OPEN leaf : an open‐source cloud‐based phenotyping system for tracking dynamic changes at leaf‐specific resolution in Arabidopsis
OPEN leaf : an open‐source cloud‐based phenotyping system for tracking dynamic changes at leaf‐specific resolution in Arabidopsis
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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
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发表时间：
2023
期刊：
影响因子：
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通讯作者：
Mendoza‐Cózatl, David G.
中科院分区：
文献类型：
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作者：
Swartz, Landon G.;Liu, Suxing;Dahlquist, Drew;Kramer, Skyler T.;Walter, Emily S.;McInturf, Samuel A.;Bucksch, Alexander;Mendoza‐Cózatl, David G.
拟南芥基因组的初稿于20多年前发布，尽管进行了密集的分子研究，但超过30%的拟南芥基因仍未被表征或没有指定功能。这在一定程度上是由于基因家族中的基因冗余或基因的本质，它们的缺失会导致致命性（即深色基因组）。高通量植物表型分析（HTPP）提供了一种自动化和公正的方法来表征由基因冗余或诱导基因沉默引起的微妙或短暂表型；然而，对商业HTPP平台的访问仍然有限。在这里，我们描述了open leaf的设计和实现，open leaf是一个开源表型系统，具有云连接和远程双边通信，以促进数据收集，共享和处理。OPEN leaf与我们的SMART成像处理管道相结合，能够在植物经历养分可用性变化时，在整个莲座水平和叶片特定分辨率上一致地记录和量化动态变化。我们的数据还表明，VIS传感器仍未得到充分利用，可以用于高通量筛选，以叶片特异性时间依赖的方式识别和表征以前未识别的表型。此外，open leaf的模块化和开源设计允许根据用户和实验需求无缝集成其他传感器。
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., thedark 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, access to commercial HTPP platforms remains limited. Here we describe the design and implementation ofOPEN leaf, an open‐source phenotyping system with cloud connectivity and remote bilateral communication to facilitate data collection, sharing and processing.OPEN leaf, coupled with our SMART imaging processing pipeline was able to consistently document and quantify dynamic changes at the whole rosette level and leaf‐specific resolution when plants experienced changes in nutrient availability. Our data also demonstrate that VIS sensors remain underutilized and can be used in high‐throughput screens to identify and characterize previously unidentified phenotypes in a leaf‐specific time‐dependent manner. Moreover, the modular and open‐source design ofOPEN leafallows seamless integration of additional sensors based on users and experimental needs.