Funded and Preparing!

Hello everyone! First of all, thank you so much to those that contributed to our successful campaign. We are waiting for the funds to arrive still, but once they do we'll immediately place our order for the FarmBots. In the meantime, we have identified the greenhouse we will be installing them in, obtained all necessary approvals, added some new collaborators to the team, and also written an additional grant proposal for funding via three sources:

•  Michigan State University Project GREEEN - two years of funding ~$50,000/year

•  NSF Graduate Research Fellowship Program (GRFP) - three years of funding ~$53,000/year

•  Michigan State University Plant Science Fellowship - up to two years of funding ~$31,000

Below is a copy of the most recent proposal for those interested:

I. PROJECT SUMMARY

Phlox is highly susceptible to powdery mildew, impacting plant health and increasing fungicide use. While resistance differs between varieties, the molecular mechanisms of age-related resistance are poorly understood due to a lack of affordable phenotyping tools. This research will develop open-source, scalable phenotyping platforms using Phlox as a novel model system, integrating tools like FarmBot to create accessible methods for studying complex traits and advancing plant science while elucidating the genetic basis for powdery mildew resistance by screening popular Phlox varieties and naturally occurring species rare in the horticultural trade. II. PROBLEM STATEMENT

Phlox is a popular ornamental genus, native to North America, within the horticultural trade, but its popularity has waned because of its susceptibility to powdery mildew (Erysiphe cichoracearum). The movement of infected materials through trade accelerates the risk of disease spread exponentially (Armitage, 2008). Plants that are affected display a powdery growth of fungal colonies on the surface of flowers, leaves, and stems that reduce the plant’s photosynthetic ability and decrease its overall attractiveness (Figure 1; McGrath & Shishkoff, 2001).

 

Due to the high degree of susceptibility to the disease, Phlox cultivation heavily relies on the use of fungicides that are both ecologically and economically expensive and must be applied every 10 to 14 days throughout the growing season to protect the ornamental value (Armitage, 2008). In 2019 Phlox accounted for over $12 million (~1.6%) of annual sales of herbaceous perennial plants in the United States with Michigan being the 5th most profitable state for the crop ($637,282 in sales), but the economic impact of powdery mildew on these sales is entirely unknown (USDA, National Agricultural Statistics Service, 2019). While resistance differs between varieties, the molecular mechanisms of age-related (ontogenic) resistance are poorly understood largely due to a lack of affordable phenotyping tools (Farinas et al., 2020; Ficke et al., 2002). Additionally, relatively few wild species have been tested, leaving gaps in understanding the genetic basis of resistance across the genus. High throughput phenotyping has been pioneered for large scale crop applications with great success (Araus & Cairns, 2014). However, specialty crops, particularly ornamental varieties, are rarely grown at the scale necessary to implement these sorts of studies or the tools required to make them high throughput can be prohibitively expensive (Iqbal, 2020). Here we propose a merging of methods in engineering, ecology, and horticulture, with adaptability and modularity at the forefront, to develop new tools that can be used across diverse research and education environments and with a wide range of plant systems. By further developing the FarmBot system (Figure 2) we will conduct the first genome-wide association study for powdery mildew resistance in Phlox addressing challenges in horticultural and agricultural systems (Aronson, 2013; Uffelmann et al., 2021).

 

III. SPECIFIC OBJECTIVES AND HYPOTHESES

• Objective 1: Develop FarmBot into a flexible open-source system for high-throughput phenotyping

• Objective 2: Perform a genome-wide association study of ontogenic resistance to powdery mildew

• Objective 3: Identify new sources of ontogenic resistance using less-frequently cultivated species

• Objective 4: Quantify the economic impact of powdery mildew on Phlox production in the US and evaluate the cost-effectiveness of integrating the upgraded FarmBot system into cultivation practices.

IV. SPECIFIC METHODS AND PROCEDURES

Objective 1: Develop FarmBot into a flexible open-source system for high-throughput phenotyping

Powdery mildew fungi are obligate biotrophs capable of infecting diverse plant hosts including both agricultural and ornamental crops. In Phlox, infection is primarily recognized by the appearance of white powdery patches of fungal growth on the surface of infected tissues. Infected leaves remain on the plant until they turn yellow, slowly becoming necrotic, until they finally senesce and fall (Sombardier et al., 2009). Resistance to powdery mildew is ontogenetic (age-related) across different powdery mildew systems, for example strawberry and grape. This factor as well as the side of the leaf that the pathogen spores land on has a potential to influence powdery mildew growth. Because of the historic popularity of Phlox in the trade, many trials have been conducted to assess new cultivars for resistance to powdery mildew (Hawke, 2011). Infection sites are more likely on the abaxial (bottom) leaf surface in non-Phlox, but curling of the leaves makes high-throughput phenotyping of this trait difficult (Farinas et al., 2019).

FarmBot provides an affordable, high-throughput solution for automating plant care and data collection. By integrating FarmBot with our BAIR imaging system, we can precisely monitor plant growth, disease progression, and resistance over time while minimizing the time required for routine plant care (McNair et al., 2024). It will enable consistent and reproducible data collection, reducing human error and allowing for larger-scale studies.

We will develop protocol libraries for rapid phenotyping of seedlings and young plants exposed to powdery mildew using FarmBot and the BAIR imaging system. The current FarmBot platform does not allow for this type of flexible experimentation. By developing open-source reproducible protocols adapting FarmBot to track disease development at the whole plant level over time, we will produce a robust phenotyping ecosystem that is more reliable than assessing disease resistance by eye.

Objective 2: Perform a genome-wide association study of ontogenic resistance to powdery mildew

Genome-wide association studies (GWAS) test hundreds of thousands of genetic variants across many genomes to find those statistically associated with a specific trait. We plan to collect DNA and phenotypic information in cultivated populations of the popular species Phlox paniculata to genotype each individual using the available P. paniculata genome (Zale & Jourdan, 2015). We will then conduct an imputation of untyped variants using haplotype phasing and reference populations to complete a statistical test of association to ultimately conduct the GWAS (Uffelmann et al., 2021).

Objective 3: Identify new sources of ontogenic resistance using less-frequently cultivated species

Horticultural research suggests that powdery mildew resistance may be limited across the Phlox genus, but relatively few species have been tested (Hawke, 2011). We plan to grow multiple other species and use our upgraded FarmBots from Objective 1 to assess their disease resistance. By developing additional assays to determine the presence of ontogenic resistance in less cultivated species of Phlox we will demonstrate the flexibility of the FarmBot platform for assessing phenotypes across species. After infecting each Phlox species with powdery mildew, we will extract RNA from each specimen, generate cNDA, and prepare libraries for sequencing on a Next-Generation Sequencing platform (Katz et al., 2010). We will then analyze the sequences and determine whether differentially expressed genes overlap with those identified by the GWAS in Objective 2 elucidating potential genetic differences in disease resistance within the Phlox-powdery mildew pathosystem. Ultimately, these sequencing results will also be used to reconstruct a more complete phylogenetic understanding of the genus where taxonomy currently remains challenging and incomplete (Zale & Jourdan, 2015).

Objective 4: Quantify the economic impact of powdery mildew on Phlox production in the US and evaluate the cost-effectiveness of integrating the upgraded FarmBot system into cultivation practices.

The cost-effectiveness analysis will involve three key steps. First, baseline data will be collected on yield losses, quality degradation, and increased management expenses associated with powdery mildew in current production systems. Primary data will be collected from growers through a reconnaissance survey and secondary data, from national reports. These metrics will then be compared against outcomes in production systems utilizing FarmBot. Finally, costs related to implementing FarmBot, including acquisition, installation, maintenance, and operation, will be compared with the benefits, such as reduced labor costs, enhanced disease detection accuracy, minimized human error, and higher yields.

V. IMPACT

The identification of the genetic basis of powdery mildew resistance will create a new path forward for Phlox breeding in alignment with the Michigan Nursery and Landscape Industry’s New Plants Program priorities. The incorporation of disease resistant, non-traditional species into breeding programs identified as part of Objective 3 will also introduce novel genetics that could greatly improve ornamental qualities of future cultivars. With the inclusion of the resulting disease resistant varieties in the trade, chemical treatments for powdery mildew should decrease, increasing profit margin for growers.

Improvement of the FarmBot system will occur in the Michigan State University Horticultural Demonstration Gardens which sees greater than 11,000 children each year through the 4H Children’s Garden programming. We will incorporate the FarmBots into the existing curriculum for garden visitors and create dedicated signage educating visitors about this project and the importance of precision agriculture tools in modern horticulture. Coupling ecology and engineering approaches as we have proposed will advance our ability to address long-standing challenges in agricultural production and plant cultivation beyond those of ornamental Phlox. FarmBot’s open-source design aligns with the McNair lab’s goal of creating accessible research tools, fostering innovation, and lowering barriers for future plant research. By developing these low-cost precision agriculture systems, scientists from all backgrounds will be empowered to ask new questions, because of their newfound access to affordable cutting-edge tools and protocols.

VI. SCOPE

We have identified a Ph.D. student (Jazlyn Salazar) to begin working on this project in August 2025. We have secured additional funds ($9,000) to purchase three FarmBot Genesis units to improve the MSU Horticulture Teaching Greenhouses via the Experiment.com Plant Biology Exploratory Research Microgrant. This proposal will gather foundational information for our understanding of Phlox disease resistance and develop the basic tools necessary to turn the FarmBot into a reliable and affordable research platform. If funded, the data gathered from this proposal will support a 2027 NSF-POSE grant application. The objectives of this proposal will continue in this stream of research based on our findings, combining our backgrounds in horticulture, economics, and novel methods development to develop a robust, economically viable hardware ecosystem for plant research and the development of new plant varieties.

VII. TIMELINE

 

Funding from Project GREEEN will be the primary source of funding for this project during the first two years, during which preliminary data for Objectives 1, 2, and 4 will be collected. The entirety of Objective 2 is planned to be completed during the first two years. Additional funds have been awarded via the Experiment.com Plant Biology Research Micro Grant. Proposals for the NSF GRFP (submitted October 2024; decision March 2025) and the Michigan State University Plant Science Fellowship (up to 2 years of funding for PhD students) are currently pending. Data collected during the first two years across all four objectives will be used to support an NSF POSE submission in 2027.

VIII. LITERATURE CITED

Araus, J. L., & Cairns, J. E. (2014). Field high-throughput phenotyping: The new crop breeding frontier. Trends in Plant Science, 19(1), 52–61. https://doi.org/10.1016/j.tplants.2013.09.008

Armitage, A. M. (2008). Herbaceous Perennial Plants: A Treatise on their Identification, Culture, and Garden Attributes. Quarto Publishing Group USA.

Aronson, R. L. (2013). FarmBot Whitepaper. https://meta.farm.bot/v2024/farmbot/intro/whitepaper

Farinas, C., Jourdan, P., Paul, P. A., & Peduto Hand, F. (2019). Development and Evaluation of Laboratory Bioassays to Study Powdery Mildew Pathogens of Phlox In Vitro. Plant Disease, 103(7), 1536–1543. https://doi.org/10.1094/PDIS-01-19-0031-RE

Farinas, C., Jourdan, P. S., Paul, P. A., Slot, J. C., Daughtrey, M. L., Ganeshan, V. D., Baysal-Gurel, F., & Hand, F. P. (2020). Phlox Species Show Quantitative and Qualitative Resistance to a Population of Powdery Mildew Isolates from the Eastern United States. Phytopathology®, 110(8), 1410–1418. https://doi.org/10.1094/PHYTO-12-19-0473-R

Ficke, A., Gadoury, D. M., & Seem, R. C. (2002). Ontogenic Resistance and Plant Disease Management: A Case Study of Grape Powdery Mildew. Phytopathology®, 92(6), 671–675. https://doi.org/10.1094/PHYTO.2002.92.6.671

Hawke, R. G. (2011). A Comparative Study of Phlox paniculata Cultivars. Plant Evaluation Notes.

Iqbal, J. (2020). Simulation and Implementation of an Autonomous Differential-drive Mobile Robot for High Throughput Phenotyping [M.S., University of Georgia]. https://www.proquest.com/docview/2447039197/abstract/A8D4810528B8448FPQ/1

Katz, Y., Wang, E. T., Airoldi, E. M., & Burge, C. B. (2010). Analysis and design of RNA sequencing experiments for identifying isoform regulation. Nature Methods, 7(12), 1009–1015. https://doi.org/10.1038/nmeth.1528

McGrath, M. T., & Shishkoff, N. (2001). Resistance to Triadimefon and Benomyl: Dynamics and Impact on Managing Cucurbit Powdery Mildew. Plant Disease, 85(2), 147–154. https://doi.org/10.1094/PDIS.2001.85.2.147

McNair, M. C., Cocioba, S. S., Pietrzyk, P., & Rife, T. W. (2024). Toward an open-source 3D-printable laboratory. Applications in Plant Sciences, 12(1), e11562. https://doi.org/10.1002/aps3.11562

Sombardier, A., Savary, S., Blancard, D., Jolivet, J., & Willocquet, L. (2009). Effects of leaf surface and temperature on monocyclic processes in Podosphaera aphanis, causing powdery mildew of strawberry. Canadian Journal of Plant Pathology, 31(4), 439–448. https://doi.org/10.1080/07060660909507618

Uffelmann, E., Huang, Q. Q., Munung, N. S., de Vries, J., Okada, Y., Martin, A. R., Martin, H. C., Lappalainen, T., & Posthuma, D. (2021). Genome-wide association studies. Nature Reviews Methods Primers 2021 1:1, 1(1), 1–21. https://doi.org/10.1038/s43586-021-00056-9

USDA, National Agricultural Statistics Service. (2019). Census of Horticultural Specialties. https://www.nass.usda.gov/Publications/AgCensus/2017/Online_Resources/Census_of_Horticulture_Specialties/index.php

Zale, P. J., & Jourdan, P. (2015). Genome Size and Ploidy of Phlox paniculata and Related Germplasm in Subsections Paniculatae and Phlox. https://doi.org/10.21273/JASHS.140.5.436