Phenotyping

An essential part of plant science is understanding how plants respond to their environment. One way our scientists can measure this is by monitoring a plant’s phenotype, such as leaf size and shape, root structure, growth rate in particular conditions, and more. In our Phenotyping Facility, the first of its kind at an academic research institute in the U.S., our scientists are able to gather an unprecedented amount of data about the plants they are studying. This data is used to develop improved and sustainable crops that are better able to withstand conditions like drought and extreme temperatures.

Bellwether Foundation Phenotyping Facility

The Bellwether Foundation Phenotyping Facility is an integrated growth chamber and imaging facility.

Applications: The Bellwether Facility provides high capacity, high-throughput phenotyping in a controlled environment to characterize how plants respond to different environments, treatments, and genetics. Results include information related to plant growth, plant development, and plant stress responses.

Conviron Growth House

Weighing and Watering

Daily Imaging

Additional Phenotyping Facility & Services

Plant Ditech Array

Applications: The Ditech PlantArray characterizes plant-water relationships, including transpiration rates, plant biomass and vigor, plant growth rates, water use efficiency, and more. This data is most useful for understanding how plant genetics and/or environmental factors affect plant growth and water use.

Description: The Ditech PlantArray System consists of two controlled-environment chambers, each with 20 units, for a total capacity of 40 plants. State-of-the-art chambers allow for precise control of two environments as well as individual treatment of water and nutrient applications to each plant to allow environmental stress application of temperature, humidity, water, nutrients, and more. Each of the 20 units provides customizable watering and other soil sensor data as well as a record of the individual plant weight and water use every 3 minutes.

PhenoVation CropReporter

Applications: The Crop Reporter provides quantification of important plant health parameters related to photosynthesis, including photosystem II efficiency, non-photochemical quenching, chlorophyll index, anthocyanin index, and plant color. Because it is a stand-alone, multi-spectral imaging unit, plants can be brought to the camera and imaged as needed rather than in the plant growth location.

Description: Whole plant, LED-induced, direct fluorescence imaging in dark-or-light-adapted conditions enables quantification of important plant health parameters visualized and quantified in a whole-plant image. Self-service and full-service options are available.

Image Analysis Software

LiCor LI-6400XT Portable Photosynthesis System

Applications: The LiCor LI-6400XT provides quantification of plant photosynthesis to determine the effect of plant genetics, product application, and environmental or biotic stress applications.

Description: This portable gas exchange system measures carbon assimilation, stomatal conductance, and more aspects of photosynthesis in a small chamber that clamps onto a leaf surface. This unit is equipped to measure leaf fluorescence for measurements of photosynthetic efficiency. Self-service and full-service options are available.

Ocean Optics FLAME VIS-NIR Spectrometer

Applications: The VIS-NIR Spectrometer provides portable measurements of plant leaf color characteristics in both the visible and near-infrared ranges. These measurements can be used to quantify differences attributed to plant genetics, management, and stress applications.

Description: This handheld device provides measurements of plant reflectance and absorbance. Wavelengths measured range from 350nm - 1μm, with an optical resolution of 1.34 nm FWHM. Self-service and full-service options are available.

Extended Services

Publications

Acknowledgments

In order to track our impact and productivity, the Phenotyping Facility appreciates acknowledgment in your publications and poster presentations as follows:

Generic Acknowledgment

”We wish to thank (staff name here) from the Bellwether Phenotyping Facility (RRID:SCR_019049) at the Donald Danforth Plant Science Center for support with (support provided)…”.

If contributions go beyond our standard fee-for-service support, including significant intellectual contribution and/or manuscript preparation, Phenotyping support staff should be considered for co-authorship.

Core facilities must charge for services rendered according to cost accounting practices set up at each institution. Charging for services does not preclude authorship on manuscripts provided the Core laboratory individual has contributed to the research in a substantial way. If authorship is anticipated, it is preferably established at the beginning of the project so that both the customer and the Core researcher are cognizant of each other’s criteria.

Important reasons for acknowledging contributions from core facilities in publications, by co-authorship or by formal mention in the acknowledgments section, include:

Core facility personnel are scientists. When they make a substantial intellectual and/or experimental contribution to a publication they deserve to be acknowledged just as any other co-author.
The existence of core facilities depends in part on proper acknowledgment in publications. This is an important metric of the value of most core facilities. Proper acknowledgment of core facilities enables them to obtain financial and other support so that they may continue to provide their essential services in the best ways possible. It also helps core personnel to advance in their careers, adding to the overall health of the core facility.

Authorship Guidelines

Activities for which authorship are recommended:

Author should make substantive contributions to the project
- Conception, design of project, critical input, or original ideas
- Acquisition of data, analysis and interpretation, beyond routine practices
- Draft the article or revise it critically for intellectual content
- Write a portion of the paper (not just materials and methods section)
- Intellectual contribution
- Final authority for the approval of article
Each author should have participated enough to accept responsibility for the content of the manuscript

The following activities do not represent intellectual contributions to a project and would not constitute authorship:

Providing funding (department chair who has no intellectual input)
Collection of data (technical skill but not involved in interpretation of data)
General supervision of research group, but no intellectual input into the project

All contributors that do not meet the criteria of authorship should be recognized in the acknowledgements section, for example:

Paid technical help
Writing assistance
Financial and material support
Scientific advice

Two examples are pertinent: (from Robert A. Day: How to Write and Publish a Scientific Paper, 5th Edition)

Example 1: Scientist A designs the experiments, and tells Technician B exactly how to do the experiments. If the experiments work and a new discovery is made and a manuscript results, Scientist A is the sole author and Technician B is recognized in the acknowledgements section.

Example 2: Scientist A designs the experiments, Technician B carries them out but they do not work. Technician B suggests some changes to the protocol, the experiments then work because of the changes and a discovery results. Scientist A and Technician B are now both authors.

Publications using our Facility

Abbasi, Arash, and Noah Fahlgren. “Naïve Bayes Pixel-Level Plant Segmentation.” 2016 IEEE Western New York Image and Signal Processing Workshop (WNYISPW), 2016, pp. 1–4, https://doi.org/10.1109/WNYIPW.2016.7904790.

Berry, Jeffrey C., et al. “An Automated, High-Throughput Method for Standardizing Image Color Profiles to Improve Image-Based Plant Phenotyping.” PeerJ, vol. 6, Oct. 2018, p. e5727, https://doi.org/10.7717/peerj.5727.

Casto, Anna, et al. “Analyzing Chlorophyll Fluorescence Images in PlantCV.” Earth and Space Science Open Archive, 17 Oct. 2021, https://doi.org/10.1002/essoar.10508322.2.

Ellsworth, Patrick Z., et al. “A Genetic Link between Leaf Carbon Isotope Composition and Whole-Plant Water Use Efficiency in the C4 Grass Setaria.” The Plant Journal: For Cell and Molecular Biology, vol. 102, no. 6, June 2020, pp. 1234–48, https://doi.org/10.1111/tpj.14696.

Fahlgren, Noah, et al. “A Versatile Phenotyping System and Analytics Platform Reveals Diverse Temporal Responses to Water Availability in Setaria.” Molecular Plant, vol. 8, no. 10, Oct. 2015, pp. 1520–35, https://doi.org/10.1016/j.molp.2015.06.005.

Feldman, Max J., Patrick Z. Ellsworth, et al. “Components of Water Use Efficiency Have Unique Genetic Signatures in the Model C4 Grass Setaria.” Plant Physiology, vol. 178, no. 2, Oct. 2018, pp. 699–715, https://doi.org/10.1104/pp.18.00146.

Feldman, Max J., Rachel E. Paul, et al. “Time Dependent Genetic Analysis Links Field and Controlled Environment Phenotypes in the Model C4 Grass Setaria.” PLoS Genetics, vol. 13, no. 6, June 2017, p. e1006841, https://doi.org/10.1371/journal.pgen.1006841.

Gehan, Malia A., et al. “PlantCV v2: Image Analysis Software for High-Throughput Plant Phenotyping.” PeerJ, vol. 5, Dec. 2017, p. e4088, https://doi.org/10.7717/peerj.4088.

Polydore, Seth, and Noah Fahlgren. “Phenotypic Analysis of a European Camelina Sativa Diversity Panel.” Earth and Space Science Open Archive, 18 Oct. 2021, https://doi.org/10.1002/essoar.10508336.2.

Qi, Mingsheng, et al. “Identification of Beneficial and Detrimental Bacteria Impacting Sorghum Responses to Drought Using Multi-Scale and Multi-System Microbiome Comparisons.” The ISME Journal, vol. 16, no. 8, Aug. 2022, pp. 1957–69, https://doi.org/10.1038/s41396-022-01245-4.

Shakoor, Nadia, et al. “Genomewide Association Study Reveals Transient Loci Underlying the Genetic Architecture of Biomass Accumulation under Cold Stress in Sorghum.” bioRxiv, 8 Sept. 2019, p. 760025, https://doi.org/10.1101/760025.

Ubbens, Jordan, et al. “Latent Space Phenotyping: Automatic Image-Based Phenotyping for Treatment Studies.” Plant Phenomics (Washington, D.C.), vol. 2020, Jan. 2020, p. 5801869, https://doi.org/10.34133/2020/5801869.

Veley, Kira M., et al. “High-Throughput Profiling and Analysis of Plant Responses over Time to Abiotic Stress.” Plant Direct, vol. 1, no. 4, Oct. 2017, p. e00023, https://doi.org/10.1002/pld3.23.

Facility Fees

The Phenotyping Facility offers competitive pricing for commercial and academic clients, with additional discounts for small businesses. For current pricing, please contact Katie Murphy, Director of Phenotyping and Principal Investigator.

Contact Katie