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: 2329282
• 负责人: Alexander Bucksch
• 金额: $ 113.74万
• 依托单位: University of Arizona
• 依托单位国家: 美国
• 项目类别: Continuing Grant
• 财政年份: 2023
• 资助国家: 美国
• 起止时间: 2023-01-01 至 2025-03-31
• 项目状态: 未结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=2329282&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都非常不同。人们还不完全了解根构型的多样性如何影响作物产量或植物生物量，部分原因是根部埋在地下，很难研究。本研究采用定量的方法来分析根结构的广泛多样性。在实验条件下生长的豆根将被成像，结果数据将被用于创建新的数学和计算工具，以辨别根部变异性的原因。结合基因组信息，分析工具将识别根形的遗传因素，以响应环境和遗传变异。这项研究将为大豆等作物的育种目标指出新的机会，并将其扩展到玉米。这项研究还与一个将计算与植物研究相结合的教育项目结合在一起，从而满足了国家对受过计算培训的植物科学劳动力的迫切需求。这些新工具将向公众开放，并利用国家网络基础设施进行部署：此外，这些技术将被整合到两门课程中，使基础科学和计算生物学能够在体验式学习环境中进行。通过植物中心和佐治亚州信息学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所取得的进展。科学和教育的结合共同开辟了一条将成果快速传播到育种项目中的途径。经过几十年对植物根的研究，如何以及为什么根结构出现在似乎无穷无尽的形状变化中仍然是一个谜。本研究引入表型谱作为一种新的定量理论，将已建立的塑性概念扩展到一个新的维度。一种基因型的表型谱由不同的根构型类型组成，假设每种根构型都与不同环境中不同的可塑性曲线有关。从理论上讲，如果每个个体根系内所有位置的所有基本几何测量都得到了，并且每个个体都用一个完整的根描述符来概括，那么一个基因群体的表型谱就会出现。具有相似特征的描述符对应于一种架构类型。因此，用目前的表型工具无法观察到光谱，这些表型工具只捕捉到每个性状在根系中的一个位置。表型谱的量化需要开发前所未有的全根性描述符和模拟技术来捕捉整个根构型的3D空间组织中的差异。在此过程中，提出了一种新的微分几何和成像方法的组合以及新发展的统计分析。这些实验将通过将温室和田间不同的根构型与所开发的描述符联系起来，提供如何描述和评估不同根构型的相互作用的理解。教育目标是通过使用开发的工具通过两门课程增加计算科学和植物科学的研究人员数量。这一奖项反映了NSF的法定使命，并通过使用基金会的智力优势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

The soil microbiome modulates the sorghum root metabolome and cellular traits with a concomitant reduction of Striga infection

• DOI: 10.1016/j.celrep.2024.113971
• 发表时间: 2024-04-23
• 期刊: CELL REPORTS
• 影响因子: 8.8
• 作者: Kawa，Dorota;Thiombiano，Benjamin;Brady，Siobhan M.
• 通讯作者: Brady，Siobhan M.

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

OPEN leaf : an open‐source cloud‐based phenotyping system for tracking dynamic changes at leaf‐specific resolution in Arabidopsis

OPEN leaf：基于开源云的表型系统，用于跟踪拟南芥叶特定分辨率的动态变化

• DOI: 10.1111/tpj.16449
• 发表时间: 2023
• 期刊: The Plant Journal
• 作者: Swartz, Landon G.;Liu, Suxing;Dahlquist, Drew;Kramer, Skyler T.;Walter, Emily S.;McInturf, Samuel A.;Bucksch, Alexander;Mendoza‐Cózatl, David G.
• 通讯作者: Mendoza‐Cózatl, David G.

Three‐dimensional phenotyping of peach tree‐crown architecture utilizing terrestrial laser scanning

• DOI: 10.1002/ppj2.20073
• 发表时间: 2023-01
• 期刊: The Plant Phenome Journal
• 作者: J. Knapp‐Wilson;Rafael Bohn Reckziegel;Srijana Thapa Magar;Alexander Bucksch;D. Chavez