A versatile phenotyping system and analytics platform reveals diverse temporal responses to water availability in Setaria

Authors: FAHLGREN, NOAH - Danforth Plant Science Center; FELDMAN, MAXIMILIAN - Danforth Plant Science Center; GEHAN, MALIA - Danforth Plant Science Center; WILSON, MELINDA - Danforth Plant Science Center; SHYU, CHRISTINE - Danforth Plant Science Center; BRYANT, DOUGLAS - Danforth Plant Science Center; HILL, STEVEN - Danforth Plant Science Center; MCENTEE, COLTON - Danforth Plant Science Center; WARNASOORIYA, SANKALPI - Danforth Plant Science Center; KUMAR, INDRAJIT - Danforth Plant Science Center; FICOR, TRACY - Danforth Plant Science Center; TURNIPSEED, STEPHANIE - Danforth Plant Science Center; GILBERT, KERRIGAN - Danforth Plant Science Center; BRUTNELL, THOMAS - Danforth Plant Science Center; CARRINGTON, JAMES - Danforth Plant Science Center; MOCKLER, TODD - Danforth Plant Science Center; Baxter, Ivan

Submitted to: Molecular Plant
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/8/2015
Publication Date: 10/5/2015
Publication URL: https://handle.nal.usda.gov/10113/61592
Citation: Fahlgren, N., Feldman, M., Gehan, M.A., Wilson, M., Shyu, C., Bryant, D.W., Hill, S.T., McEntee, C.J., Warnasooriya, S.N., Kumar, I., Ficor, T., Turnipseed, S., Gilbert, K.B., Brutnell, T.P., Carrington, J.C., Mockler, T.C., Baxter, I.R. 2015. A versatile phenotyping system and analytics platform reveals diverse temporal responses to water availability in Setaria. Molecular Plant. 8:1520-1535.

Interpretive Summary: Plant growth is a dynamic process that responds to a changing environment. Most of the methods that we have for measuring plant properties are static and collecting information throughout a plants lifecycle is labor and cost prohibitive. Advances in imaging and robotics technology have enabled novel approaches to understanding how plants adapt to the environment. Here, the Bellwether Phenotyping platform, a system for controlling the environment where plants growth and recording their properties over time, is described. The conveyor-based system has capacity for 1,140 plants, which pass daily through stations to record fluorescence images for photosynethsis, near infrared images for water content, and visible images for size, shape and color. Data management and analysis systems, including PhenoFront for data management and Plant Computer Vision (PlantCV) for quantitative image analysis, were developed. PlantCV open-source analysis tools are platform independent and can serve as a community resource. The utility of the platform and software to reveal distinct temporal responses to controlled water-deficit in wild Setaria viridis, and domesticated Setaria italica (lab plant models for maize), was shown during a four-week experiment involving the acquisition of ~79,000 images, which are publically available. Setaria viridis and Setaria italica had fundamentally different responses to water deficit. Setaria italica shifted to water use-efficient growth, while Setaria viridis reduced growth, under limited water conditions. These systems and approaches can be used to understand how model and crop plants respond to environmental stresses, which will lead to more efficient crops.

Technical Abstract: With rapid advances in DNA sequencing, phenotyping has become the rate-limiting step in using large-scale genomic data to understand and improve agricultural crops. Here, the Bellwether Phenotyping platform for controlled-environment plant growth and automated, multimodal phenotyping is described. The conveyor-based system has capacity for 1,140 plants, which pass daily through stations to record fluorescence images, near infrared images, and visible images. Data management and analysis systems, including PhenoFront for data management and Plant Computer Vision (PlantCV) for quantitative image analysis, were developed. PlantCV open-source analysis tools are platform independent and can serve as a community resource for image-based phenomics. The utility of the platform and software to reveal distinct temporal responses to controlled water-deficit in wild Setaria viridis, and domesticated Setaria italica, was shown during a four-week experiment involving the acquisition of ~79,000 images, which are publically available. Setaria viridis and Setaria italica had fundamentally different responses to water deficit. Setaria italica shifted to water use-efficient growth, while Setaria viridis reduced growth, under limited water conditions. Overall, the Bellwether Phenotyping platform and PlantCV software detected significant effects of genotype, and environment on height, biomass, water-use efficiency, color, plant architecture and near-infrared traits.