title: A Versatile Phenotyping System and Analytics Platform Reveals Diverse Temporal Responses to Water Availability in Setaria.
abstract: 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 system has capacity for 1140 plants, which pass daily through stations to record fluorescence, near-infrared, and visible images. Plant Computer Vision (PlantCV) was developed as open-source, hardware platform-independent software for quantitative image analysis. In a 4-week experiment, wild Setaria viridis and domesticated Setaria italica had fundamentally different temporal responses to water availability. While both lines produced similar levels of biomass under limited water conditions, Setaria viridis maintained the same water-use efficiency under water replete conditions, while Setaria italica shifted to less efficient growth. 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 tissue water status traits. All ∼ 79,000 images acquired during the course of the experiment are publicly available.
authors.affiliation: Donald Danforth Plant Science Center, St. Louis, MO 63132, USA.
authors.forename: Noah
authors.initials: N
authors.lastname: Fahlgren
authors.affiliation: Donald Danforth Plant Science Center, St. Louis, MO 63132, USA.
authors.forename: Maximilian
authors.initials: M
authors.lastname: Feldman
authors.affiliation: Donald Danforth Plant Science Center, St. Louis, MO 63132, USA.
authors.forename: Malia A
authors.initials: MA
authors.lastname: Gehan
authors.affiliation: Donald Danforth Plant Science Center, St. Louis, MO 63132, USA.
authors.forename: Melinda S
authors.initials: MS
authors.lastname: Wilson
authors.affiliation: Donald Danforth Plant Science Center, St. Louis, MO 63132, USA.
authors.forename: Christine
authors.initials: C
authors.lastname: Shyu
authors.affiliation: Donald Danforth Plant Science Center, St. Louis, MO 63132, USA.
authors.forename: Douglas W
authors.initials: DW
authors.lastname: Bryant
authors.affiliation: Donald Danforth Plant Science Center, St. Louis, MO 63132, USA.
authors.forename: Steven T
authors.initials: ST
authors.lastname: Hill
authors.affiliation: Donald Danforth Plant Science Center, St. Louis, MO 63132, USA.
authors.forename: Colton J
authors.initials: CJ
authors.lastname: McEntee
authors.affiliation: Donald Danforth Plant Science Center, St. Louis, MO 63132, USA.
authors.forename: Sankalpi N
authors.initials: SN
authors.lastname: Warnasooriya
authors.affiliation: Donald Danforth Plant Science Center, St. Louis, MO 63132, USA.
authors.forename: Indrajit
authors.initials: I
authors.lastname: Kumar
authors.affiliation: Donald Danforth Plant Science Center, St. Louis, MO 63132, USA.
authors.forename: Tracy
authors.initials: T
authors.lastname: Ficor
authors.affiliation: Donald Danforth Plant Science Center, St. Louis, MO 63132, USA.
authors.forename: Stephanie
authors.initials: S
authors.lastname: Turnipseed
authors.affiliation: Donald Danforth Plant Science Center, St. Louis, MO 63132, USA.
authors.forename: Kerrigan B
authors.initials: KB
authors.lastname: Gilbert
authors.affiliation: Donald Danforth Plant Science Center, St. Louis, MO 63132, USA.
authors.forename: Thomas P
authors.initials: TP
authors.lastname: Brutnell
authors.affiliation: Donald Danforth Plant Science Center, St. Louis, MO 63132, USA.
authors.forename: James C
authors.initials: JC
authors.lastname: Carrington
authors.affiliation: Donald Danforth Plant Science Center, St. Louis, MO 63132, USA.
authors.forename: Todd C
authors.initials: TC
authors.lastname: Mockler
authors.affiliation: USDA-ARS, Donald Danforth Plant Science Center, St. Louis, MO 63132, USA. Electronic address: ivan.baxter@ars.usda.gov.
authors.forename: Ivan
authors.initials: I
authors.lastname: Baxter
mesh_terms: D019295:Computational Biology; D010641:Phenotype; D032983:Setaria Plant / Q000378:metabolism*; D014867:Water / Q000378:metabolism*
chemical_list: D014867:Water
keywords: abiotic/environmental stress; bioinformatics; development; phenotyping; water relations