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

Abstract

The first draft of the Arabidopsis genome was released more than 20 years ago and despite intensive molecular research, more than 30% of Arabidopsis genes remained uncharacterized or without an assigned function. This is in part due to gene redundancy within gene families or the essential nature of genes, where their deletion results in lethality (i.e., the dark genome). High-throughput plant phenotyping (HTPP) offers an automated and unbiased approach to characterize subtle or transient phenotypes resulting from gene redundancy or inducible gene silencing; however, commercial HTPP platforms remain unaffordable. Here we describe the design and implementation of OPEN leaf, an open-source HTPP system with cloud connectivity and remote bilateral communication to facilitate data collection, sharing and processing. OPEN leaf, coupled with the SMART imaging processing package was able to consistently document and quantify dynamic morphological changes over time at the whole rosette level and also at leaf-specific resolution when plants experienced changes in nutrient availability. The modular design of OPEN leaf allows for additional sensor integration. Notably, our data demonstrate that VIS sensors remain underutilized and can be used in high-throughput screens to identify characterize previously unidentified phenotypes in a leaf-specific manner. Significance StatementMany bottlenecks exist in high-throughput phenotyping involving computing power for processing and a lack of focus on abiotic stresses that has prevented an advancement in phenotyping on par with genotyping. Therefore, we create an automated HTP system that performs nutrient studies on Arabidopsis thaliana with cloud-based image processing that quantifies plant traits at a whole and leaf-level.

Plant phenotyping relevance

OPEN leafは、葉単位の形態形質を画像から自動取得・定量するオープンソース高スループット表現型解析システムの設計・実装が中心であり、明確に収載対象です。

Code and data availability

The paper's image-analysis pipeline (SMART) used for rosette and leaf-specific phenotyping is explicitly released as public source code on GitHub and as a prepackaged Docker container. Phenotype data tables are only in supplementary material without a public URL, and other code repos (OPEN Controller, OPEN-leaf-cloud)'