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Open research questions in Plant Molecular Biology Research

90 unresolved questions extracted from the limitations and future-work sections of 459 Plant Molecular Biology Research papers in our library. Each links back to the study that raised it.

What the literature leaves open

  • However, the PHD finger gene family has not been systematically identified in Panax ginseng, and its association with ginsenoside biosynthesis remains unclear.

    Comprehensive Genome Identification of the PHD Gene Family in Panax ginseng and Expression Analysis of PgPHD Genes in Response to MeJA · 2026 · DOI

  • While the molecular mechanism by which EgrARF10 acts remains unknown, these findings provide the first evidence for the role of a class C ARF in xylem SCW biology.

    Eucalyptus grandis Auxin Response Factor 10 (EgrARF10) is associated with the modulation of secondary xylem cell wall chemistry · 2026 · DOI

  • While GATA families have been well characterized in model plants and Solanaceae crops, their evolutionary and functional features remain poorly defined in eggplant (Solanum melongena L.

    Genome-Wide Identification and Stress Response Analysis of the GATA Gene Family in Eggplant (Solanum melongena L.) · 2026 · DOI

  • Abscisic acid (ABA) mediates these adaptations; however, it remains unclear which cells produce ABA, whether ABA synthesis shifts during stress, and whether ABA movement is required for its adaptive functions.

    Water stress adaptive responses in plants require movement of ABA and AB-aldehyde from vascular to target tissues · 2026 · DOI

  • Beyond its established role in flowering-time regulation, FLD has been implicated in plant immunity, particularly in systemic acquired resistance (SAR), although the mechanistic basis of its immune function remains poorly understood.

    FLD Is Required for N-Hydroxypipecolic Acid Accumulation and Associated Growth Defects in Arabidopsis pmr4 Mutant · 2026 · DOI

  • Although the mechanisms of GA action have been extensively characterized in other developmental processes, their role in SE remains poorly understood.

    The multifaceted role of gibberellins in somatic embryogenesis: from in vitro culture to molecular networks · 2026 · DOI

  • Gibberellin (GA) promotes germination, but how GA signaling achieves self-amplification at the early stage of germination to drive rapid germination remains unknown.

    CYCLING DOF FACTOR 2 (LdCDF2) functions as a positive regulator integrating GA signaling and biosynthesis to drive bulb germination in <i>Lilium</i> · 2026 · DOI

  • Brassinosteroid (BR) signalling, mediated by glycogen synthase kinase-like (GSK-like) kinases, modulates both stress tolerance and plant growth; however, its role under fluctuating cold-related temperature conditions has not been explored in detail.

    Omics-based characterization of physiological and transcriptomic resilience during cold de-acclimation and re-acclimation in GSK-like kinase mutants · 2026 · DOI

  • We previously identified the Rs locus (CsSHN1), encoding an AP2/ERF transcription factor, as a major determinant of cucumber skin netting, but how fruit growth is temporally coupled to periderm formation remains unclear.

    Natural variants of <i>CsSHN1</i> orchestrate a temporal regulatory cascade driving fruit skin netting in cucumber · 2026 · DOI

  • Leaf senescence directly affects lettuce quality and postharvest shelf life, but the regulatory roles of miR319-targeted and non-target CIN-TCP transcription factors remain unclear.

    miR319-targeted LsTCP4 and non-target LsTCP17 act in parallel to promote leaf senescence in lettuce · 2026 · DOI

  • I show how within a single cell oscillations are limited to a small parameter domain, with constraints intensifying due to the presence of multiple AUX/IAA and ARF types as well as auxin export.

    The (un)likelihood of clock-driven lateral root priming; A modeling exploration · 2026 · DOI

  • CO‐mediated FT activation must be properly controlled to prevent an excessive florigen production and precocious flowering under inductive photoperiods, but the underlying mechanism remains elusive.

    Auto‐Downregulation of the Florigen FT Production Prevents Precocious Flowering in Plants · 2026 · DOI

  • However, in plants, where the known de novo DNA methylation mechanism (RdDM) targets euchromatin, how heterochromatin is formed in a region-specific manner remains unclear.

    Antagonistic histone H2A variants and autonomous heterochromatin formation shape epigenomic patterns in Arabidopsis · 2026 · DOI

  • Epigenetic changes in DNA methylation and small RNAs have been implicated, yet how their temporal dynamics govern the establishment and erasure of immune memory remains unclear.

    Contrasting epigenetic dynamics in chromosome arms and pericentromeres during ROS1-induced plant immune memory · 2026 · DOI

  • Although this model remains to be tested experimentally, it pro- vides a more specific framework for future investigation. Several limitations of the present study should be acknowl- edged. It is not yet known whether TRQA1 acts primarily through transcriptional regulation, protein interaction, plastid-associated metabolic processes, or a combination of these mechanisms.

    The Brassicaceae-restricted gene TRQA1, acting opposite to QQS, modulates starch and protein accumulation in Arabidopsis · 2026 · DOI

  • Because little is known empirically about the timing and frequency of such exchanges, these assumptions would need to be considered carefully, as exchanges introduced at different developmental stages could have different consequences for the resulting VAF spectra.

    simSOMA: a cell-lineage based simulator of the somatic VAF spectrum in plants · 2026 · DOI

  • Future work should address OsPR1 expression patterns under biotic and abiotic stresses, subcellular localization, and targeted functional studies, including validation of pre- dicted protein–protein interactions. PPI network and KEGG pathway analyses suggest potential functional associations with nitrogen and purine metabolism, although these relation- ships remain to be experimentally validated.

    The pathogenesis-related protein 1 (PR-1) gene in rice ( <i>Oryza sativa</i> ) · 2026 · DOI

  • The GA–GID1–DELLA module is a prototypical plant hormone signaling system built on de-repression. Canoni- cally, GA binding to GID1 enables DELLA recognition by SCF ubiquitin ligases and 26S proteasome degradation, thereby derepressing growth (McGinnis et al. 2003; Dill et al. 2004; Murase et al. 2008; Harberd et al. 2009). This logic explains how plants can rapidly shift gene expression and growth in response to changes in GA levels. Recent work broadens this canonical view. GA–GID1 can suppress DELLA output in a proteolysis-independent Singh et al. manner (Ariizumi et al. 2008; Dahal et al. 2025), DELLA activity can be tuned via chromatin association and phos- phorylation (Huang et al. 2024), DELLA repression can be maintained through recruitment of chromatin modifiers (Li et al. 2023), and in specific physiological settings GA can promote DELLA degradation via autophagy (Zhang et al. 2025). Together, these findings strengthen the view that DELLA proteins are integrative hubs whose output depends on abundance, conformation, modifications, interaction partners, and chromatin engagement. For crop improvement, the hub view suggests that precision tuning will outperform blunt stabilization. The most promising interventions are likely to be those that adjust DELLA output in the right tissue, at the right time, and under the right environmental conditions. With expanding structural insight, chromatin mechanisms, and genome editing capacity, the GA–DELLA module remains a compelling target for rational design of growth and yield stability traits.

    Beyond proteolysis: the GA–GID1–DELLA module as a transcriptional control hub in plants · 2026 · DOI

  • Utilising genome assemblies of representative Cyphostemma species, we demonstrate that specific long terminal repeat retrotransposon (LTR-RT) lineages thrived through the radiation of Cyphostemma and led to substantial intron expansion, a phenomenon rarely studied in eudicots.

    Genomic and ecological drivers of parallel arid adaptation in tree grapes (Vitaceae) · 2026 · DOI

  • Gibberellin (GA) promotes plant growth primarily by triggering degradation of DELLA transcription regulators, yet how DELLA activity is fine-tuned dynamically by phosphorylation independently of proteolysis remains poorly understood.

    CDK8 phosphorylation of DELLA limits Mediator recruitment in gibberellin signaling · 2026 · DOI

  • Results indicate limited evidence of parallel local adaptation along elevation, suggesting that dwarf inflorescences are selected for in multiple mountain tops, while bet-hedging prevails in cold and seasonally dry sky-islands, and divergent selection along elevation in other traits can evolve in mountains with milder climates.

    Genomic history and ecology of local adaptation in sky-island Arabidopsis thaliana · 2026 · DOI

  • In the field of CAMTA-CRE biology, several research areas require strategic focus in the next years. A primary objective is to develop a CRE atlas for CAMTA target promoters through systematic chromatin immunoprecipitation sequencing (ChIP-seq) and ATAC-seq profiling. This comprehensive approach would provide datasets analogous to the mammalian ENCODE initiative, facilitating the identification of all CGCG-core and ABRE-CE elements appropriate for genome-wide editing. Establishment of high-throughput CRE variant libraries through massively parallel reporter assays (MPRAs) would enable systematic evaluation of thousands of CRE variant sequences derived from targeted mutagenesis of CGCG areas, generating quantitative models linking CAMTA-binding affinities to gene expression outcomes. This would enhance CRE editing precision, enabling the achievement of designated expression levels rather than just binary on/off outcomes. Development of multi-stress CRE modules is equally important, given that many crops encounter several environmental challenges concurrently. Engineering promoters capable of simultaneously responding to multiple stress signals, such as CGCG/Ca2+, ABRE/ ABA, and DRE/DREB, would enable the development of crops resilient to diverse stressors through a single editing intervention. Epigenome editing is an emerging discipline that emphasizes the significance of chromatin accessibility for the correct functioning of CREs. Techniques deploying dCas9 fused to histone acetyltransferases or DNA demethylases have been shown to activate target loci in plant systems (Morelli et al., 2021), and application of this approach to CAMTA-responsive CREs under stress conditions is a tractable avenue for enhancing the durationalong with the intensity of stress-responsive gene expression in crops that suppress these genes via epigenetic mechanisms. AI-enhanced synthetic CRE design has significant potential. Machine learning models utilizing datasets of plant promoters to forecast gene expression from CRE sequences, combined with CAMTA-CRE binding data, enable the creation of entirely computer-designed synthetic stress-responsive promoters tailored to specific crops, stressors, and desired expression profiles. Despite these opportunities, several challenges must be addressed before deploying CAMTA-centered cis-engineering at scale. Several CAMTA promoters and their downstream targets remain insufficiently characterized at high resolution. The function of motifs is contingent upon the environment and the activity of the same cis element vary based on the chromatin state or the adjacent sequences. Additional genome-wide binding and promoter-editing investigations in economically significant crop species are required.

    Cis-regulatory elements in CAMTA-mediated stress signalling: mechanisms and prospects for CRISPR-based crop improvement · 2026 · DOI

  • The field of developmental biology aims to understand the highly organised and complex processes that govern cellular differ- entiation and tissue formation. In plants, these processes employ GRNs to maintain stem cells to provide a constant supply of new cells for the formation of shoot and root tissues. Thanks to a combination of genetic, molecular, and imaging approaches sub- stantial insight into the formation and development of the SAM have now been achieved (Figure 2). Additionally, networking approaches and mathematical models have frequently been used to probe our understanding of apical systems in silico. Since the ‘Omics’ revolution, a significant contribution to these discoveries is a result of the generation of ‘big data’ produced by advances in high- throughput sequencing techniques and decreasing sequencing costs. GRNs employing machine learning or Bayesian algorithms are now making use of the large volumes of transcriptomic data, and are ever-improving with the integration epigenetic data (such as ChIP data), increasing precision and accuracy by honing in on direct, causal interactions (Chen et al., 2020; Klein et al., 2020; Sauta et al., 2020; De Clercq et al., 2021; Lechon et al., 2025). On a similar note, an investigation into regulators of reactive oxygen species (ROS) signalling used a supervised machine learning method to incorporate seven GRNs comprised of transcription factor motif, open chromatin, co-expression, and ChIP-binding data to create an integrative GRN (iGRN) (De Clercq et al., 2021). The iGRN also incorporated conserved non-coding regions across 13 dicotyledonous genomes using a comparative motif mapping algorithm (Van de Velde et al., 2016). The iGRN was able to recapitulate known regulatory interactions as well as predicting novel ones, later validated in vivo. As this model outperformed the individual input models, it highlights how using a broad range of omics data can vastly improve network inference. It will be interesting to see how the use of such networks will shed more light on conserved network hubs between plant species and core facets of shoot development. Despite the widespread use of these advanced techniques to investigate SAM processes, features of experimental design such as the use of bulk tissue and single timepoint “snapshot” studies have limited their potential. As a result, a true representation of the continuous and dynamic nature of SAM GRNs as well as the cross- talk between different systems remains elusive (Zhang et al., 2021a). Trends in experimental design are now rapidly shifting towards the integration of multiple genome-wide approaches with single cell analysis to analyse stem cell differentiation in the SAM (Scofield et al., 2018; Sijacic et al., 2018; Ma et al., 2019; Tian et al., 2019; Mahajan and Yadav, 2020; Zhang et al., 2021a) and in developing floral meristems (reviewed in Pelayo and Yamaguchi, 2023). Furthermore, insights into the genome-wide chromatin landscape of the SAM is now being explored at the bulk tissue and single cell level (Zhang et al., 2012; Zhu et al., 2015; Sijacic et al., 2018). Future single cell studies of SAM chromatin and organ primordia tissues will provide greater insight to the chromatin landscape. Combining this with other epigenetic and transcriptomic data would contribute to resolving these GRNs to the cellular level. Due to the nature of high-throughput sequencing data, vast amounts of transcriptome and chromatin accessibility information have been generated and uploaded to public repositories for com- munity use. For example, the Plant Public RNA-seq Database compiles ~100,000 RNA-seq libraries across multiple plant species to explore gene co-expression across multiple tissues and experimental conditions (Yu et al., 2022b). Likewise, the Arabidopsis Shoot Cell Atlas hosts the published scRNA-seq data from Zhang et al. (2021), providing an interactive interface with the data. SAM research will greatly benefit from leveraging these large single cell omics datasets with the latest bioinformatics tools, though current GRN techniques will likely require new innovations to supplement the spatial data produced by scRNA-seq (Zinati et al., 2024).

    Big data approaches to understanding gene regulatory networks in the shoot apical meristem and de novo shoot regeneration · 2026 · DOI

  • A key limitation of this study is that the identification of cAMP-responsive genes (CRGs) and the subsequent pro- tein–protein interaction (PPI) network are based on tran- scriptomic data, which may not directly reflect protein abundance due to post-transcriptional and post-translational regulation.

    Endogenous cAMP elevation regulates proteostasis networks to integrate stress signaling, metabolic reprogramming, and immune defense in Arabidopsis · 2026 · DOI

  • sRNAs exert pivotal regulatory functions across all eukaryotic organisms, yet critical knowledge gaps persist in fungal sRNA research. First, it remains to be clarified whether novel classes of fungal sRNAs exist beyond the currently identified subtypes. While preliminary evidence has confirmed that sRNAs modulate core fungal biological processes—including growth, development, and stress adaptation—the precise molecular mechanisms underlying their activity are far from fully elucidated. Key unresolved questions include defining the context-specific functions of individual sRNA molecules, characterizing their spatiotemporal expression patterns, dissecting the structural dynamics and functional specificities of sRNA-associated protein complexes, and unraveling the evolutionary drivers that have shaped the diversity of fungal sRNA pathways (Chand et al., 2017). Technical bottlenecks continue to hinder the comprehensive study of fungal sRNAs. Although advancements have been made in detecting, isolating, and characterizing fungal sRNAs, limitations such as low sensitivity for detecting low-abundance sRNA species and the technical complexity of purifying structurally modified sRNAs restrict the scope of exploratory studies. Moreover, functional validation of fungal sRNAs is hindered by the recalcitrance of many fungal species to efficient genetic transformation. The lack of robust protocols for targeted gene knockout or in vivo overexpression in non-model fungi compromises the accuracy and reproducibility of sRNA functional assays (Hamby et al., 2020). Compounding these challenges is the extreme intricacy of fungal sRNA regulatory networks, involving numerous interactions between sRNAs, their target mRNAs, and downstream signaling cascades. Unraveling these interactions presents a major challenge for researchers aiming to elucidate the full scope of sRNA-mediated gene regulation. Nevertheless, with the rapid advancement of computational science, bioinformatics, and biotechnology, biological research has entered the era of whole-genome studies.

    Fungal small RNA: unveiling the breakthroughs and promising applications · 2026 · DOI

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90 open questions have been extracted from the limitations and future-work passages of 459 Plant Molecular Biology Research papers in our library. Each one below links back to the study that raised it, so you can read the original claim in context.

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