Center for Environment, Energy, and EconomyHarrisburg University of Science and TechnologyHarrisburgPennsylvaniaUSA
| | - Carl J. Bernacchi
- The Carl R. Woese Institute for Genomic BiologyUniversity of Illinois at Urbana‐ChampaignUrbanaIllinois
- USDA‐ARS Global Change and Photosynthesis Research UnitUrbanaIllinoisUSA
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Weih M, Adam E, Vico G, Rubiales D. Application of Crop Growth Models to Assist Breeding for Intercropping: Opportunities and Challenges. FRONTIERS IN PLANT SCIENCE 2022; 13:720486. [PMID: 35185972 PMCID: PMC8854142 DOI: 10.3389/fpls.2022.720486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 01/17/2022] [Indexed: 06/14/2023]
Abstract
Intercropping of two or more species on the same piece of land can enhance biodiversity and resource use efficiency in agriculture. Traditionally, intercropping systems have been developed and improved by empirical methods within a specific local context. To support the development of promising intercropping systems, the individual species that are part of an intercrop can be subjected to breeding. Breeding for intercropping aims at resource foraging traits of the admixed species to maximize niche complementarity, niche facilitation, and intercrop performance. The breeding process can be facilitated by modeling tools that simulate the outcome of the combination of different species' (or genotypes') traits for growth and yield development, reducing the need of extensive field testing. Here, we revisit the challenges associated with breeding for intercropping, and give an outlook on applying crop growth models to assist breeding for intercropping. We conclude that crop growth models can assist breeding for intercropping, provided that (i) they incorporate the relevant plant features and mechanisms driving interspecific plant-plant interactions; (ii) they are based on model parameters that are closely linked to the traits that breeders would select for; and (iii) model calibration and validation is done with field data measured in intercrops. Minimalist crop growth models are more likely to incorporate the above elements than comprehensive but parameter-intensive crop growth models. Their lower complexity and reduced parameter requirement facilitate the exploration of mechanisms at play and fulfil the model requirements for calibration of the appropriate crop growth models.
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Affiliation(s)
- Martin Weih
- Department of Crop Production Ecology, Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden
| | | | - Giulia Vico
- Department of Crop Production Ecology, Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden
| | - Diego Rubiales
- Institute for Sustainable Agriculture, Consejo Superior de Investigaciones Científicas (CSIC), Córdoba, Spain
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O’Sullivan H, Raumonen P, Kaitaniemi P, Perttunen J, Sievänen R. Integrating terrestrial laser scanning with functional-structural plant models to investigate ecological and evolutionary processes of forest communities. ANNALS OF BOTANY 2021; 128:663-684. [PMID: 34610091 PMCID: PMC8557364 DOI: 10.1093/aob/mcab120] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 09/13/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND Woody plants (trees and shrubs) play an important role in terrestrial ecosystems, but their size and longevity make them difficult subjects for traditional experiments. In the last 20 years functional-structural plant models (FSPMs) have evolved: they consider the interplay between plant modular structure, the immediate environment and internal functioning. However, computational constraints and data deficiency have long been limiting factors in a broader application of FSPMs, particularly at the scale of forest communities. Recently, terrestrial laser scanning (TLS), has emerged as an invaluable tool for capturing the 3-D structure of forest communities, thus opening up exciting opportunities to explore and predict forest dynamics with FSPMs. SCOPE The potential synergies between TLS-derived data and FSPMs have yet to be fully explored. Here, we summarize recent developments in FSPM and TLS research, with a specific focus on woody plants. We then evaluate the emerging opportunities for applying FSPMs in an ecological and evolutionary context, in light of TLS-derived data, with particular consideration of the challenges posed by scaling up from individual trees to whole forests. Finally, we propose guidelines for incorporating TLS data into the FSPM workflow to encourage overlap of practice amongst researchers. CONCLUSIONS We conclude that TLS is a feasible tool to help shift FSPMs from an individual-level modelling technique to a community-level one. The ability to scan multiple trees, of multiple species, in a short amount of time, is paramount to gathering the detailed structural information required for parameterizing FSPMs for forest communities. Conventional techniques, such as repeated manual forest surveys, have their limitations in explaining the driving mechanisms behind observed patterns in 3-D forest structure and dynamics. Therefore, other techniques are valuable to explore how forests might respond to environmental change. A robust synthesis between TLS and FSPMs provides the opportunity to virtually explore the spatial and temporal dynamics of forest communities.
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Affiliation(s)
- Hannah O’Sullivan
- Department of Life Sciences, Imperial College London, Silwood Park, Ascot, Berkshire, SL5 7PY, UK
- Royal Botanic Gardens, Kew, Richmond, UK
| | - Pasi Raumonen
- Mathematics, Tampere University, Korkeakoulunkatu 7, FI-33720 Tampere, Finland
| | - Pekka Kaitaniemi
- Hyytiälä Forestry Field Station, Faculty of Agriculture and Forestry, University of Helsinki, Hyytiäläntie 124, FI-35500 Korkeakoski, Finland
| | - Jari Perttunen
- Natural Resources Institute Finland, Latokartanontie 9, 00790 Helsinki, Finland
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8
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Blanc E, Barbillon P, Fournier C, Lecarpentier C, Pradal C, Enjalbert J. Functional-Structural Plant Modeling Highlights How Diversity in Leaf Dimensions and Tillering Capability Could Promote the Efficiency of Wheat Cultivar Mixtures. FRONTIERS IN PLANT SCIENCE 2021; 12:734056. [PMID: 34659301 PMCID: PMC8511389 DOI: 10.3389/fpls.2021.734056] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 08/30/2021] [Indexed: 06/02/2023]
Abstract
Increasing the cultivated diversity has been identified as a major leverage for the agroecological transition as it can help improve the resilience of low input cropping systems. For wheat, which is the most cultivated crop worldwide in terms of harvested area, the use of cultivar mixtures is spreading in several countries, but studies have seldom focused on establishing mixing rules based on plant architecture. Yet, the aerial architecture of plants and the overall canopy structure are critical for field performance as they greatly influence light interception, plant interactions and yield. The very high number of trait combinations in wheat mixtures makes it difficult to conduct experimentations on this issue, which is why a modeling approach appears to be an appropriate solution. In this study, we used WALTer, a functional structural plant model (FSPM), to simulate wheat cultivar mixtures and try to better understand how differences between cultivars in key traits of the aerial architecture influence mixture performance. We simulated balanced binary mixtures of cultivars differing for different critical plant traits: final height, leaf dimensions, leaf insertion angle and tillering capability. Our study highlights the impact of the leaf dimensions and the tillering capability on the performance of the simulated mixtures, which suggests that traits impacting the plants' leaf area index (LAI) have more influence on the performance of the stand than traits impacting the arrangement of the leaves. Our results show that the performance of mixtures is very variable depending on the values of the explored architectural traits. In particular, the best performances were achieved by mixing cultivars with different leaf dimensions and different tillering capability, which is in agreement with numerous studies linking the diversity of functional traits in plant communities to their productivity. However, some of the worst performances were also achieved by mixing varieties differing in their aerial architecture, which suggests that diversity is not a sufficient criterion to design efficient mixtures. Overall, these results highlight the importance of simulation-based explorations for establishing assembly rules to design efficient mixtures.
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Affiliation(s)
- Emmanuelle Blanc
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE—Le Moulon, Gif-sur-Yvette, France
| | - Pierre Barbillon
- Université Paris-Saclay, AgroParisTech, INRAE, UMR MIA-Paris, 75005, Paris, France
| | | | | | - Christophe Pradal
- CIRAD, UMR AGAP Institut, Montpellier, France
- INRIA and LIRMM, Univ Montpellier, CNRS, Montpellier, France
| | - Jérôme Enjalbert
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE—Le Moulon, Gif-sur-Yvette, France
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9
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Reprint of: Functional-structural plant models to boost understanding of complementarity in light capture and use in mixed-species forests. Basic Appl Ecol 2021. [DOI: 10.1016/j.baae.2021.01.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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10
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Chen BJW, Huang L, During HJ, Wang X, Wei J, Anten NPR. No neighbour-induced increase in root growth of soybean and sunflower in mesh-divider experiments after controlling for nutrient concentration and soil volume. AOB PLANTS 2021; 13:plab020. [PMID: 33995993 PMCID: PMC8112762 DOI: 10.1093/aobpla/plab020] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 04/12/2021] [Indexed: 05/11/2023]
Abstract
Root competition is a key factor determining plant performance, community structure and ecosystem productivity. To adequately estimate the extent of root proliferation of plants in response to neighbours independently of nutrient availability, one should use a set-up that can simultaneously control for both nutrient concentration and soil volume at plant individual level. With a mesh-divider design, which was suggested as a promising solution for this problem, we conducted two intraspecific root competition experiments: one with soybean (Glycine max) and the other with sunflower (Helianthus annuus). We found no response of root growth or biomass allocation to intraspecific neighbours, i.e. an 'ideal free distribution' (IFD) norm, in soybean; and even a reduced growth as a negative response in sunflower. These responses are all inconsistent with the hypothesis that plants should produce more roots even at the expense of reduced fitness in response to neighbours, i.e. root over-proliferation. Our results suggest that neighbour-induced root over-proliferation is not a ubiquitous feature in plants. By integrating the findings with results from other soybean studies, we conclude that for some species this response could be a genotype-dependent response as a result of natural or artificial selection, or a context-dependent response so that plants can switch from root over-proliferation to IFD depending on the environment of competition. We also critically discuss whether the mesh-divider design is an ideal solution for root competition experiments.
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Affiliation(s)
- Bin J W Chen
- College of Biology and the Environment, Nanjing Forestry University, Longpan Road 159, Xuanwu District, Nanjing 210037, China
| | - Li Huang
- College of Biology and the Environment, Nanjing Forestry University, Longpan Road 159, Xuanwu District, Nanjing 210037, China
| | - Heinjo J During
- Section of Ecology and Biodiversity, Institute of Environmental Biology, Utrecht University, Padualaan 8, 3584CH Utrecht, The Netherlands
| | - Xinyu Wang
- College of Biology and the Environment, Nanjing Forestry University, Longpan Road 159, Xuanwu District, Nanjing 210037, China
| | - Jiahe Wei
- College of Biology and the Environment, Nanjing Forestry University, Longpan Road 159, Xuanwu District, Nanjing 210037, China
| | - Niels P R Anten
- Centre for Crop Systems Analysis, Wageningen University, P.O. Box 430, 6700AK Wageningen, The Netherlands
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11
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Li S, van der Werf W, Zhu J, Guo Y, Li B, Ma Y, Evers JB. Estimating the contribution of plant traits to light partitioning in simultaneous maize/soybean intercropping. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:3630-3646. [PMID: 33608704 DOI: 10.1093/jxb/erab077] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Accepted: 02/18/2021] [Indexed: 06/12/2023]
Abstract
Spatial configuration and plant phenotypic plasticity contribute to increased light capture in relay intercropping, but there is little information on whether these factors also increase light capture in simultaneous intercropping. We developed and validated a three-dimensional functional-structural plant model to simulate light capture in maize and soybean sole crops and intercrop scenarios, using species traits observed in sole crops and intercrops. The intercrop maize phenotype had 2% greater light capture than the sole crop phenotype in a pure stand. The soybean intercrop phenotype had 5-10% lower light capture than the sole crop phenotype in a pure stand. The intercrop configuration increased the light capture of maize by 29% and reduced the light capture of soybean by 42%, compared with the light capture expected from sole crops. However, intercrop configuration only marginally affected total light capture by the intercrop system (+1%). Testing of individual soybean plant traits revealed that plasticity in leaf dimensions was the main reason for differences in light capture by soybean in simulated sole crops and intercrops. The results of this study illustrate a major shift of light capture from shorter species (soybean) to the taller component (maize) in a simultaneous strip intercrop. Plastic plant traits modulate this overall effect, but only marginally.
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Affiliation(s)
- Shuangwei Li
- College of Land Science and Technology, China Agricultural University, Beijing 100193,China
- Key Laboratory of Arable Land Conservation in North China, Ministry of Agriculture and Rural Affairs, Beijing 100193, China
- Key Laboratory of Agricultural Land Quality, Ministry of Natural Resources, Beijing 100193, China
- Centre for Crop Systems Analysis, Wageningen University, PO Box 430, Wageningen 6700 AK, The Netherlands
| | - Wopke van der Werf
- Centre for Crop Systems Analysis, Wageningen University, PO Box 430, Wageningen 6700 AK, The Netherlands
| | - Junqi Zhu
- The New Zealand Institute for Plant & Food Research Ltd, Marlborough Research Centre, PO Box 845, Blenheim 7240, New Zealand
| | - Yan Guo
- College of Land Science and Technology, China Agricultural University, Beijing 100193,China
- Key Laboratory of Arable Land Conservation in North China, Ministry of Agriculture and Rural Affairs, Beijing 100193, China
- Key Laboratory of Agricultural Land Quality, Ministry of Natural Resources, Beijing 100193, China
| | - Baoguo Li
- College of Land Science and Technology, China Agricultural University, Beijing 100193,China
- Key Laboratory of Arable Land Conservation in North China, Ministry of Agriculture and Rural Affairs, Beijing 100193, China
- Key Laboratory of Agricultural Land Quality, Ministry of Natural Resources, Beijing 100193, China
| | - Yuntao Ma
- College of Land Science and Technology, China Agricultural University, Beijing 100193,China
- Key Laboratory of Arable Land Conservation in North China, Ministry of Agriculture and Rural Affairs, Beijing 100193, China
- Key Laboratory of Agricultural Land Quality, Ministry of Natural Resources, Beijing 100193, China
| | - Jochem B Evers
- Centre for Crop Systems Analysis, Wageningen University, PO Box 430, Wageningen 6700 AK, The Netherlands
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12
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A Scientometric Analysis of Worldwide Intercropping Research Based on Web of Science Database between 1992 and 2020. SUSTAINABILITY 2021. [DOI: 10.3390/su13052430] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Intercropping has been practiced worldwide in both traditional and sustainable agriculture to feed the growing population. This study aims to analyze the research status and evolution of intercropping, to identify the influential authors, research centers, and articles, and to reveal the main research topics between 1992 and 2020 based on the Web of Science Core Collection database. The results show that the volume of publications in this field has increased rapidly over the past three decades. The analysis identifies the top three authors (i.e., Meine Van Noordwijk, Wenyu Yang, and Teja Tscharntke), top three contributing organizations (i.e., the World Agroforestry Center (ICRAF), the Chinese Academy of Science, and the INRA), and three most productive countries (i.e., the USA, India, and China). Co-occurrence analysis demonstrates that studies on intercropping can be divided into four clusters as centered by keywords of intercropping/maize, biodiversity/conservation, agroforestry, and carbon, respectively. Lal 2004 is the most influential study with the greatest number of citations and Agroforestry Systems is the most utilized journal. Perspectives on future studies were also given. This study helps researchers to clarify the current research status in the field of intercropping and put forward its future research.
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Bourke PM, Evers JB, Bijma P, van Apeldoorn DF, Smulders MJM, Kuyper TW, Mommer L, Bonnema G. Breeding Beyond Monoculture: Putting the "Intercrop" Into Crops. FRONTIERS IN PLANT SCIENCE 2021; 12:734167. [PMID: 34868116 PMCID: PMC8636715 DOI: 10.3389/fpls.2021.734167] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 10/22/2021] [Indexed: 05/15/2023]
Abstract
Intercropping is both a well-established and yet novel agricultural practice, depending on one's perspective. Such perspectives are principally governed by geographic location and whether monocultural practices predominate. Given the negative environmental effects of monoculture agriculture (loss of biodiversity, reliance on non-renewable inputs, soil degradation, etc.), there has been a renewed interest in cropping systems that can reduce the impact of modern agriculture while maintaining (or even increasing) yields. Intercropping is one of the most promising practices in this regard, yet faces a multitude of challenges if it is to compete with and ultimately replace the prevailing monocultural norm. These challenges include the necessity for more complex agricultural designs in space and time, bespoke machinery, and adapted crop cultivars. Plant breeding for monocultures has focused on maximizing yield in single-species stands, leading to highly productive yet specialized genotypes. However, indications suggest that these genotypes are not the best adapted to intercropping systems. Re-designing breeding programs to accommodate inter-specific interactions and compatibilities, with potentially multiple different intercropping partners, is certainly challenging, but recent technological advances offer novel solutions. We identify a number of such technology-driven directions, either ideotype-driven (i.e., "trait-based" breeding) or quantitative genetics-driven (i.e., "product-based" breeding). For ideotype breeding, plant growth modeling can help predict plant traits that affect both inter- and intraspecific interactions and their influence on crop performance. Quantitative breeding approaches, on the other hand, estimate breeding values of component crops without necessarily understanding the underlying mechanisms. We argue that a combined approach, for example, integrating plant growth modeling with genomic-assisted selection and indirect genetic effects, may offer the best chance to bridge the gap between current monoculture breeding programs and the more integrated and diverse breeding programs of the future.
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Affiliation(s)
- Peter M. Bourke
- Plant Breeding, Wageningen University & Research, Wageningen, Netherlands
- Peter M. Bourke,
| | - Jochem B. Evers
- Centre for Crops Systems Analysis, Wageningen University & Research, Wageningen, Netherlands
| | - Piter Bijma
- Animal Breeding and Genomics, Wageningen University & Research, Wageningen, Netherlands
| | - Dirk F. van Apeldoorn
- Farming Systems Ecology Group, Wageningen University & Research, Wageningen, Netherlands
- Field Crops, Wageningen University & Research, Lelystad, Netherlands
| | | | - Thomas W. Kuyper
- Soil Biology, Wageningen University & Research, Wageningen, Netherlands
| | - Liesje Mommer
- Plant Ecology and Nature Conservation, Wageningen University & Research, Wageningen, Netherlands
| | - Guusje Bonnema
- Plant Breeding, Wageningen University & Research, Wageningen, Netherlands
- *Correspondence: Guusje Bonnema,
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Functional-structural plant models to boost understanding of complementarity in light capture and use in mixed-species forests. Basic Appl Ecol 2020. [DOI: 10.1016/j.baae.2020.09.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Distel RA, Arroquy JI, Lagrange S, Villalba JJ. Designing Diverse Agricultural Pastures for Improving Ruminant Production Systems. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2020. [DOI: 10.3389/fsufs.2020.596869] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
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Braghiere RK, Gérard F, Evers JB, Pradal C, Pagès L. Simulating the effects of water limitation on plant biomass using a 3D functional-structural plant model of shoot and root driven by soil hydraulics. ANNALS OF BOTANY 2020; 126:713-728. [PMID: 32249296 PMCID: PMC7489072 DOI: 10.1093/aob/mcaa059] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 04/02/2020] [Indexed: 05/28/2023]
Abstract
BACKGROUND AND AIMS Improved modelling of carbon assimilation and plant growth to low soil moisture requires evaluation of underlying mechanisms in the soil, roots, and shoots. The feedback between plants and their local environment throughout the whole spectrum soil-root-shoot-environment is crucial to accurately describe and evaluate the impact of environmental changes on plant development. This study presents a 3D functional structural plant model, in which shoot and root growth are driven by radiative transfer, photosynthesis, and soil hydrodynamics through different parameterisation schemes relating soil water deficit and carbon assimilation. The new coupled model is used to evaluate the impact of soil moisture availability on plant productivity for two different groups of flowering plants under different spatial configurations. METHODS In order to address different aspects of plant development due to limited soil water availability, a 3D FSP model including root, shoot, and soil was constructed by linking three different well-stablished models of airborne plant, root architecture, and reactive transport in the soil. Different parameterisation schemes were used in order to integrate photosynthetic rate with root water uptake within the coupled model. The behaviour of the model was assessed on how the growth of two different types of plants, i.e. monocot and dicot, is impacted by soil water deficit under different competitive conditions: isolated (no competition), intra, and interspecific competition. KEY RESULTS The model proved to be capable of simulating carbon assimilation and plant development under different growing settings including isolated monocots and dicots, intra, and interspecific competition. The model predicted that (1) soil water availability has a larger impact on photosynthesis than on carbon allocation; (2) soil water deficit has an impact on root and shoot biomass production by up to 90 % for monocots and 50 % for dicots; and (3) the improved dicot biomass production in interspecific competition was highly related to root depth and plant transpiration. CONCLUSIONS An integrated model of 3D shoot architecture and biomass development with a 3D root system representation, including light limitation and water uptake considering soil hydraulics, was presented. Plant-plant competition and regulation on stomatal conductance to drought were able to be predicted by the model. In the cases evaluated here, water limitation impacted plant growth almost 10 times more than the light environment.
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Affiliation(s)
- Renato K Braghiere
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, USA
- Joint Institute for Regional Earth System Science and Engineering, University of California at Los Angeles, Los Angeles, CA, USA
- Eco&Sols, Univ. Montpellier, CIRAD, INRAE, IRD, SupAgro, Montpellier, France
| | - Frédéric Gérard
- Eco&Sols, Univ. Montpellier, CIRAD, INRAE, IRD, SupAgro, Montpellier, France
| | - Jochem B Evers
- Centre for Crop Systems Analysis (CSA), Wageningen University, Wageningen, The Netherlands
| | - Christophe Pradal
- CIRAD, UMR AGAP, Montpellier, France
- AGAP, Univ. Montpellier, CIRAD, INRAE, SupAgro, Montpellier, France
- INRIA, Univ. Montpellier, France
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Louarn G, Barillot R, Combes D, Escobar-Gutiérrez A. Towards intercrop ideotypes: non-random trait assembly can promote overyielding and stability of species proportion in simulated legume-based mixtures. ANNALS OF BOTANY 2020; 126:671-685. [PMID: 32004372 PMCID: PMC7489071 DOI: 10.1093/aob/mcaa014] [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: 07/07/2019] [Accepted: 01/29/2020] [Indexed: 05/27/2023]
Abstract
BACKGROUNDS AND AIMS A major challenge when supporting the development of intercropping systems remains the design of efficient species mixtures. The ecological processes that sustain overyielding of legume-based mixtures compared to pure crops are well known, but their links to plant traits remain to be unravelled. A common assumption is that enhancing trait divergence among species for resource acquisition when assembling plant mixtures should increase species complementarity and improve community performance. METHODS The Virtual Grassland model was used to assess how divergence in trait values between species on four physiological functions (namely light and mineral N acquisition, temporal development, and C-N use efficiency) affected overyielding and mixture stability in legume-based binary mixtures. A first step allowed us to identify the model parameters that were most important to interspecies competition. A second step involved testing the impact of convergent and divergent parameter (or trait) values between species on virtual mixture performance. RESULTS Maximal overyielding was achieved in cases where trait values were divergent for the physiological functions controlling N acquisition and temporal development but convergent for light interception. It was also found that trait divergence should not affect competitive abilities of legume and non-legumes at random. Indeed, random trait combinations frequently led to reduced mixture yields when compared to a perfectly convergent neutral model. Combinations with the highest overyielding also tended to be associated with mixture instability and decreasing legume biomass proportion. Achieving both high overyielding and mixture stability was only found to be possible under low or moderate N levels, using combinations of traits adapted to each environment. CONCLUSIONS No simple assembly rule based on trait divergence could be confirmed. Plant models able to infer plant-plant interactions can be helpful for the identification of major interaction traits and the definition of ideotypes adapted to a targeted intercropping system.
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Zhang B, DeAngelis DL. An overview of agent-based models in plant biology and ecology. ANNALS OF BOTANY 2020; 126:539-557. [PMID: 32173742 PMCID: PMC7489105 DOI: 10.1093/aob/mcaa043] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Accepted: 03/12/2020] [Indexed: 05/22/2023]
Abstract
Agent-based modelling (ABM) has become an established methodology in many areas of biology, ranging from the cellular to the ecological population and community levels. In plant science, two different scales have predominated in their use of ABM. One is the scale of populations and communities, through the modelling of collections of agents representing individual plants, interacting with each other and with the environment. The other is the scale of the individual plant, through the modelling, by functional-structural plant models (FSPMs), of agents representing plant building blocks, or metamers, to describe the development of plant architecture and functions within individual plants. The purpose of this review is to show key results and parallels in ABM for growth, mortality, carbon allocation, competition and reproduction across the scales from the plant organ to populations and communities on a range of spatial scales to the whole landscape. Several areas of application of ABMs are reviewed, showing that some issues are addressed by both population-level ABMs and FSPMs. Continued increase in the relevance of ABM to environmental science and management will be helped by greater integration of ABMs across these two scales.
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Affiliation(s)
- Bo Zhang
- Department of Environmental Science and Policy, University of California, Davis, CA, USA
| | - Donald L DeAngelis
- U. S. Geological Survey, Wetland and Aquatic Research Center, Davie, FL, USA
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Louarn G, Song Y. Two decades of functional-structural plant modelling: now addressing fundamental questions in systems biology and predictive ecology. ANNALS OF BOTANY 2020; 126:501-509. [PMID: 32725187 PMCID: PMC7489058 DOI: 10.1093/aob/mcaa143] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 07/25/2020] [Indexed: 05/16/2023]
Abstract
BACKGROUND Functional-structural plant models (FSPMs) explore and integrate relationships between a plant's structure and processes that underlie its growth and development. In the last 20 years, scientists interested in functional-structural plant modelling have expanded greatly the range of topics covered and now handle dynamical models of growth and development occurring from the microscopic scale, and involving cell division in plant meristems, to the macroscopic scales of whole plants and plant communities. SCOPE The FSPM approach occupies a central position in plant science; it is at the crossroads of fundamental questions in systems biology and predictive ecology. This special issue of Annals of Botany features selected papers on critical areas covered by FSPMs and examples of comprehensive models that are used to solve theoretical and applied questions, ranging from developmental biology to plant phenotyping and management of plants for agronomic purposes. Altogether, they offer an opportunity to assess the progress, gaps and bottlenecks along the research path originally foreseen for FSPMs two decades ago. This review also allows discussion of current challenges of FSPMs regarding (1) integration of multidisciplinary knowledge, (2) methods for handling complex models, (3) standards to achieve interoperability and greater genericity and (4) understanding of plant functioning across scales. CONCLUSIONS This approach has demonstrated considerable progress, but has yet to reach its full potential in terms of integration and heuristic knowledge production. The research agenda of functional-structural plant modellers in the coming years should place a greater emphasis on explaining robust emergent patterns, and on the causes of possible deviation from it. Modelling such patterns could indeed fuel both generic integration across scales and transdisciplinary transfer. In particular, it could be beneficial to emergent fields of research such as model-assisted phenotyping and predictive ecology in managed ecosystems.
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Affiliation(s)
| | - Youhong Song
- Anhui Agricultural University, School of Agronomy, Hefei, Anhui Province, PR China
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Muller B, Martre P. Plant and crop simulation models: powerful tools to link physiology, genetics, and phenomics. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:2339-2344. [PMID: 31091319 DOI: 10.1093/jxb/erz175] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Affiliation(s)
- Bertrand Muller
- UMR LEPSE, Univ Montpellier, INRA, Montpellier SupAgro, Montpellier, France
| | - Pierre Martre
- UMR LEPSE, Univ Montpellier, INRA, Montpellier SupAgro, Montpellier, France
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Gaudio N, Escobar-Gutiérrez AJ, Casadebaig P, Evers JB, Gérard F, Louarn G, Colbach N, Munz S, Launay M, Marrou H, Barillot R, Hinsinger P, Bergez JE, Combes D, Durand JL, Frak E, Pagès L, Pradal C, Saint-Jean S, Van Der Werf W, Justes E. Current knowledge and future research opportunities for modeling annual crop mixtures. A review. AGRONOMY FOR SUSTAINABLE DEVELOPMENT 2019; 39:20. [PMID: 0 DOI: 10.1007/s13593-019-0562-6] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 02/04/2019] [Indexed: 05/27/2023]
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