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AI-summarized plant biology research papers from bioRxiv

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Latest 38 Papers

Molecular basis of delayed leaf senescence induced by short-term treatment with low phosphate in rice

Authors: Martin-Cardoso, H., Bundo, M., Garcia-Molina, A., San Segundo, B.

Date: 2026-01-24 · Version: 1
DOI: 10.64898/2026.01.23.701354

Category: Plant Biology

Model Organism: Oryza sativa

AI Summary

The study demonstrates that short‑term low phosphate treatment delays leaf senescence in rice by increasing photosynthetic pigments, enhancing antioxidant enzyme activities, and reducing oxidative damage, whereas high phosphate accelerates senescence. CRISPR/Cas9 editing of MIR827 to lower Pi levels also postpones senescence, while overexpression of MIR827 or MIR399, which raises Pi, speeds it up. Transcriptomic profiling reveals coordinated changes in senescence‑associated and metabolic pathways underlying the low‑phosphate response.

phosphate deficiency leaf senescence Oryza sativa CRISPR/Cas9 transcriptomic analysis

Features affecting Cas9-Induced Editing Efficiency and Patterns in Tomato: Evidence from a Large CRISPR Dataset

Authors: Cucuy, A., Ben-Tov, D., Melamed-Bessudo, C., Honig, A., Cohen, B. A., Levy, A. A.

Date: 2026-01-07 · Version: 1
DOI: 10.64898/2026.01.06.696182

Category: Plant Biology

Model Organism: Solanum lycopersicum

AI Summary

The study generated a dataset of 420 sgRNAs targeting promoters, exons, and introns of 137 tomato genes in protoplasts, linking editing efficiency to chromatin accessibility, genomic context, and sequence features. Open chromatin sites showed higher editing rates, while transcriptional activity had little effect, and a subset of guides produced near‑complete editing with microhomology‑mediated deletions. Human‑trained prediction models performed poorly, highlighting the need for plant‑specific guide design tools.

CRISPR/Cas9 ATAC-seq chromatin accessibility microhomology‑mediated end joining tomato

Do stomatal movements have a limited dynamic range?

Authors: Muraya, F., Siqueira, J. A., Very, A.-A., Roelfsema, R.

Date: 2025-12-26 · Version: 1
DOI: 10.64898/2025.12.22.695892

Category: Plant Biology

Model Organism: Arabidopsis thaliana

AI Summary

The study examined the roles of AtKUP2, AtKUP6, AtKUP8, and GORK potassium transport proteins in guard cell function by performing gas-exchange measurements on mature Arabidopsis leaves. Loss of KUP2/6/8 reduced stomatal conductance, whereas a GORK loss‑of‑function mutant showed increased conductance, yet the magnitude of light‑ and ABA‑induced transpiration changes remained similar across genotypes, suggesting a limited dynamic range for rapid stomatal movements that relies on small ionic osmolytes.

stomatal conductance potassium transporters GORK channel AtKUP2/6/8 Arabidopsis

Comparative Evaluation of Conventional Inorganic Fertilization and Sesbania rostrata Green Manuring on Soil Properties and the Growth and Development of Oryza sativa L. Pant Basmati 1

Authors: Joshi, H. C., Patni, B., Guru, S. K., Bhatt, M. K., Singh, M.

Date: 2025-12-26 · Version: 1
DOI: 10.64898/2025.12.24.696455

Category: Plant Biology

Model Organism: Oryza sativa

AI Summary

A two‑year field trial compared conventional and organic nutrient management on the Basmati rice cultivar Pant Basmati 1, revealing that conventional fertilizer enhanced later‑stage growth and grain yield, while organic inputs increased early plant height and markedly improved soil health and harvest index in the second year. Despite some yield differences, organic management achieved comparable productivity with superior soil macro‑ and micronutrient status, water‑holding capacity, aggregate stability, and enzyme activities, supporting its sustainability as an alternative nutrient regime.

Oryza sativa organic nutrient management soil health harvest index Basmati rice

FLOWERING LOCUS T genes MtFTb1 and MtFTb2 act redundantly to promote flowering under long days in Medicago truncatula

Authors: Perez Santangelo, S., Macknight, R. C.

Date: 2025-12-17 · Version: 1
DOI: 10.64898/2025.12.15.694442

Category: Plant Biology

Model Organism: Medicago truncatula

AI Summary

The study identifies MtFTb1 and MtFTb2 as essential, redundant regulators of long‑day flowering in the legume Medicago truncatula, demonstrating that they are required for up‑regulating MtFTa1 under vernalised long‑day conditions. Using CRISPR/Cas9‑generated single and double mutants, the authors show that double mutants are specifically delayed in flowering under long days while retaining vernalization responsiveness, and transcriptomic analyses reveal that MtFTb1/2 activate MADS‑box genes and other flowering regulators.

flowering time FT genes Medicago truncatula CRISPR/Cas9 long‑day photoperiod

High-frequency sorghum transformation toolkit enhances Cas9 efficiency and expands promoter-editing capability with SpRY

Authors: Shen, J., Aregawi, K., Anwar, S., Miller, T., Groover, E. D., Rajkumar, M., Savage, D. F., Lemaux, P. G.

Date: 2025-12-07 · Version: 2
DOI: 10.1101/2025.01.21.634149

Category: Plant Biology

Model Organism: Sorghum bicolor

AI Summary

The study presents an optimized Agrobacterium-mediated transformation toolkit for Sorghum bicolor that achieves up to 95.7% editing efficiency using CRISPR/Cas9 targeting the SbPDS gene, and demonstrates comparable performance with a PAM‑broadened SpRY variant. This platform enables multiplex genome editing and is positioned for integration of advanced tools such as prime and base editors to accelerate sorghum breeding.

Sorghum bicolor CRISPR/Cas9 Agrobacterium-mediated transformation SpRY (PAM‑flexible Cas9) high-efficiency genome editing

Vacuolar invertase knockout enhances drought tolerance in potato plants

Authors: Roitman, M., Teper-Bamnolker, P., Doron-Faigenboim, A., Sikron, N., Fait, A., Vrobel, O., Tarkowski, P., Moshelion, M., Bocobza, S., Eshel, D.

Date: 2025-12-02 · Version: 1
DOI: 10.64898/2025.12.01.691554

Category: Plant Biology

Model Organism: Solanum tuberosum

AI Summary

CRISPR/Cas9 knockout of the vacuolar invertase gene (StVInv) in potato enhanced drought resilience, with mutants maintaining higher stomatal conductance, transpiration, and photosynthetic efficiency, leading to improved agronomic water-use efficiency and biomass under water limitation. Metabolomic profiling showed accumulation of galactinol and raffinose, while ABA levels were reduced, indicating altered osmoprotective and hormonal responses that support sustained growth during drought.

drought stress vacuo lar invertase knockout CRISPR/Cas9 raffinose family oligosaccharides water-use efficiency

The Pik NLR pair accumulates at the plasma membrane as a hetero-oligomeric sensor-helper immune protein complex prior to activation

Authors: Pai, H., Contreras, M. P., Salguero Linares, J., Luedke, D., Posbeyikian, A., Kourelis, J., Kamoun, S., Marchal, C.

Date: 2025-12-02 · Version: 1
DOI: 10.64898/2025.11.30.691369

Category: Plant Biology

Model Organism: Oryza sativa

AI Summary

The study examined the pre‑activation state of the rice NLR pair Pik‑1 (sensor) and Pik‑2 (helper) when transiently expressed in Nicotiana benthamiana leaves. Both wild‑type and engineered Pik‑1 variants constitutively associate with Pik‑2 to form ~1 MDa hetero‑oligomeric complexes that localize to the plasma membrane in the absence of effector. These results reveal that some NLRs exist as pre‑assembled membrane‑associated complexes prior to pathogen perception.

NLR oligomerization Pik-1/Pik-2 sensor‑helper pair resting state complex plasma membrane localization Oryza sativa

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

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
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