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AI is creating new plants that can help fight climate change

By focusing on root systems, researchers aim to create new plants, using an artificial intelligence (AI) tool called SLEAP, that can store more carbon for extended periods.

For this intriguing new study, scientists are leveraging AI to optimize plants’ natural ability to draw carbon dioxide out of the atmosphere, a crucial step in combating climate change and limiting global temperature rise.

SLEAP: Game-changing AI tool that creates plants

Talmo Pereira and Professor Wolfgang Busch from Salk’s Harnessing Plants Initiative have joined forces to apply SLEAP, a sophisticated AI software initially designed for tracking animal movement, to the study of plants.

Their research introduces a new protocol for using SLEAP to analyze plant root phenotypes, such as depth, width, and mass.

“This collaboration is truly a testament to what makes Salk science so special and impactful,” says Pereira. “We’re not just ‘borrowing’ from different disciplines — we’re really putting them on equal footing in order to create something greater than the sum of its parts.”

Streamlining plant analysis with AI

Prior to SLEAP, analyzing plant and animal characteristics was a labor-intensive process that slowed scientific progress.

Researchers had to manually flag parts of images frame-by-frame, part-by-part, and pixel-by-pixel before older AI models could process the data.

SLEAP’s unique combination of computer vision and deep learning allows researchers to skip this intermediary step, jumping straight from image input to defined plant features.

This approach significantly reduces analysis time and human error while emphasizing accessibility and ease of use.

sleap-roots: Digging deep into plant biology

The Salk team developed sleap-roots, a downloadable toolkit for SLEAP that enables the software to process biological traits of root systems, such as depth, mass, and angle of growth.

The toolkit, available as open-source software, was tested on various plants, including soybeans, rice, canola, and Arabidopsis thaliana.

“We 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 — and it required no changes to the actual SLEAP software,” says Elizabeth Berrigan, a bioinformatics analyst in Busch’s lab.

Deciphering the secrets of climate-saving plants

By connecting phenotypic data, such as a plant’s deep root system, with genotype data obtained through genome sequencing efforts, researchers can identify the genes responsible for creating desirable traits.

This step is crucial in Salk’s mission to create plants with AI that hold on to more carbon for longer periods, as these plants will require root systems designed to be deeper and more robust.

“We have already been able to create the most extensive catalogue of plant root system phenotypes to date, which is really accelerating our research to create carbon-capturing plants that fight climate change,” says Busch, the Hess Chair in Plant Science at Salk.

“SLEAP has been so easy to apply and use, thanks to Talmo’s professional software design, and it’s going to be an indispensable tool in my lab moving forward,” Busch concluded.

Understanding the hidden world of plant root systems

To further clarify, plant root systems are intricate networks of roots that play a crucial role in anchoring plants to the soil, absorbing water and nutrients, and storing essential compounds.

There are two main types of root systems exist in plants: taproot systems and fibrous root systems.

  • Taproot systems feature a single, dominant root that grows vertically downward, with smaller lateral roots branching off from it.
  • Fibrous root systems, on the other hand, consist of numerous small roots that grow outward from the base of the plant, forming a dense network.

Functions of root systems

Root systems perform several critical functions for plants:

  • Anchoring: Roots secure plants to the soil, providing stability and preventing them from toppling over.
  • Absorption: Fine root hairs absorb water and dissolved nutrients from the soil, which are then transported to the rest of the plant.
  • Storage: Some plants, such as carrots and beets, use their roots to store carbohydrates and other essential compounds.

Factors influencing root growth

Several factors influence the growth and development of plant root systems:

  • Soil type: Different soil types, such as sandy, loamy, or clay soils, affect root growth and distribution.
  • Water availability: Plants adapt their root systems in response to water availability, with some species growing deeper roots to access water in times of drought.
  • Nutrient availability: The presence or absence of essential nutrients in the soil can impact root growth and architecture.

Healthy root systems are essential for overall plant health and productivity. Well-developed roots enable plants to efficiently absorb water and nutrients, leading to stronger growth and increased resilience to stresses such as drought or disease.

AI and the future of climate-saving plants

The accessibility and reproducibility of SLEAP and sleap-roots have the potential to revolutionize plant research worldwide. The Salk team has already begun discussions with NASA scientists hoping to utilize the tool to guide carbon-sequestering plants on Earth and to study plants in space.

In summary, the Salk Institute’s pioneering research in plant-based carbon capture, powered by the innovative SLEAP software and sleap-roots toolkit, paves the way for a greener future.

As scientists continue to refine and expand these tools, they accelerate the development of climate-saving plants with optimized root systems capable of storing more carbon for longer periods.

The accessibility and reproducibility of SLEAP and sleap-roots invite researchers worldwide to join the fight against climate change, fostering global collaboration and innovation.

With the Harnessing Plants Initiative at the forefront, Salk scientists are rooting for change, digging deep into plant biology, and branching out to make a lasting impact on our planet’s future.

The full study was published in the journal Plant Phenomics.


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