A custom pipeline for building computational models of plant tissue

IF 4.5 1区 农林科学 Q1 AGRONOMY European Journal of Agronomy Pub Date : 2024-09-16 DOI:10.1016/j.eja.2024.127356
Stephen S.B. Clarke , Alice Benzecry , Norbert Bokros , Seth DeBolt , Daniel J. Robertson , Christopher J. Stubbs
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Abstract

Stalk lodging in the monocot Zea mays is an important agricultural issue that requires the development of a genome-to-phenome framework, mechanistically linking intermediate and high-level phenotypes. As part of that effort, tools are needed to enable better mechanistic understanding of the microstructure in herbaceous plants. A method was therefore developed to create finite element models using CT scan data for Zea mays. This method represents a pipeline for processing the image stacks and developing the finite element models. 2-dimensional finite element models, 3-dimensional watertight models, and 3-dimensional voxel-based finite element models were developed. The finite element models contain both the cell and cell wall structures that can be tested in silico for phenotypes such as structural stiffness and predicted tissue strength. This approach was shown to be successful, and a number of example analyses were presented to demonstrate its usefulness and versatility. This pipeline is important for two reasons: (1) it helps inform which microstructure phenotypes should be investigated to breed for more lodging-resistant stalks, and (2) represents an essential step in the development of a mechanistic hierarchical framework for the genome-to-phenome modeling of herbaceous plant stalk lodging.

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建立植物组织计算模型的定制管道
单子叶植物玉米的茎秆萎缩是一个重要的农业问题,需要开发一个基因组到表型组的框架,从机理上将中间表型和高级表型联系起来。作为这项工作的一部分,需要一些工具来更好地从机理上理解草本植物的微观结构。因此,我们开发了一种方法,利用玉米的 CT 扫描数据创建有限元模型。该方法是处理图像堆栈和开发有限元模型的流水线。开发了二维有限元模型、三维水密模型和基于体素的三维有限元模型。这些有限元模型包含细胞和细胞壁结构,可对结构刚度和预测组织强度等表型进行硅测试。这种方法证明是成功的,并介绍了一些实例分析,以证明其有用性和多功能性。这种方法有两个重要原因:(1) 它有助于了解应该研究哪些微观结构表型,以培育更多的抗茎秆宿存能力;(2) 它是为草本植物茎秆宿存的基因组到表型组建模开发机理层次框架的重要一步。
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来源期刊
European Journal of Agronomy
European Journal of Agronomy 农林科学-农艺学
CiteScore
8.30
自引率
7.70%
发文量
187
审稿时长
4.5 months
期刊介绍: The European Journal of Agronomy, the official journal of the European Society for Agronomy, publishes original research papers reporting experimental and theoretical contributions to field-based agronomy and crop science. The journal will consider research at the field level for agricultural, horticultural and tree crops, that uses comprehensive and explanatory approaches. The EJA covers the following topics: crop physiology crop production and management including irrigation, fertilization and soil management agroclimatology and modelling plant-soil relationships crop quality and post-harvest physiology farming and cropping systems agroecosystems and the environment crop-weed interactions and management organic farming horticultural crops papers from the European Society for Agronomy bi-annual meetings In determining the suitability of submitted articles for publication, particular scrutiny is placed on the degree of novelty and significance of the research and the extent to which it adds to existing knowledge in agronomy.
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