Abstract
BackgroundChemical genetics provides a powerful alternative to conventional genetics for understanding gene function. However, its application to plants has been limited by the lack of a technology that allows detailed phenotyping of whole-seedling development in the context of a high-throughput chemical screen. We have therefore sought to develop an automated micro-phenotyping platform that would allow both root and shoot development to be monitored under conditions where the phenotypic effects of large numbers of small molecules can be assessed.ResultsThe ‘Microphenotron’ platform uses 96-well microtitre plates to deliver chemical treatments to seedlings of Arabidopsis thaliana L. and is based around four components: (a) the ‘Phytostrip’, a novel seedling growth device that enables chemical treatments to be combined with the automated capture of images of developing roots and shoots; (b) an illuminated robotic platform that uses a commercially available robotic manipulator to capture images of developing shoots and roots; (c) software to control the sequence of robotic movements and integrate these with the image capture process; (d) purpose-made image analysis software for automated extraction of quantitative phenotypic data. Imaging of each plate (representing 80 separate assays) takes 4 min and can easily be performed daily for time-course studies. As currently configured, the Microphenotron has a capacity of 54 microtitre plates in a growth room footprint of 2.1 m2, giving a potential throughput of up to 4320 chemical treatments in a typical 10 days experiment. The Microphenotron has been validated by using it to screen a collection of 800 natural compounds for qualitative effects on root development and to perform a quantitative analysis of the effects of a range of concentrations of nitrate and ammonium on seedling development.ConclusionsThe Microphenotron is an automated screening platform that for the first time is able to combine large numbers of individual chemical treatments with a detailed analysis of whole-seedling development, and particularly root system development. The Microphenotron should provide a powerful new tool for chemical genetics and for wider chemical biology applications, including the development of natural and synthetic chemical products for improved agricultural sustainability.
Highlights
Chemical genetics provides a powerful alternative to conventional genetics for understanding gene function
Chemical genetics has become an important tool in many areas of research, and in the development of pharmaceuticals and agrochemicals [3,4,5], it has been less enthusiastically adopted by plant researchers, with some notable exceptions (e.g. [6,7,8,9,10]). This is despite the number of Burrell et al Plant Methods (2017) 13:10 advantages that chemical genetics offers over conventional genetic approaches [1, 2], most notably its ability to overcome the problem of functional redundancy that can prevent single gene mutations having a discernible effect on the phenotype [11]
The ‘Phytostrip’: a novel plant growth device to enable automated imaging and analysis of root architecture in the context of a chemical screen In the original version of the micro-phenotyping technique, commercially available strips of PCR tubes were filled with solid nutrient medium and their tips excised to allow chemical treatments to be applied by diffusion from the wells of a microtitre plate [17]
Summary
Chemical genetics provides a powerful alternative to conventional genetics for understanding gene function. Its application to plants has been limited by the lack of a technology that allows detailed phenotyping of whole-seedling development in the context of a high-throughput chemical screen. Burrell et al Plant Methods (2017) 13:10 advantages that chemical genetics offers over conventional genetic approaches [1, 2], most notably its ability to overcome the problem of functional redundancy that can prevent single gene mutations having a discernible effect on the phenotype [11]. It is likely that one key reason for the low engagement with chemical genetics in plants is the limited range of plant phenotypes that it has been possible to screen for in a high-throughput format. Alternative approaches have used plant cell cultures [15] or germinating pollen [16], but again severely restricting the range of traits that it is possible to screen
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