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AI-summarized plant biology research papers from bioRxiv

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Golden Promise-rapid, a fast-cycling barley genotype with high transformation efficiency

Authors: Buchmann, G., Haraldsson, E. B., Schüller, R., Rütjes, T., Walla, A. A., von Korff Schmising, M., Liu, S.

Date: 2025-10-31 · Version: 1
DOI: 10.1101/2025.10.31.685778

Category: Plant Biology

Model Organism: Hordeum vulgare

AI Summary

The authors created a fast‑cycling, isogenic barley line (GP‑rapid) by introgressing the wild‑type Ppd‑H1 allele from Igri into the Golden Promise cultivar and performing two backcrosses to limit the donor genome, achieving a 25% reduction in generation time under speed‑breeding conditions while retaining high transformation efficiency. CRISPR/Cas9‑mediated editing of Ppd‑H1 showed regeneration and transformation rates comparable to the original Golden Promise, establishing GP‑rapid as a rapid platform for transgenic and gene‑edited barley research.

Golden Promise Ppd-H1 speed breeding CRISPR/Cas9 transformation efficiency

Engineering compact Physalis peruviana (goldenberry) to promote its potential as a global crop

Authors: Santo Domingo, M., Fitzgerald, B., Robitaille, G. M., Ramakrishnan, S., Swartwood, K., Karavolias, N., Schatz, M., Van Eck, J., Lippman, Z.

Date: 2025-10-24 · Version: 2
DOI: 10.1101/2025.08.15.670557

Category: Plant Biology

Model Organism: Physalis peruviana

AI Summary

The study applied CRISPR/Cas9 gene editing to Physalis peruviana to modify plant‑architecture genes and create a compact growth ideotype. This compact phenotype is intended to increase per‑plot yield and support future breeding efforts for this nutritionally valuable minor crop.

Physalis peruviana Goldenberry CRISPR/Cas9 plant architecture compact ideotype

Role of AtCPK5 and AtCPK6 in the regulation of the plant immune response triggered by rhamnolipids in Arabidopsis

Authors: STANEK, J., FERNANDEZ, O., BOUDSOCQ, M., AGGAD, D., VILLAUME, S., PARENT, L., DHONDT CORDELIER, S., CROUZET, J., DOREY, S., CORDELIER, S.

Date: 2025-10-23 · Version: 1
DOI: 10.1101/2025.10.22.683368

Category: Plant Biology

Model Organism: Arabidopsis thaliana

AI Summary

The study examined how Arabidopsis calcium‑dependent protein kinases AtCPK5 and AtCPK6 modulate immunity triggered by bacterial rhamnolipids, finding that RLs up‑regulate these kinases and that mutants, especially cpk5/6, show altered reactive oxygen species production and defense gene expression. However, these kinases did not influence RL‑induced electrolyte leakage or resistance to Pseudomonas syringae pv. tomato DC3000, indicating additional signaling components are involved.

rhamnolipids calcium dependent protein kinases Arabidopsis thaliana immunity reactive oxygen species defense gene expression

Spatiotemporal Analysis Reveals Mechanisms Controlling Reactive Oxygen Species and Calcium Interplay Following Root Compression

Authors: Vinet, P., Audemar, V., Durand-Smet, P., Frachisse, J.-M., Thomine, S.

Date: 2025-10-23 · Version: 1
DOI: 10.1101/2025.10.22.683952

Category: Plant Biology

Model Organism: General

AI Summary

Using a microfluidic valve rootchip, the study simultaneously tracked ROS and calcium dynamics in compressed roots and found three kinetic phases linking mechanosensitive channel activity, NADPH oxidase‑dependent ROS accumulation, and secondary calcium influx. Pharmacological inhibition revealed that a fast calcium response is mediated by plasma‑membrane mechanosensitive channels, while a slower calcium increase is driven by ROS production.

mechanotransduction reactive oxygen species calcium signaling microfluidic compression root biology

Phosphoproteomics uncovers rapid and specific transition from plant two-component system signaling to Ser/Thr phosphorylation by the intracellular redox sensor AHK5

Authors: Drechsler, T., Li, Z., Schulze, W. X., Harter, K. J. W.

Date: 2025-10-14 · Version: 1
DOI: 10.1101/2025.10.13.682113

Category: Plant Biology

Model Organism: Arabidopsis thaliana

AI Summary

A comparative phosphoproteomics study using Arabidopsis thaliana ahk5 loss‑of‑function mutants and wild‑type seedlings revealed that the histidine kinase AHK5 mediates a rapid shift from multistep phosphorelay signaling to serine/threonine phosphorylation in response to H2O2. AHK5 controls ROS‑responsive phosphorylation of plasma‑membrane nanodomain proteins and orchestrates distinct ABA‑independent stomatal closure and ABA‑dependent root development pathways by modulating key components such as RBOHD, CAS, HPCA1, and auxin transporters.

AHK5 reactive oxygen species phosphoproteomics Arabidopsis thaliana nanodomain signaling

Cis-regulatory architecture downstream of FLOWERING LOCUS T underlies quantitative control of flowering

Authors: Zhou, H.-R., Doan, D. T. H., Hartwig, T., Turck, F.

Date: 2025-09-25 · Version: 1
DOI: 10.1101/2025.09.23.678055

Category: Plant Biology

Model Organism: Arabidopsis thaliana

AI Summary

The study used CRISPR/Cas9 to edit the downstream region of the Arabidopsis thaliana FLOWERING LOCUS T (FT) gene, identifying a 2.3‑kb segment containing the Block E enhancer as crucial for normal FT expression and flowering. Fine‑scale deletions pinpointed a 63‑bp core module with CCAAT‑ and G‑boxes, and revealed a cryptic CCAAT‑box that becomes active when repositioned, highlighting the importance of local chromatin context and motif arrangement for enhancer function.

FLOWERING LOCUS T enhancer architecture cis‑regulatory logic CRISPR/Cas9 chromatin accessibility

Choosing the Best Route: Comparative Optimization of Wheat Transformation Methods for Improving Yield by Targeting TaARE1-D with CRISPR/Cas9

Authors: Tek, M. I., Budak Tek, K., Sarikaya, P., Ahmed, A. R., Fidan, H.

Date: 2025-09-12 · Version: 1
DOI: 10.1101/2025.09.11.675438

Category: Plant Biology

Model Organism: Triticum aestivum

AI Summary

The study optimized three wheat transformation methods—immature embryo, callus, and in planta injection—by systematically adjusting Agrobacterium strain, bacterial density, acetosyringone concentration, and incubation conditions, achieving transformation efficiencies up to 66.84%. Using these protocols, CRISPR/Cas9 knockout of the negative regulator TaARE1-D produced mutants with increased grain number, spike length, grain size, and a stay‑green phenotype, demonstrating the platform’s potential to accelerate yield and stress‑tolerance improvements in wheat.

Triticum aestivum CRISPR/Cas9 Agrobacterium-mediated transformation TaARE1-D yield improvement

Calcium-dependent protein kinases participate in RBOH-mediated sustained ROS burst during plant immune cell death

Authors: Hino, Y., Yoshioka, M., Adachi, H., Yoshioka, H.

Date: 2025-09-01 · Version: 1
DOI: 10.1101/2025.09.01.672762

Category: Plant Biology

Model Organism: Nicotiana benthamiana

AI Summary

The study demonstrates that calcium-dependent protein kinases NbCDPK4 and NbCDPK5 directly phosphorylate the NADPH oxidase NbRBOHB at Ser‑123, enhancing sustained ROS production during effector-triggered immunity in Nicotiana benthamiana. Constitutively active CDPKs also upregulate NbRBOHB transcription, and phosphorylation of Ser‑123 is amplified by Ca2+ influx triggered by an autoactive helper NLR (NRC4). These results define a NbCDPK‑NbRBOHB signaling module that links NLR activation to prolonged ROS bursts in ETI.

effector-triggered immunity calcium-dependent protein kinases NADPH oxidase reactive oxygen species Nicotiana benthamiana

The improved auxin signalling via entire mutation enhances aluminium tolerance in tomato

Authors: Silva, R., Siqueira, J. A., Batista-Silva, W., Ferreira-Silva, M., Thiago, W., Vargas, J. R., Vilela, G., Robson, R., Neto, D. F. M., Azevedo, A. A., Ribeiro, C., Fernie, A., Nunes-Nesi, A., Araujo, W.

Date: 2025-09-01 · Version: 1
DOI: 10.1101/2025.08.29.673006

Category: Plant Biology

Model Organism: Tomato

AI Summary

The study investigates how auxin signaling influences aluminium tolerance using tomato mutants with altered auxin sensitivity, showing that the auxin‑hypersensitive entire mutant tolerates Al stress while the auxin‑reduced dgt mutant is more sensitive. Differences in reactive oxygen species accumulation and root transition‑zone cell differentiation correlate with distinct metabolic responses, suggesting that modifying auxin perception can enhance crop Al tolerance.

aluminium toxicity auxin signaling tomato mutants reactive oxygen species metabolite profiling

tRNA-Based Polycistronic CRISPR/Cas9 System Boosts Efficiency of Multi-Gene Deletion in the Moss Physcomitrella.

Authors: Kozgunova, E.

Date: 2025-08-01 · Version: 1
DOI: 10.1101/2025.07.29.667574

Category: Plant Biology

Model Organism: Physcomitrium patens

AI Summary

The authors introduced a polycistronic tRNA‑gRNA array for CRISPR/Cas9 editing in Physcomitrium patens that doubled the frequency of large, targeted deletions compared with conventional single‑gRNA constructs. Using dual‑gRNA targeting, they achieved simultaneous deletion of two to four genes (katanin and TPX2 families) in a single transformation, reaching up to 42% efficiency per gene, though efficiency depended on gRNA pair design.

CRISPR/Cas9 polycistronic tRNA‑gRNA array large gene deletion multiplex editing Physcomitrium patens
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