KVL Collaborates on Plant Biology Publication

Overview

KVL collaborated with Professor Mark Tester (KAUST) and Prof. Magdalena Julkowska (Boyce Thompson Insitute) and others resulting in a recent publication in eLife Sciences journal. The paper titled "Natural variation in salt-induced changes in root:shoot ratio reveals SR3G as a negative regulator of root suberization and salt resilience in Arabidopsis" identified and studied the Salt Root:Shoot Ratio Regulator Gene (SR3G) that is involved in plants' loss of coordination between roots and shoots growth rates when exposed to salt stress. Ronell Sicat, a KVL scientist, developed PlantSeg - an open-source Matlab app that was developed for this particular research project that helped segment and analyze hundreds of plant root/shoot images used in the study. The paper is available with below details:

Maryam Rahmati Ishka, Hayley Sussman, Yunfei Hu, Mashael Daghash Alqahtani, Eric Craft, Ronell Sicat, Minmin Wang, Li'ang Yu, Rachid Ait-Haddou, Bo Li, Georgia Drakakaki, Andrew DL Nelson, Miguel Pineros, Arthur Korte, Łukasz Jaremko, Christa Testerink, Mark Tester, Magdalena M Julkowska (2025) Natural variation in salt-induced changes in root:shoot ratio reveals SR3G as a negative regulator of root suberization and salt resilience in Arabidopsis eLife 13:RP98896. https://doi.org/10.7554/eLife.98896.4.

The open-source Matlab tool can be found in github: https://github.com/ronellsicat/PlantSeg. The tool uses color space partitioning for segmentation, and also provides simple manual segmentation tools for proofreading. Results are also automatically exported to csv files for easy access for post-processing and analysis. Technical details and algorithms used in the tool are described in this document.