CAREER: The phenotypic spectrum: Quantifying new patterns of architecture variation in crop roots

职业：表型谱：量化作物根部结构变异的新模式

• 批准号: 1845760
• 负责人: Alexander Bucksch
• 金额: $ 113.74万
• 依托单位: University of Georgia Research Foundation Inc
• 依托单位国家: 美国
• 项目类别: Continuing Grant
• 财政年份: 2019
• 资助国家: 美国
• 起止时间: 2019-04-01 至 2023-06-30
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1845760&HistoricalAwards=false
• 关键词: CAREER; phenotypic; spectrum; Quantifying; new

Plant roots are remarkably diverse in size and shape. It is not fully understood how the diversity in root architecture contributes to crop yields or plant biomass in part because roots are buried underground and difficult to study. This research takes a quantitative approach to analyze the wide diversity of root architectures. Bean roots grown under experimental conditions will be imaged and the resulting data will be used to create new mathematical and computational tools to discern causes of root variability. Combined with genomic information, the analytical tools will identify genetic elements underlying root shapes in response to environmental and genetic variation. The research will point to new opportunities for breeding targets in crops such as bean and extended to maize. The research also couples with an education program that integrates computation with plant research, thus addressing the critical national need for a computationally trained plant science workforce. The novel tools will be publicly available and deployed using national cyberinfrastructure: further the technologies will be integrated into two courses that enable basic science and computational biology within an experiential learning environment. A new student award is implemented through the Plant Center and the Georgia Informatics Institute to highlight advances attained by working at the computational and plant science interface. Together, the integration of science and education sets forth a path for fast dissemination of results into breeding programs. After decades of research on plant roots it is still a mystery how and why root architecture arises in seemingly endless variations of shapes. The research introduces the phenotypic spectrum as a new quantitative theory that extends the established concept of plasticity by a new dimension. The phenotypic spectrum of one genotype consists of distinct root architecture types, each of which is hypothesized to be associated with a different plasticity curve across environments. Theoretically, the phenotypic spectrum emerges for a population of one genotype if all elementary geometric measurements at all locations within each individual root system are taken and each individual is summarized by a whole root descriptor. Descriptors with similar characteristics correspond to one architecture type. Hence, the spectrum is not observable with current phenotyping tools that capture only one location in a root system per trait. Quantifying the phenotypic spectrum demands the development of unprecedented whole root descriptors and simulation techniques to capture the differences in the 3D spatial organization of the whole root architecture. In doing so, a new combination of differential geometry and imaging approaches as well as a newly developed statistical analysis is proposed. The experiments will provide an understanding of how to describe and evaluate the interplay of different root architecture types in the greenhouse and the field by linking both with the developed descriptors. The educational goal is to increase the number of researchers at the interface of computational and plant sciences through two courses using the developed tools.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.

植物的根在大小和形状上差别很大。根系结构的多样性对作物产量或植物生物量的影响尚不完全清楚，部分原因是根系埋在地下，难以研究。本研究采用定量方法来分析根系结构的多样性。在实验条件下生长的豆根将被成像，结果数据将用于创建新的数学和计算工具，以识别根变异的原因。结合基因组信息，分析工具将识别响应环境和遗传变异的根形状的遗传因素。这项研究将为豆类等作物的育种目标指明新的机会，并将其扩展到玉米。该研究还与一个将计算与植物研究相结合的教育计划相结合，从而解决了国家对计算训练有素的植物科学劳动力的关键需求。这些新工具将公开提供，并使用国家网络基础设施进行部署：此外，这些技术将整合到两门课程中，使基础科学和计算生物学能够在体验式学习环境中学习。通过植物中心和佐治亚信息研究所实施了一个新的学生奖，以突出在计算和植物科学接口工作中取得的进步。科学和教育的结合为育种计划快速传播成果开辟了一条道路。经过几十年对植物根系的研究，根系结构如何以及为什么以看似无穷无尽的形状出现仍然是一个谜。本研究引入表型谱作为一种新的定量理论，将已建立的可塑性概念扩展了一个新的维度。一种基因型的表型谱由不同的根构型类型组成，每种类型都被假设与不同环境下不同的可塑性曲线相关。从理论上讲，如果在每个个体根系的所有位置进行所有基本几何测量，并且每个个体都被一个完整的根系描述符概括，那么就会出现一个基因型群体的表型谱。具有相似特征的描述符对应于一种体系结构类型。因此，目前的表型工具只能捕获根系中每个性状的一个位置，因此无法观察到光谱。量化表型谱需要前所未有的全根描述符和模拟技术的发展，以捕捉整个根结构的三维空间组织的差异。在此过程中，提出了微分几何和成像方法的新组合以及新开发的统计分析。通过将温室和田间不同根系构型类型与已开发的描述符联系起来，这些实验将使人们了解如何描述和评估温室和田间不同根系构型类型的相互作用。教育目标是通过使用开发的工具的两门课程来增加计算和植物科学界面的研究人员数量。该奖项反映了美国国家科学基金会的法定使命，并通过使用基金会的知识价值和更广泛的影响审查标准进行评估，被认为值得支持。

项目成果

Quantification of Phenotypic Responses to Root-Root Interactions Among Common Beans in a Specialized Mesocosm

特殊中生态系统中常见豆类根-根相互作用表型反应的量化

• 发表时间: 2022
• 期刊: CROPS 2022
• 作者: William LaVoy, Limeng Xie

3D imaging and quantitative analysis of peach tree architecture via TreeQSM

通过 TreeQSM 对桃树结构进行 3D 成像和定量分析

• DOI: 10.17660/actahortic.2022.1352.41
• 发表时间: 2022
• 期刊: Acta Horticulturae
• 作者: Knapp-Wilson, J.;Bohn Reckziegel, R.;Bucksch, A.;Chavez, D.J.
• 通讯作者: Chavez, D.J.

TESTING THE THEORY OF THE PHENOTYPIC SPECTRUM ON 3-DIMENSIONAL ROOT ARCHITECTURE OF MAIZE

检验玉米三维根结构表型谱理论

• 发表时间: 2022
• 期刊: Crops 2022
• 作者: Jitrana Kengkanna, Molly Hanlon

Comparison of open-source image-based reconstruction pipelines for 3D root phenotyping of field-grown maize

用于田间种植玉米 3D 根表型分析的基于开源图像的重建流程的比较

• DOI: 10.1002/essoar.10508794.2
• 发表时间: 2022
• 期刊: 2022 NAPPN Conference Proceedings
• 作者: Liu, Suxing Bonelli

Comparison of open‐source three‐dimensional reconstruction pipelines for maize‐root phenotyping

• DOI: 10.1002/ppj2.20068
• 发表时间: 2023-01
• 期刊: The Plant Phenome Journal
• 作者: Suxing Liu;Wesley Paul Bonelli;P. Pietrzyk;Alexander Bucksch