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AI-summarized plant biology research papers from bioRxiv

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Latest 21 Papers

Physics-Informed Neural Network Methods for Predicting Plant Height Development

Authors: Shao, Y., van Eeuwijk, F., Peeters, C., Zumsteg, O., Athanasiadis, I., van Voorn, G.

Date: 2026-01-14 · Version: 1
DOI: 10.64898/2026.01.14.699475

Category: Plant Biology

Model Organism: Triticum aestivum

AI Summary

The study introduces a hybrid modeling framework that integrates a logistic ordinary differential equation with a Long Short-Term Memory neural network to form a Physics-Informed Neural Network (PINN) for predicting wheat plant height. Using only time and temperature as inputs, the PINN outperformed other longitudinal growth models, achieving the lowest average RMSE and reduced variability across multiple random initializations. The results suggest that embedding biological growth constraints within data‑driven models can substantially improve prediction accuracy for plant traits.

Physics-Informed Neural Network logistic ODE Long Short-Term Memory plant height prediction wheat

Evolution of HMA-integrated tandem kinases accompanied by expansion of target pathogens

Authors: Asuke, S., Tagle, A. G., Hyon, G.-S., Koizumi, S., Murakami, T., Horie, A., Niwamoto, D., Katayama, E., Shibata, M., Takahashi, Y., Islam, M. T., Matsuoka, Y., Yamaji, N., Shimizu, M., Terauchi, R., Hisano, H., Sato, K., Tosa, Y.

Date: 2025-12-16 · Version: 1
DOI: 10.64898/2025.12.15.692859

Category: Plant Biology

Model Organism: Multi-species

AI Summary

The study cloned the resistance genes Rmo2 and Rwt7 from barley and wheat, revealing them as orthologous tandem kinase proteins (TKPs) with an N‑terminal heavy metal‑associated (HMA) domain. Domain‑swapping experiments indicated that the HMA domain dictates effector specificity, supporting a model of TKP diversification into paralogs and orthologs that recognize distinct pathogen effectors.

tandem kinase proteins HMA domain disease resistance barley wheat

Targeting granule initiation and amyloplast structure to create giant starch granules in wheat

Authors: McNelly, R., Esch, L., Ngai, Q. Y., Pohan, K., Stringer, R., Fahy, B., Warren, F., Seung, D.

Date: 2025-12-15 · Version: 1
DOI: 10.64898/2025.12.12.693964

Category: Plant Biology

Model Organism: Triticum aestivum

AI Summary

Mutations in the plastid division gene PARC6 and the granule initiation gene BGC1 were combined to generate wheat plants with dramatically enlarged A-type starch granules, some exceeding 50 µm, without affecting plant growth, grain size, or overall starch content. The parc6 bgc1 double mutant was evaluated in both glasshouse and field trials, and the giant granules displayed altered viscosity and pasting temperature, offering novel functional properties for food and industrial applications.

starch granule size PARC6 BGC1 wheat giant starch granules

Glycosylated diterpenes associate with early containment of Fusarium culmorum infection across wheat (Triticum aestivum L.) genotypes under field conditions

Authors: Pieczonka, S. A., Dick, F., Bentele, M., Ramgraber, L., Prey, L., Kupczyk, E., Seidl-Schulz, J., Hanemann, A., Noack, P. O., Asam, S., Schmitt-Kopplin, P., Rychlik, M.

Date: 2025-12-04 · Version: 1
DOI: 10.64898/2025.12.02.691979

Category: Plant Biology

Model Organism: Triticum aestivum

AI Summary

The researchers performed a large‑scale field trial with 105 wheat (Triticum aestivum) genotypes inoculated by Fusarium culmorum, combining quantitative deoxynivalenol (DON) profiling and untargeted metabolomics to uncover molecular signatures of infection. Sesquiterpene‑derived metabolites tracked toxin accumulation, whereas glycosylated diterpene conjugates were enriched in low‑DON samples, indicating a potential defensive metabolic pathway.

wheat Fusarium head blight deoxynivalenol untargeted metabolomics diterpene conjugates

Identification and Development of Functional Markers Associated with Triple Pistil Phenotype in Wheat

Authors: Raza, Q., Song, Q., Rehman, S. u., Ali, Z.

Date: 2025-11-10 · Version: 1
DOI: 10.1101/2025.11.09.687415

Category: Plant Biology

Model Organism: Triticum aestivum

AI Summary

The study characterizes the triple pistil (TP) phenotype in wheat, identifying two tightly linked mutations (TraesCS2D02G490900 and TraesCS2D02G491600) that co‑segregate with the trait and developing functional markers for early‑generation selection. CRISPR‑Cas9 editing of one candidate gene altered grain set, and field evaluation showed TP wheat increases grains per spike without reducing grain weight, highlighting its value for hybrid wheat breeding.

triple pistil wheat CRISPR-Cas9 functional markers grain yield

Dual recognition of structurally unrelated mildew effectors underlies the broad-spectrum resistance of Pm3e in wheat

Authors: Kunz, L., Bernasconi, Z., Heuberger, M., Isaksson, J., Sotiropoulos, A. G., Stirnemann, U., Jigisha, J., Menardo, F., Wicker, T., Mueller, M. C., Keller, B.

Date: 2025-10-30 · Version: 2
DOI: 10.1101/2025.10.26.683672

Category: Plant Biology

Model Organism: Triticum aestivum (wheat)

AI Summary

The study investigates the wheat Pm3 NLR allelic series, revealing that near-identical Pm3d and Pm3e alleles confer broad-spectrum resistance by recognizing multiple, structurally diverse powdery mildew effectors. Using chimeric NLR constructs, the authors pinpoint specificity-determining polymorphisms and demonstrate that engineered combinations of Pm3d and Pm3e further expand effector recognition, showcasing the potential for durable wheat protection through NLR engineering.

broad-spectrum resistance NLR receptors Pm3 alleles powdery mildew effectors wheat

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 researchers optimized Agrobacterium‑mediated transformation parameters for immature embryo, callus, and in‑planta methods in wheat, achieving efficiencies of up to 66.84% and shortening the callus induction stage by about one month. Validation with CRISPR/Cas9 knockout of the negative regulator TaARE1‑D produced mutants showing increased grain number, spike length, grain size, thousand‑grain weight, and a stay‑green phenotype, demonstrating the protocol’s potential to accelerate yield‑enhancing gene editing.

wheat CRISPR/Cas9 transformation optimization Agrobacterium yield traits

Spatial transcriptomics identifies distinct domains regulating yield-related traits of the wheat ear

Authors: Qu, Y., Tan, C., Yang, L., Pasquariello, M., Alabdullah, A. K., Sun, S., Iqbal, M., Salamon, J., Boden, S.

Date: 2025-08-13 · Version: 1
DOI: 10.1101/2025.08.12.670006

Category: Plant Biology

Model Organism: Triticum aestivum

AI Summary

The study used spatial transcriptomics to map gene expression dynamics in wheat inflorescences, revealing two distinct regions— a primordium region with RAMOSA2 activity and a boundary region expressing ALOG1 and bract‑suppression regulators—that govern spikelet architecture. Developmental assays linked meristematic differentiation to vascular formation in the rachis, identifying key regulators and potential targets for enhancing spikelet number and yield.

spikelet development spatial transcriptomics RAMOSA2 ALOG1 wheat

Dynamic structural changes in wheat vegetative development as an adaptive response to drought stress

Authors: Leszczuk, A., Kutyrieva-Nowak, N.

Date: 2025-08-07 · Version: 1
DOI: 10.1101/2025.08.07.669084

Category: Plant Biology

Model Organism: Triticum aestivum

AI Summary

The study examined wheat seedling cell‑wall remodeling under drought, targeting hydroxyproline‑rich glycoproteins, xylan and pectic compounds. Within five days of water deficit, organ‑specific changes included polymer aggregation and degradation, deposition of un‑esterified homogalacturonans and AGPs, and calcium cross‑linking that increases wall rigidity and aids intracellular water preservation.

drought stress wheat cell wall remodeling homogalacturonans AGPs

An aphid resistant wheat variety reduces the transmission of Barley Yellow Dwarf Virus (BYDV) by Rhopalosiphum padi (L.)

Authors: Qonaah, I. A., Simon, A. L., Warner, D., Bruce, T. J. A., Ray, R. V.

Date: 2025-08-02 · Version: 1
DOI: 10.1101/2025.07.30.667415

Category: Plant Biology

Model Organism: Triticum aestivum

AI Summary

The winter wheat variety G1 emits the aphid‑repellent volatile 2‑tridecanone, limiting phloem access by viruliferous Rhopalosiphum padi and reducing Barley Yellow Dwarf Virus (BYDV) transmission compared with resistant (RGT Wolverine) and susceptible (RGT Illustrious) cultivars. While G1 curtails virus spread via aphid resistance, RGT Wolverine restricts systemic BYDV infection despite high transmission, indicating distinct defense mechanisms that could be combined in breeding programs.

aphid resistance Barley Yellow Dwarf Virus 2-tridecanone electrical penetration graph wheat
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