Plant roots play a pivotal role in the survival and growth of nearly all terrestrial plants. They are responsible for water and nutrient uptake, anchoring the plant, and can serve as storage organs. Many of these functions are intimately linked to the spatial distribution of roots within a root system in the soil. 

This spatial configuration is defined as root system architecture (RSA). RSA indicates the volume of soil explored by a root system and the root surface area that is the interface between roots and soil. Therefore, RSA is crucial for the uptake of nutrients and water, resources distributed non-uniformly in the soil, and it is linked to plant survival and productivity.

The Intergovernmental Panel on Climate Change (IPCC) has declared that removing carbon from the atmosphere is now essential to fighting climate change and limiting the rise in global temperature. To support these efforts, Salk Institute scientists are harnessing plants’ natural ability to draw carbon dioxide out of the air by optimizing their root systems to store more carbon for an extended period of time.

Climate saving plants

To design climate-saving plants, scientists in Salk’s Harnessing Plants Igniting are leveraging a new research tool called SLEAP. It is an easy-to-use artificial intelligence (AI) software that tracks multiple features of root growth. SLEAP is created by Salk Fellow Talmo Pereira. Initially designed to track animal movement in the lab, Pereira has teamed up with plant scientist and Salk colleague Professor Wolfgang Busch to apply SLEAP to plants.

Busch and Pereira debuted a new protocol for using SLEAP to analyze plant root phenotypes in a study published in Plant Phenomics. It explained how deep and wide they grow, how massive their root systems become, and other physical qualities that—before SLEAP—were tedious to measure. The application of SLEAP to plants has already enabled researchers to establish the most extensive catalogue of plant root system phenotypes to date.

Furthermore, tracking these physical root system characteristics helps scientists find genes affiliated with those characteristics and determine whether multiple root characteristics are determined by the same genes or independently. It aids Salk Tea in determining which genes are most beneficial to their plant designs.

According to Pereira, this collaboration is truly a testament to what makes Salk science unique and impactful. They are not just ‘borrowing’ from different disciplines but putting them on equal footing to create something greater than the sum of its parts.

Different approach

SLEAP differs from other tools due to its unique use of computer vision (the ability of computers to understand images) and deep learning (an AI approach for training a computer to learn and work like the human brain). This combination allows researchers to process images without moving pixel by pixel, instead skipping this intermediate labour-intensive step to jump straight from image input to defined plant features.

According to the study’s first author, Elizabeth Berrigan, they created a robust protocol validated in multiple plant types that cuts down on analysis time and human error while emphasizing accessibility and ease of use. It required no changes to the actual SLEAP software.

The researchers already created the most extensive catalogue of plant root system phenotypes to date, accelerating our research to develop carbon-capturing plants that fight climate change. The researchers are now in conversation with NASA, hoping to utilize the tool not only to help guide carbon-sequestering plants on Earth but also to study plants in space.

Phys Org

Plant Phenomics

Image: Unsplash