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bioRxiv · 10.1101/2025.09.03.673899

A multigenic quantitative trait locus underlies natural variation in Arabidopsis thaliana root system architecture and transcriptional responses to microbiota-derived Pseudomonas

Copeland, C.·Logemann, E.·Malisic, M.·Amrhein, A.·Valisi, A.·Schulze-Lefert, P.
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Abstract

Plants interact with structured microbial communities called the microbiota, which can have a profound impact on plant growth and health. However, how plants perceive and respond to specific core microbiota members at a molecular level is still unclear. We identified natural variation in Arabidopsis thaliana root responses to bacterial strains of the genus Pseudomonas, a core genus of the plant microbiota. Some A. thaliana accessions such as Van-0 show strong root responses to Pseudomonas strains, including changes in root system architecture and transcriptional reprogramming. Through a forward genetic screen using Pseudomonas isolate R569, we found that the nuo NADH dehydrogenase complex, part of the bacterial electron transport chain, contributes to the bacterial activity on Van-0 roots. Using recombinant inbred lines, we further mapped a multigenic quantitative trait locus in the host that is associated with the root responses. In Van-0, the exocyst subunit EXO70E2 positively contributes to the response, while Col-0 haplotypes of malectin-like and leucine-rich-repeat domain-containing receptor-like kinases play an inhibitory role. The identification of these components in the bacteria and the host establishes a genetic framework for how root developmental plasticity is integrated with the microbe-rich soil environment and is subject to intraspecific natural variation.

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Copeland, C., Logemann, E., Malisic, M., Amrhein, A., Valisi, A., Schulze-Lefert, P.. 2025-09-05. A multigenic quantitative trait locus underlies natural variation in Arabidopsis thaliana root system architecture and transcriptional responses to microbiota-derived Pseudomonas. https://doi.org/10.1101/2025.09.03.673899

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