Comparative gene regulatory network mapping of Brassicaceae members with differential drought tolerance

Pandiarajan, R.; Lin, C.-W.; Sauer, M.; Rothballer, S. T.; Marin-de la Rosa, N.; Schwehn, P.; Papadopoulou, E.; Mairhormann, B.; Falter-Braun, P.

doi:10.1101/2025.08.24.668636

bioRxiv · 10.1101/2025.08.24.668636

Comparative gene regulatory network mapping of Brassicaceae members with differential drought tolerance

Pandiarajan, R.·Lin, C.-W.·Sauer, M.·Rothballer, S. T.·Marin-de la Rosa, N.·Schwehn, P.·Papadopoulou, E.·Mairhormann, B.·Falter-Braun, P.

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Abstract

Climate change is projected to intensify weather extremes like droughts that threaten global crop yields. While many crops are sensitive to water deprivation, they have drought-tolerant wild relatives; however, the molecular basis for this differential tolerance among closely related species remains unclear. We previously investigated this using transcriptomics in the Brassicaceae family, comparing the drought-sensitive reference plant Arabidopsis thaliana (Ath) with its drought-tolerant relatives Arabidopsis lyrata (Aly) and Eutrema salsugineum (Esa), uncovering key differences that may underlie their respective phenotypes. Here, to elucidate the regulatory architecture driving these differences, we mapped drought-responsive gene regulatory networks (GRNs) for all three species using the yeast one-hybrid (Y1H) approach. We cloned promoters of orthologs with divergent drought-induced expression patterns and screened them against the Ath transcription factor (TF) collection, generating a quality-controlled cross-species drought-responsive GRN map encompassing 1,137 high-confidence TF-promoter interactions. Comparative analysis revealed that the tolerant species share greater regulatory similarity and exhibit higher network connectivity than Ath. An Esa-specific expansion of bZIP TF interactions was observed, consistent with an enrichment of G-box motifs in its genome and in drought-upregulated genes. Several observed changes affect the ABA signalling pathway: Ath gained a susceptibility linked GBF3-CYP707A1 edge, whereas Esa acquired tolerance associated ABF-mTERF10 interactions. Furthermore, network-rewiring analysis uncovered a novel role for ASIL2 in stress response. Finally, our network highlights TFs (CSDP1, ERF4, HB6, and MYB73) that likely contribute to the "stress-primed" state of Aly and Esa. Our work provides a broadly applicable framework for comparative GRN mapping and a valuable resource for improving drought tolerance in crops.

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Pandiarajan, R., Lin, C.-W., Sauer, M., Rothballer, S. T., Marin-de la Rosa, N., Schwehn, P., Papadopoulou, E., Mairhormann, B., Falter-Braun, P.. 2025-08-25. Comparative gene regulatory network mapping of Brassicaceae members with differential drought tolerance. https://doi.org/10.1101/2025.08.24.668636

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