Garin Guillaume, Fournier Christian, Andrieu Bruno, Houlès Vianney, Robert Corinne, Pradal Christophe
Ann Bot. 2014 Sep;114(4):795-812. doi: 10.1093/aob/mcu101.
Sustainable agriculture requires the identification of new, environmentally responsible strategies of crop protection. Modelling of pathosystems can allow a better understanding of the major interactions inside these dynamic systems and may lead to innovative protection strategies. In particular, functional-structural plant models (FSPMs) have been identified as a means to optimize the use of architecture-related traits. A current limitation lies in the inherent complexity of this type of modelling, and thus the purpose of this paper is to provide a framework to both extend and simplify the modelling of pathosystems using FSPMs.
Different entities and interactions occurring in pathosystems were formalized in a conceptual model. A framework based on these concepts was then implemented within the open-source OpenAlea modelling platform, using the platform's general strategy of modelling plant-environment interactions and extending it to handle plant interactions with pathogens. New developments include a generic data structure for representing lesions and dispersal units, and a series of generic protocols to communicate with objects representing the canopy and its microenvironment in the OpenAlea platform. Another development is the addition of a library of elementary models involved in pathosystem modelling. Several plant and physical models are already available in OpenAlea and can be combined in models of pathosystems using this framework approach.
Two contrasting pathosystems are implemented using the framework and illustrate its generic utility. Simulations demonstrate the framework's ability to simulate multiscaled interactions within pathosystems, and also show that models are modular components within the framework and can be extended. This is illustrated by testing the impact of canopy architectural traits on fungal dispersal.
This study provides a framework for modelling a large number of pathosystems using FSPMs. This structure can accommodate both previously developed models for individual aspects of pathosystems and new ones. Complex models are deconstructed into separate 'knowledge sources' originating from different specialist areas of expertise and these can be shared and reassembled into multidisciplinary models. The framework thus provides a beneficial tool for a potential diverse and dynamic research community.
可持续农业需要确定新的、对环境负责的作物保护策略。对病理系统进行建模可以更好地理解这些动态系统中的主要相互作用，并可能带来创新的保护策略。特别是，功能-结构植物模型（FSPM）已被视为优化利用与结构相关性状的一种手段。目前的一个限制在于这类建模固有的复杂性，因此本文的目的是提供一个框架，以扩展并简化使用FSPM对病理系统进行的建模。
在一个概念模型中对病理系统中发生的不同实体和相互作用进行了形式化。然后，基于这些概念的一个框架在开源的OpenAlea建模平台中得以实现，采用该平台对植物-环境相互作用进行建模的通用策略，并将其扩展以处理植物与病原体的相互作用。新的进展包括用于表示病斑和传播单元的通用数据结构，以及一系列与OpenAlea平台中表示冠层及其微环境的对象进行通信的通用协议。另一项进展是增加了一个参与病理系统建模的基本模型库。OpenAlea中已经有几个植物模型和物理模型，可使用这种框架方法组合到病理系统模型中。
使用该框架实现了两个截然不同的病理系统，并展示了其通用效用。模拟结果证明了该框架模拟病理系统内多尺度相互作用的能力，还表明模型是框架内的模块化组件，可以进行扩展。通过测试冠层结构性状对真菌传播的影响对此进行了说明。
本研究提供了一个使用FSPM对大量病理系统进行建模的框架。这种结构既可以容纳先前针对病理系统各个方面开发的模型，也可以容纳新模型。复杂模型被解构为源自不同专业领域的单独“知识源”，这些知识源可以共享并重新组合成多学科模型。因此，该框架为潜在的多样化和动态研究群体提供了一个有益的工具。
