Search bioRxiv⌕ Search
Home/Archive/bioRxiv

bioRxiv · 10.1101/2025.10.16.682766

Leaf-age specific flood resilience in Arabidopsis thaliana is determined by distinct processes contributing to post-submergence recovery

Rankenberg, T.·Sanclemente, M.-A.·Zhang, H.·Leeggangers, M. A.·Devaiah, M.·Chao, J.·van Veen, H.·Theodoulou, F. L.·Sasidharan, R.
View original source ↗Export metadata ↓

Abstract

While the molecular mechanisms mediating submergence tolerance have been extensively studied, those underpinning age-dependent resilience remain poorly characterized. In Arabidopsis thaliana, submergence elicits a leaf-age dependent phenotype in which senescence and death progress across an age gradient starting with older leaves. Here we sought to investigate the mechanisms mediating this observed differential flood resilience by interrogating leaf age-specific transcriptome and proteome changes during submergence and recovery. Following submergence, most age-dependent differences were in the magnitude or speed of transcript abundance changes, whereas qualitative leaf-age dependent responses were most apparent during recovery. This included a strong desiccation response in old leaves despite a stronger ABA-signaling response. Physiological measurements suggested that faster dehydration was facilitated by a combination of submergence-mediated reduction of ABA sensitivity and higher conductance in old leaves. We also observed a stronger induction in young shoot tissue of genes associated with endoplasmic reticulum (ER) stress and the unfolded protein response (UPR). Mutants disabled in the two UPR signaling branches were affected in new leaf formation and the ability to restore the proteome, but not in senescence, suggesting that young tissues activate ER stress recovery to permit continuation of growth. Of the mitochondrial membrane proteins differentially regulated in young leaves, loss of mitochondrial voltage-dependent anion channel function impacted submergence-recovery tolerance. Our data reveal multiple mechanisms underlying leaf age-dependent differential submergence recovery and demonstrate how tolerance is determined by an interplay between age related developmental traits and stress signaling pathways.

Source connections

Explore related subjects

plant biologyPreprint

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

Rankenberg, T., Sanclemente, M.-A., Zhang, H., Leeggangers, M. A., Devaiah, M., Chao, J., van Veen, H., Theodoulou, F. L., Sasidharan, R.. 2025-10-16. Leaf-age specific flood resilience in Arabidopsis thaliana is determined by distinct processes contributing to post-submergence recovery. https://doi.org/10.1101/2025.10.16.682766

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related preprints

bioRxiv2026

MpILR1 Hydrolyzes Jasmonate-Amino Acid Conjugates to Activate dn-iso-OPDA Signaling in Marchantia polymorpha.

Jasmonates are essential phytohormones that coordinate defense responses and developmental programs across land plants. In angiosperms, the active jasmonate ligand jasmonoyl-L-isoleucine (JA-Ile), is produced through GH3-mediated conjugation of jasmonic acid to isoleucine and JA-Ile homeostasis is further shaped by ILR1/ILL-family amidohydrolases. In contrast, the primary bioactive jasmonate ligand in bryophytes, dinor-12-oxo-phytodienoic acid (dn-iso-OPDA), is inactivated through conjugation with amino acids, raising the question of whether these conjugates constitute a reversible hormone reservoir or an irreversible catabolic end point. Although the ILR1-like family has been characterized extensively for its role in auxin and jasmonate homeostasis in angiosperms, its function in bryophytes remains basically unexplored. Here we show that MpILR1, the sole Marchantia ortholog of the ILR1/ILL family, hydrolyzes a specific subset of dn-iso-OPDA-amino acid conjugates in vivo. Loss-of-function Mpilr1 mutants exhibit enhanced accumulation of dn-iso-OPDA conjugated to hydrophobic amino acids (Val, Leu and Ile) but not to hydrophilic residues (His, Glu and Gln), demonstrating substrate-selective hydrolysis. MpILR1 hydrolytic activity is required for full dn-iso-OPDA-mediated responses, including transcriptional activation and defense against gastropod herbivory. These findings establish MpILR1 as a key positive regulator of jasmonate signaling in Marchantia polymorpha and suggest that hormone conjugation/deconjugation is an ancient regulatory mechanism evolved during plant terrestrialization.

plant biology↗
bioRxiv2026

Drought-Spec-Net: Early Tomato Drought Detection and Potential Yield-Impact Assessment Using Vis NIR Data

Drought stress significantly reduces tomato (Solanum lycopersicum L.) productivity, and early detection is critical to minimize yield losses through timely interventions. In this study, we developed Drought-Spec-Net, a hybrid 1D convolutional neural network that integrates local and global spectral feature extraction to detect early drought stress from visible and near infrared (Vis NIR) spectra data of tomato seedlings. The model was trained on 378 samples using an 80:20 train test split, with 20% of the training set reserved for validation. DroughtSpecNet outperformed the evaluated baseline and state of the art models, achieving 97% accuracy, 95% precision, 98% recall, and an F1 score of 97%. To improve the agronomic interpretation of the model outputs, predicted drought probabilities were converted into a literature-informed potential yield impact indicator using a maximum impact level of 60%. On the test set (76 samples), mapped potential yield-impact values ranged from 0% to 60%, with an average reduction of 12.97%. We also conducted an initial experiment using our greenhouse RGB dataset, collected daily from drought treated and well-watered tomato plants at West Virginia State University (WVSU). From this dataset, 44 images were selected for ilastik-based canopy segmentation, producing plant-level drought severity indices (DSI) with a mean of 0.28, median of 0.14, and range of 0.01 to 0.91. Additionally, we trained and fine-tuned a large language model (LLM) based on PLLaMA7BInstruct, called AgriLLaMA, for automated agronomic report generation from Drought-Spec-Net outputs. The generated reports summarize predicted stress levels, mapped potential yield impacts, and preliminary management considerations. This integrated approach not only improves early drought stress detection but also delivers quantitative and interpretable estimates of potential productivity losses, providing a complete framework connecting physiological stress detection to actionable agricultural outcomes.

plant biology↗
bioRxiv2026

BSA101: Unlocking Historical Mutant Collections with BSA-Seq

Forward genetics is a powerful approach for gene discovery, but identifying causal mutations becomes difficult when mutants are maintained in heterogeneous populations with uncertain pedigrees. This is exemplified by classical tasselseed (ts) mutants, which have long served as a genetic model for studying sex determination and carpel suppression. Decades of repeated outcrossing to diverse inbred lines have created substantial genetic heterogeneity, limiting the effectiveness of conventional bulked-segregant analysis sequencing (BSA-Seq). To address this, we developed a BSA-Seq framework that integrates flexible experimental designs, multiple reference genomes, and complementary statistical methods tailored for genetically heterogeneous populations. Applying this framework revealed that reference genome selection is critical for mapping success and that Euclidean distance raised to the fourth power (ED4) outperformed homozygosity mapping (HM). Furthermore, the framework enables simultaneous mapping of multiple mutations within a single population, eliminating the need for additional mapping populations. Applying this framework to 26 ts mutant stocks from the Maize Genetics Cooperation Stock Center, we successfully mapped 24 mutants to genomic intervals containing known ts genes, while the remaining mutants mapped to distinct genomic intervals, defining novel candidate regions underlying carpel suppression. Together, these results demonstrate that historical mutant collections represent an underutilized resource for gene discovery and establish a generalizable mapping strategy for unlocking their genetic potential across diverse species.

plant biology↗