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Laurans M, Munoz F, Charles-Dominique T, Heuret P, Fortunel C, Isnard S, Sabatier SA, Caraglio Y, Violle C. Why incorporate plant architecture into trait-based ecology? Trends Ecol Evol 2024; 39:524-536. [PMID: 38212187 DOI: 10.1016/j.tree.2023.11.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 11/20/2023] [Accepted: 11/23/2023] [Indexed: 01/13/2024]
Abstract
Trait-based ecology has improved our understanding of the functioning of organisms, communities, ecosystems, and beyond. However, its predictive ability remains limited as long as phenotypic integration and temporal dynamics are not considered. We highlight how the morphogenetic processes that shape the 3D development of a plant during its lifetime affect its performance. We show that the diversity of architectural traits allows us to go beyond organ-level traits in capturing the temporal and spatial dimensions of ecological niches and informing community assembly processes. Overall, we argue that consideration of multilevel topological, geometrical, and ontogenetic features provides a dynamic view of the whole-plant phenotype and a relevant framework for investigating phenotypic integration, plant adaptation and performance, and community structure and dynamics.
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Affiliation(s)
- Marilyne Laurans
- CIRAD, UMR AMAP, F-34398 Montpellier, France; AMAP, Université de Montpellier, CIRAD, CNRS, INRAE, IRD, Montpellier, France.
| | - François Munoz
- LiPhy, Université Grenoble-Alpes, CNRS, Grenoble, France
| | - Tristan Charles-Dominique
- AMAP, Université de Montpellier, CIRAD, CNRS, INRAE, IRD, Montpellier, France; CNRS UMR7618, Institute of Ecology and Environmental Sciences, Paris, Sorbonne University, Paris, France
| | - Patrick Heuret
- AMAP, Université de Montpellier, CIRAD, CNRS, INRAE, IRD, Montpellier, France
| | - Claire Fortunel
- AMAP, Université de Montpellier, CIRAD, CNRS, INRAE, IRD, Montpellier, France
| | - Sandrine Isnard
- AMAP, Université de Montpellier, CIRAD, CNRS, INRAE, IRD, Montpellier, France
| | - Sylvie-Annabel Sabatier
- CIRAD, UMR AMAP, F-34398 Montpellier, France; AMAP, Université de Montpellier, CIRAD, CNRS, INRAE, IRD, Montpellier, France
| | - Yves Caraglio
- CIRAD, UMR AMAP, F-34398 Montpellier, France; AMAP, Université de Montpellier, CIRAD, CNRS, INRAE, IRD, Montpellier, France
| | - Cyrille Violle
- CEFE, Université de Montpellier, CNRS, EPHE, IRD, Montpellier, France
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Guédon Y, Caraglio Y, Granier C, Lauri PÉ, Muller B. Identifying Developmental Patterns in Structured Plant Phenotyping Data. Methods Mol Biol 2022; 2395:199-225. [PMID: 34822155 DOI: 10.1007/978-1-0716-1816-5_10] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Technological breakthroughs concerning both sensors and robotized plant phenotyping platforms have totally renewed the plant phenotyping paradigm in the last two decades. This has impacted both the nature and the throughput of data with the availability of data at high-throughput from the tissular to the whole plant scale. Sensor outputs often take the form of 2D or 3D images or time series of such images from which traits are extracted while organ shapes, shoot or root system architectures can be deduced. Despite this change of paradigm, many phenotyping studies often ignore the structure of the plant and therefore loose the information conveyed by the temporal and spatial patterns emerging from this structure. The developmental patterns of plants often take the form of succession of well-differentiated phases, stages or zones depending on the temporal, spatial or topological indexing of data. This entails the use of hierarchical statistical models for their identification.The objective here is to show potential approaches for analyzing structured plant phenotyping data using state-of-the-art methods combining probabilistic modeling, statistical inference and pattern recognition. This approach is illustrated using five different examples at various scales that combine temporal and topological index parameters, and development and growth variables obtained using prospective or retrospective measurements.
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Affiliation(s)
- Yann Guédon
- AGAP, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Yves Caraglio
- AMAP, Univ Montpellier, CIRAD, CNRS, INRAE, IRD, Montpellier, France.
| | - Christine Granier
- AGAP, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Pierre-Éric Lauri
- ABSys, Univ Montpellier, CIHEAM-IAMM, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Bertrand Muller
- LEPSE, Univ Montpellier, INRAE, Institut Agro, Montpellier, France
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Guédon Y, Costes E, Rakocevic M. Modulation of the yerba-mate metamer production phenology by the cultivation system and the climatic factors. Ecol Modell 2018. [DOI: 10.1016/j.ecolmodel.2018.06.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Peyhardi J, Caraglio Y, Costes E, Lauri PÉ, Trottier C, Guédon Y. Integrative models for joint analysis of shoot growth and branching patterns. THE NEW PHYTOLOGIST 2017; 216:1291-1304. [PMID: 28892159 DOI: 10.1111/nph.14742] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Accepted: 07/09/2017] [Indexed: 06/07/2023]
Abstract
Plants exhibit dependences between shoot growth and branching that generate highly structured patterns. The characterization of the patterning mechanism is still an open issue because of the developmental processes involved with both succession of events (e.g. internode elongation, axillary shoot initiation and elongation) and complex dependences among neighbouring positions along the parent shoot. Statistical models called semi-Markov switching partitioned conditional generalized linear models were built on the basis of apple and pear tree datasets. In these models, the semi-Markov chain represents both the succession and lengths of branching zones, whereas the partitioned conditional generalized linear models represent the influence of parent shoot growth variables on axillary productions within each branching zone. Parent shoot growth variables were shown to influence specific developmental events. On this basis, the growth and branching patterns of two apple tree (Malus domestica) cultivars, as well as of pear trees (Pyrus spinosa) between two successive growing cycles, were compared. The proposed integrative statistical models were able to decipher the roles of successive developmental events in the growth and branching patterning mechanisms. These models could incorporate other parent shoot explanatory variables, such as the local curvature or the maximum growth rate of the leaf.
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Affiliation(s)
- Jean Peyhardi
- CIRAD, UMR AGAP and Inria, Virtual Plants, 34095, Montpellier, France
- Université de Montpellier, Institut Montpelliérain Alexander Grothendieck, 34095, Montpellier, France
| | | | | | | | - Catherine Trottier
- Université de Montpellier, Institut Montpelliérain Alexander Grothendieck, 34095, Montpellier, France
| | - Yann Guédon
- CIRAD, UMR AGAP and Inria, Virtual Plants, 34095, Montpellier, France
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Yang W, Pallas B, Durand JB, Martinez S, Han M, Costes E. The impact of long-term water stress on tree architecture and production is related to changes in transitions between vegetative and reproductive growth in the 'Granny Smith' apple cultivar. TREE PHYSIOLOGY 2016; 36:1369-1381. [PMID: 27587485 DOI: 10.1093/treephys/tpw068] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Revised: 06/06/2016] [Accepted: 06/28/2016] [Indexed: 06/06/2023]
Abstract
Water stress (WS) generates a number of physiological and morphological responses in plants that depend on the intensity and duration of stress as well as the plant species and development stage. In perennial plants, WS may affect plant development through cumulative effects that modify plant functions, architecture and production over time. Plant architecture depends on the fate of the terminal and axillary buds that can give rise, in the particular case of apple, to reproductive or vegetative growth units (GUs) of different lengths. In this study, the impact of long-term WS (7 years) on the fate of terminal and axillary buds was investigated in relation to flowering occurrence and production pattern (biennial vs regular) in the 'Granny Smith' cultivar. It was observed that WS decreased the total number of GUs per branch, regardless of their type. Conversely, WS did not modify the timing of the two successive developmental phases characterized by the production of long and medium GUs and an alternation of floral GUs over time, respectively. The analysis of GU successions over time using a variable-order Markov chain that included both the effects of the predecessor and water treatment revealed that WS reduced the transition towards long and medium GUs and increased the transition toward floral, short and dead GUs. WS also slightly increased the proportion of axillary floral GUs. The higher relative frequency of floral GUs compared with vegetative ones reduced the tendency to biennial bearing under WS. The accelerated ontogenetic trend observed under WS suggests lower vegetative growth that could, in turn, be beneficial to floral induction and fruit set.
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Affiliation(s)
- Weiwei Yang
- INRA, UMR AGAP, Equipe Architecture et Fonctionnement des Espèces Fruitières, Avenue d'Agropolis - TA-A-108/03, 34398 Montpellier Cedex 5, France
- College of Horticulture, Northwest A&F University, No. 3 Taicheng Road, Yangling, Shaanxi 712100, China
| | - Benoît Pallas
- INRA, UMR AGAP, Equipe Architecture et Fonctionnement des Espèces Fruitières, Avenue d'Agropolis - TA-A-108/03, 34398 Montpellier Cedex 5, France
| | - Jean-Baptiste Durand
- Grenoble University, Laboratoire Jean Kuntzmann, BP53, 38041 Grenoble Cedex 9, France
- Inria-CIRAD-INRA, Virtual Plants Team, UMR AGAP, 860 rue de St Priest, 34095 Montpellier Cedex 5, France
| | - Sébastien Martinez
- INRA, UMR AGAP, Equipe Architecture et Fonctionnement des Espèces Fruitières, Avenue d'Agropolis - TA-A-108/03, 34398 Montpellier Cedex 5, France
| | - Mingyu Han
- College of Horticulture, Northwest A&F University, No. 3 Taicheng Road, Yangling, Shaanxi 712100, China
| | - Evelyne Costes
- INRA, UMR AGAP, Equipe Architecture et Fonctionnement des Espèces Fruitières, Avenue d'Agropolis - TA-A-108/03, 34398 Montpellier Cedex 5, France
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Lièvre M, Granier C, Guédon Y. Identifying developmental phases in the Arabidopsis thaliana rosette using integrative segmentation models. THE NEW PHYTOLOGIST 2016; 210:1466-78. [PMID: 26853434 DOI: 10.1111/nph.13861] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Accepted: 12/15/2015] [Indexed: 05/26/2023]
Abstract
The change in leaf size and shape during ontogeny associated with heteroblastic development is a composite trait for which extensive spatiotemporal data can be acquired using phenotyping platforms. However, only part of the information contained in such data is exploited, and developmental phases are usually defined using a selected organ trait. We here introduce new methods for identifying developmental phases in the Arabidopsis rosette using various traits and minimum a priori assumptions. A pipeline of analysis was developed combining image analysis and statistical models to integrate morphological, shape, dimensional and expansion dynamics traits for the successive leaves of the Arabidopsis rosette. Dedicated segmentation models called semi-Markov switching models were built for selected genotypes in order to identify rosette developmental phases. Four successive developmental phases referred to as seedling, juvenile, transition and adult were identified for the different genotypes. We show that the degree of covering of the leaf abaxial surface with trichomes is insufficient to define these developmental phases. Using our pipeline of analysis, we were able to identify the supplementary seedling phase and to uncover the structuring role of various leaf traits. This enabled us to compare on a more objective basis the vegetative development of Arabidopsis mutants.
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Affiliation(s)
- Maryline Lièvre
- INRA, UMR LEPSE, 34060, Montpellier, France
- CIRAD, UMR AGAP and Inria, Virtual Plants, 34095, Montpellier, France
| | | | - Yann Guédon
- CIRAD, UMR AGAP and Inria, Virtual Plants, 34095, Montpellier, France
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Taugourdeau O, Caraglio Y, Sabatier S, Guédon Y. Characterizing the respective importance of ontogeny and environmental constraints in forest tree development using growth phase duration distributions. Ecol Modell 2015. [DOI: 10.1016/j.ecolmodel.2014.12.022] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Pope KS, Dose V, Da Silva D, Brown PH, Leslie CA, Dejong TM. Detecting nonlinear response of spring phenology to climate change by Bayesian analysis. GLOBAL CHANGE BIOLOGY 2013; 19:1518-25. [PMID: 23505006 DOI: 10.1111/gcb.12130] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2012] [Accepted: 12/10/2012] [Indexed: 05/18/2023]
Abstract
The impact of climate change on the advancement of plant phenological events has been heavily studied in the last decade. Although the majority of spring plant phenological events have been trending earlier, this is not universally true. Recent work has suggested that species that are not advancing in their spring phenological behavior are responding more to lack of winter chill than increased spring heat. One way to test this hypothesis is by evaluating the behavior of a species known to have a moderate to high chilling requirement and examining how it is responding to increased warming. This study used a 60-year data set for timing of leaf-out and male flowering of walnut (Juglans regia) cultivar 'Payne' to examine this issue. The spring phenological behavior of 'Payne' walnut differed depending on bud type. The vegetative buds, which have a higher chilling requirement, trended toward earlier leaf-out until about 1994, when they shifted to later leaf-out. The date of male bud pollen shedding advanced over the course of the whole record. Our findings suggest that many species which have exhibited earlier bud break are responding to warmer spring temperatures, but may shift into responding more to winter temperatures (lack of adequate chilling) as warming continues.
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Affiliation(s)
- Katherine S Pope
- Department of Plant Sciences, University of California, Davis, CA 95616, USA.
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