Higher temperatures across the globe are causing an increase in the frequency and severity of droughts. In agricultural crops, this results in reduced yields, financial losses for farmers, and increased food costs at the supermarket. Root architecture plays a major role in a plant’s ability to survive and perform under drought conditions but phenotyping root growth to determine the genetic and environmental factors involved is extremely difficult due to roots being under the soil. RootBot is an automated high-throughput phenotyper that eliminates many of the difficulties and time constraints for performing multiple drought-stress studies. RootBot can simulate plant growth conditions during the first 72 hours of growth using transparent plates filled with soil (as opposed to synthetic media such as agar). RootBot has the capacity for up to 50 plates at a time, however, designing a system to organize these plates, image them at the appropriate times, and save and analyze the data for many plates simultaneously is challenging. To improve upon the pipeline, we incorporate strategies from existing phenotyping pipelines into the imaging and measurement processes. We will also investigate the genotypes using GWAS to identify sequence variants associated with drought tolerance or lack thereof. This pipeline will improve RootBot’s abilities in high-throughput phenotyping and the information gathered will be helpful towards future genetic engineering and breeding.

Anthropogenic factors such as climate change, harsh agricultural practices, and mining have contributed to increases in soil salinization and heavy metal contamination. Highly saline environments drastically lower yield for crop species and elevated levels of toxic metals like cadmium are carcinogenic in the environment. Some plants that have evolved in high-salinity habitats or in soils with heavy metals could be used to remediate contaminated soils. Halophytes are plants with various adaptations that allow them to survive and reproduce in saline conditions. General mechanisms for salt tolerance/uptake in halophytes are hypothesized to help deal with other stresses like heavy metals. Plants with these traits could be utilized to extract salt and heavy metals from affected soils in a process called phytoremediation. We plan to develop Sea Rocket (Cakile maritima) in the Mustard family as a model system to understand mechanisms of salt (NaCl) and cadmium uptake and tolerance, as it has been shown to accumulate both. As part of this study, we will hydroponically grow C. maritima in different stress treatments using salt and cadmium. As the plants uptake the pollutants, the conductivity of the solution will change. We will develop an automated pipeline to track these changes in real-time using conductivity sensors. In addition, we will sample root and leaf tissues at various time points to measure salt and cadmium uptake using ICP-OES elemental analysis. This data will provide insights into salt and cadmium uptake/tolerance and paves a path toward efficient and viable solutions improving phytoremediation approaches.

Generating data has become cheaper and easier, but alone is not sufficient to answer biological questions – data must be analyzed and interpreted. However, many algorithms can create or exacerbate biases (e.g., facial-recognition, ancestry, and disease risk). This necessitates incorporating diverse perspectives to confront both the moral and technical “big data challenges”. To move to a future where this is possible, it is necessary for researchers to develop skills in data management, processing, and analytics. Specifically, the field of plant phenotyping has moved from time consuming hand measurements to the use and development of high-throughput phenotyping. These systems require data-enabled/fluent users, yet academic programs in biology do not provide sufficient data science training. Here we present the Bioinformatics in Plant Science (BIPS) program at the University of Missouri (MU) as a model for training the next generation of data-enabled/fluent scientists. BIPS aims to mentor undergraduate students to build foundational skills in plant biology, research, and computational science. Our program pairs biology and computer science students to address biological questions through computational methods, with many focusing on plant phenotyping methods. The students learn to tackle problems using multidisciplinary approaches, alongside learning how to work in teams while building science communication skills (e.g., professional conferences, research forums, presenting to lawmakers). Through peer learning, BIPS students can understand and incorporate diverse perspectives from both the biological and computational side to address one of NSF’s 10 big ideas: harnessing the data revolution.

Anthropogenic factors such as climate change, harsh agricultural practices, and mining have contributed to increases in soil salinization and heavy metal contamination. Highly saline environments drastically lower yield for crop species and elevated levels of toxic metals like cadmium are carcinogenic in the environment. Some plants that have evolved in high-salinity habitats or in soils with heavy metals could be used to remediate contaminated soils. Halophytes are plants with various adaptations that allow them to survive and reproduce in saline conditions. General mechanisms for salt tolerance/uptake in halophytes are hypothesized to help deal with other stresses like heavy metals. Plants with these traits could be utilized to extract salt and heavy metals from affected soils in a process called phytoremediation. We plan to develop Sea Rocket (Cakile maritima) in the Mustard family as a model system to understand mechanisms of salt (NaCl) and cadmium uptake and tolerance, as it has been shown to accumulate both. As part of this study, we will hydroponically grow C. maritima in different stress treatments using salt and cadmium. As the plants uptake the pollutants, the conductivity of the solution will change. We will develop an automated pipeline to track these changes in real-time using conductivity sensors. In addition, we will sample root and leaf tissues at various time points to measure salt and cadmium uptake using ICP-OES elemental analysis. This data will provide insights into salt and cadmium uptake/tolerance and paves a path toward efficient and viable solutions improving phytoremediation approaches.