A Field-to-Parameter Pipeline for Analyzing and Simulating Root System Architecture of Woody Perennials: Application to Grapevine Rootstocks.

Abstract

Understanding root system architecture (RSA) is essential for improving crop resilience to climate change, yet assessing root systems of woody perennials under field conditions remains a challenge. This study introduces a pipeline that combines field excavation, in situ 3-dimensional digitization, and transformation of RSA data into an interoperable format to analyze and model the growth and water uptake of grapevine rootstock genotypes. Eight root systems of each of 3 grapevine rootstock genotypes ("101-14", "SO4", and "Richter 110") were excavated and digitized 3 and 6 months after planting. We validated the precision of the digitization method, compared in situ and ex situ digitization, and assessed root loss during excavation. The digitized RSA data were converted to root system markup language (RSML) format and imported into the CPlantBox modeling framework, which we adapted to include a static initial root system and a probabilistic tropism function. We then parameterized it to simulate genotype-specific growth patterns of grapevine rootstocks and integrated root hydraulic properties to derive a standard uptake fraction (SUF) for each genotype. Results demonstrated that excavation and in situ digitization accurately reflected the spatial structure of root systems, despite some underestimation of fine root length. Our experiment revealed significant genotypic variations in RSA over time and provided new insights into genotype-specific water acquisition capabilities. Simulated RSA closely resembled the specific features of the field-grown and digitized root systems. This study provides a foundational methodology for future research aimed at utilizing RSA models to improve the sustainability and productivity of woody perennials under changing climatic conditions.

Plant phenotyping relevance

圃場での根系3次元デジタル化、精度検証、データ形式変換、モデル化を統合した根系表現型取得・解析パイプラインが研究の中心である。

Code and data availability

The paper describes field excavation, 3D digitization (DigiTool), RSML conversion, and CPlantBox-based simulation of grapevine rootstock RSA, but the supplied blocks contain no public deposit of the digitized RSA datasets, RSML files, or the authors' customized R/CPlantBox scripts. The only URLs present (R, RStudio) in

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