Salk Institute researchers are making the first attempt to engineer climate-resistant crops to combat climate change and prevent global temperature rises.
Using plants’ natural ability to absorb carbon dioxide from the atmosphere, scientists are developing root systems to store carbon more efficiently and for longer periods of time.
At the forefront of this initiative is the development of SLEAP, an innovative artificial intelligence program designed to track animal behavior in laboratory settings.
Adapted for plant research by Salk Fellow Talmo Pereira and Professor Wolfgang Busch, SLEAP enables comprehensive monitoring of various root growth characteristics important for carbon uptake.
Scientists use SLEAP to closely examine root phenotypes, revealing intricate details such as root depth, width, and other physical characteristics that were previously difficult to detect.
These findings help create an extensive catalog of plant root system phenotypes, allowing researchers to identify genes associated with traits needed to engineer climate-tolerant plants.
Elizabeth Berrigan, a bioinformatics analyst involved in the work, emphasized the efficiency and accessibility of the protocol developed for SLEAP, which significantly reduces analysis time and reduces human error.
In addition, the team has made the SLEAP toolkit available as open source software, increasing its applicability to various plant species.
The efficiency of the SLEAP-based approach has been confirmed to be superior to previous methods on model organisms such as Arabidopsis thaliana and on various plant species including canola, rice, and soybeans.
In particular, the SLEAP-based methodology has demonstrated higher speed and accuracy in annotation, AI model training, and plant structure prediction, marking a new era in plant research.
Salk Fellow Talmo Pereira said, “This partnership is a testament to how unique and influential Salk’s science is. We don’t just “borrow” from different disciplines, we actually give equal rights to create something greater than the sum of its parts.”
Combining genotype and phenotype data is considered essential for engineering plants with advanced carbon storage capabilities.
By seamlessly linking desired phenotypes to gene targeting, researchers aim to accelerate the development of plants with deeper and stronger root systems, which are essential for long-term carbon uptake.
Pereira focused on reproducibility and accessibility in the development of SLEAP and Roots, both tools are freely available for global use.
Researchers are exploring collaborations with NASA scientists to demonstrate the potential global impact of their work to study vegetation in space and use these tools to aid carbon research efforts on Earth.
Salk colleague Professor Wolfgang Busch said: “We have been able to create the most extensive catalog of plant root system phenotypes to date, which really accelerates our research into creating carbon sequestering plants that combat climate change. Thanks to Talmo’s professional software design, SLEAP is easy use and use, and it will be an important tool in my lab moving forward.”
