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AI-summarized plant biology research papers from bioRxiv

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Latest 59 Papers

KDM7-mediated oxygen sensing reprograms chromatin to enhance hypoxia tolerance in the root

Authors: Zhang, D., Chirinos, X., Del Chiaro, A., Shukla, V., Ryder, A., Beltran, A. D. P., Iacopino, S., Bota, P., Zivkovic, D., Fioriti, F., Telara, Y., Ellison, C. J., Costa, F., Elliott, P. R., Giorgi, F., Giuntoli, B., Flashman, E. G., Abreu, I., Licausi, F.

Date: 2025-11-26 · Version: 1
DOI: 10.1101/2025.11.24.690241

Category: Plant Biology

Model Organism: Arabidopsis thaliana

AI Summary

The study shows that Arabidopsis root tips adapt to hypoxia by increasing H3K4me3 levels, linked to the inhibition of group 7 demethylases (KDM7s). Genetic loss of KDM7s mimics hypoxic conditions, activating genes that sustain meristem survival, suggesting KDM7s act as root‑specific oxygen sensors that prime epigenetic tolerance mechanisms.

hypoxia root meristem H3K4 trimethylation KDM7 demethylase Arabidopsis

The mRNA covalent modification dihydrouridine regulates transcript turnover and photosynthetic capacity during plant abiotic stress

Authors: Yu, L., Melandri, G., Dittrich, A. C., Calleja, S., Rozzi, B., Ganguly, D. R., Palos, K., Srinivasan, A., Brewer, E. K., Fischer, H., Obata, T., Elgawad, H. A., Beemster, G. T. S., Henderson, R., Garcia, C. D., Zhang, X., Stern, D., Eveland, A., Schroeder, S. J., Skirycz, A., Lyons, E., Arnold, E. A., Gregory, B. D., Nelson, A. D. L., Pauli, D.

Date: 2025-11-24 · Version: 3
DOI: 10.1101/2025.01.17.633510

Category: Plant Biology

Model Organism: Arabidopsis thaliana

AI Summary

The study integrates multi-omics data from six Sorghum bicolor accessions under field drought to link RNA covalent modifications (RCMs) with photosynthetic performance, identifying the enzyme SbDUS2 that produces dihydrouridine (DHU) on transcripts. Loss‑of‑function dus2 mutants in Arabidopsis thaliana reveal that DHU deficiency leads to hyperstability of photosynthesis‑related mRNAs, impairing germination, development, and stress‑induced CO2 assimilation. The authors propose DHU as a post‑transcriptional mark that promotes rapid mRNA turnover during abiotic stress, enhancing plant resilience.

RNA covalent modifications dihydrouridine (DHU) drought stress photosynthesis RNA stability

Mobility-enhanced virus vectors enable meristem genome editing in model and crop plants

Authors: Chiu, K. T., Higgs, H., Antunes, M. S., Lin, Y. T., McGarry, R. C.

Date: 2025-11-19 · Version: 1
DOI: 10.1101/2025.11.19.689159

Category: Plant Biology

Model Organism: Nicotiana benthamiana

AI Summary

The study engineered Tobacco rattle virus vectors incorporating distinct RNA secondary structures as mobility factors to improve guide RNA delivery to plant meristems. Using Nicotiana benthamiana plants expressing Cas9, optimal virus constructs were identified that generated both somatic and heritable edits, and these constructs were successfully applied to edit the emerging oilseed crop pennycress (Thlaspi arvense).

CRISPR/Cas9 Tobacco rattle virus (TRV) RNA mobility factors meristem editing virus-mediated gRNA delivery

Developing a Molecular Toolkit to ENABLE all to apply CRISPR/Cas9-based Gene Editing in planta

Authors: Abate, B. A., Hahn, F., Chirivi, D., Betti, C., Fornara, F., Molloy, J. C., Krainer, K. M. C.

Date: 2025-11-09 · Version: 1
DOI: 10.1101/2025.11.09.687425

Category: Plant Biology

Model Organism: Multi-species

AI Summary

The authors introduce the ENABLE(R) Gene Editing in planta toolkit, a streamlined two‑step cloning system for creating CRISPR/Cas9 knockout vectors suitable for transient or stable transformation. Validation was performed in Oryza sativa protoplasts and Arabidopsis thaliana plants, and the toolkit includes low‑cost protocols aimed at facilitating adoption in the Global South.

CRISPR/Cas9 plant gene editing low‑cost cloning Global South agriculture ENABLE(R) toolkit

Effects of carbon dioxide enrichment and environmental factors on photosynthesis, growth and yield and their interaction in cucumber: a meta-analysis

Authors: Liu, X., Liu, X., Xu, Y., Wang, Z., Sun, Q., Liu, S., Liu, B., Li, Q.

Date: 2025-11-01 · Version: 1
DOI: 10.1101/2025.10.31.685732

Category: Plant Biology

Model Organism: Cucumis sativus

AI Summary

A meta‑analysis of 73 studies on cucumber (Cucumis sativus) under elevated CO₂ (eCO₂) revealed that eCO₂ significantly increased net photosynthetic rate (+56.31%), biomass (+27.75%) and yield (+21.98%), while reducing stomatal conductance (‑36.07%) and transpiration (‑30.42%). The authors recommend maintaining eCO₂ levels between 800–1200 ppm together with higher light, temperature, optimal humidity, and adequate fertilization to optimise greenhouse cucumber production under climate‑change scenarios.

elevated CO₂ cucumber (Cucumis sativus) photosynthesis biomass and yield meta‑analysis

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

Deciphering Photosynthetic Protein Networks: A Crosslinking-MS Strategy for Studying Functional Thylakoid Membranes

Authors: Frances, N., Giustini, C., Finazzi, G., Ferro, M., Albanese, P.

Date: 2025-10-08 · Version: 1
DOI: 10.1101/2025.10.07.681025

Category: Plant Biology

Model Organism: Multi-species

AI Summary

The study introduces an enhanced crosslinking mass spectrometry workflow that preserves native protein interactions within functional thylakoid membranes of Arabidopsis and spinach, while electron transport remains active. Mapping the obtained crosslinks to known structures validates complex integrity and reveals novel assemblies, facilitating in situ exploration of photosynthetic membrane protein networks.

photosynthesis thylakoid membranes crosslinking mass spectrometry protein complexes Arabidopsis thaliana

KATANIN promotes cell elongation and division to generate proper cell numbers in maize organs

Authors: Martinez, S. E., Lau, K. H., Allsman, L. A., Irahola, C., Habib, C., Diaz, I. Y., Ceballos, I., Panteris, E., Bommert, P., Wright, A. J., Weil, C., Rasmussen, C.

Date: 2025-10-06 · Version: 1
DOI: 10.1101/2025.10.05.680529

Category: Plant Biology

Model Organism: Zea mays

AI Summary

The study identifies two maize genes, Discordia3a and Discordia3b, that encode the microtubule‑severing protein KATANIN. Loss‑of‑function allele combinations reduce microtubule severing, impair cell elongation, delay mitotic entry, and disrupt preprophase band and nuclear positioning, leading to dwarfed, misshapen plants.

KATANIN microtubule severing Zea mays preprophase band cell elongation

Microclimatic Effects on Functional Traits of Arctostaphylos crustacea ssp. crustacea in Alameda County, California, USA

Authors: Hsiao, L.

Date: 2025-10-06 · Version: 1
DOI: 10.1101/2025.10.03.680375

Category: Plant Biology

Model Organism: Arctostaphylos crustacea ssp. crustacea

AI Summary

The study examined how microclimatic factors influence leaf morphology and photosynthetic productivity in Arctostaphylos crustacea ssp. crustacea across two chaparral sites in California, finding that higher light and lower soil moisture increased leaf mass per area, leaf angle steepness, and photosynthetic rates. Linear mixed‑model analysis identified light level as the strongest predictor, with vapor pressure deficit, soil moisture, leaf temperature, and leaf angle also contributing, highlighting the role of combined microclimatic interactions in driving intraspecific trait variation.

microclimate leaf mass per area (LMA) photosynthesis intraspecific trait variation chaparral ecosystems
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