Open research questions in Plant Molecular Biology Research
1,308 gap statements mined from Plant Molecular Biology Research papers in our 7.9M-paper local library, which holds 5,097 papers on the topic — drawn mostly from each paper's own stated research gap, future-work, challenge and limitation notes, and its abstract. The ones listed below are a selection still marked open; each names the study that raised it, with a DOI link where the paper has one.
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What the literature leaves open
The slow growth rate of plant cells, which requires slower-maturing fluorescent timers. The lower growth temperatures for plants, which further slow fluorophore maturation. The need to balance cell growth rate, temperature, and fluorophore maturation kinetics for adapting fluorescent timers to plants. The potential interference of large-sized tandem fluorescent timers with protein mobility.
A suite of fluorescent timers for visualizing protein spatiotemporal dynamics in plants · 2026 · DOIThe study faced challenges in identifying expansin genes in bryophytes and green algae due to the lack of prior knowledge. The phylogenetic analysis of the expansin gene families was challenging due to the complexity of the data. The study also faced challenges in determining the relationships between the expansin gene families in bryophytes and green algae.
The research required the development of a comprehensive rhizome transcriptome for D. roosii at three distinct developmental stages. The study needed to validate the transcript abundance of DEGs obtained from RNA-Seq using quantitative real-time PCR analysis.
The regulatory networks and metabolite variations during rhizome development in Drynaria roosii Nakaike · 2026 · DOIThe lack of understanding of the LdERF gene subfamily's role in bulblet regeneration. The need for a comprehensive genome-wide analysis of the LdERF gene subfamily.
Genome-Wide Analysis of the LdERF Gene Subfamily and Functional Characterization of LdERF179 During Bulblet Regeneration in Lilium · 2026 · DOIFunctional annotation of genes with domains of unknown function (DUFs) is a significant challenge. Understanding the population-level diversity and potential functions of the DUF668 gene family in maize is a complex task. Characterizing the expression of DUF668 genes under various abiotic stress conditions is a technical challenge.
Pan-Genome-Wide Identification, Evolutionary Analysis, and Stress-Responsive Expression Profiling of the Maize DUF668 Gene Family · 2026 · DOIThe mechanism of interaction between ELF3 homologs and R2R3-MYB TFs is not well understood. The regulation of flowering and floral development by the ELF3-R2R3-MYB module is not clearly defined.
The FaesMYB15-FaesELF3 module regulates flowering time, floral organ number, and floral color in red flower long-homostyle common buckwheat · 2026 · DOILimited genome-wide information on the PIN gene family in Populus euphratica. Poor understanding of the molecular processes regulating the development of different leaf forms in P. euphratica. Lack of functional characterization of PePIN genes in relation to leaf development and adaptation to arid conditions.
Genome-Wide Analysis of the PIN-FORMED Gene Family in Populus euphratica and Functional Characterization of PePIN1a Through Heterologous Expression in Arabidopsis thaliana · 2026 · DOIIt highlights the need for further research on the potential applications of AP2/ERF TFs in crop improvement.
It highlights the need to elucidate the complex roles of DNA methylation, histone modifications, histone variants, and non-coding RNAs in plant adaptation to salt stress.
The dynamic and spatiotemporal organization of the molecular interactions between BES1/BZR1 and their interacting partners remain poorly understood. The paper identifies a gap in understanding how BES1/BZR1 determine their interacting partners and establish a complex regulatory network.
Traditional biochemical and genetic approaches are not ideal for high-efficiency peptide identification. There is a need for novel peptidomics, bioinformatics screening, and biochemical and genetic validation methods for peptide identification.
The need to identify key genes and metabolites involved in the cold tolerance of Chrysanthemum. The challenge of understanding the molecular mechanisms underlying the cold tolerance of Chrysanthemum.
Integrated Metabolomics and Transcriptomics Reveal the Key Role of Flavonoids in the Cold Tolerance of Chrysanthemum · 2024 · DOIThe need to allocate resources according to physiological need in response to biotic and abiotic cues.
The evolutionary history of the expansin superfamily in early-diverging land plants and green algae is not well understood. There is a lack of knowledge about the expansin gene families in bryophytes and green algae. The study aims to fill this gap by examining the expansin superfamilies in these organisms.
The specific biochemical and molecular mechanisms regulating D. roosii Nakaike growth and development remain poorly understood. There is a limited investigation on transcriptional changes through the developmental phases. The study aims to fill this knowledge gap by utilizing Illumina paired-end sequencing to develop a comprehensive rhizome transcriptome for D. roosii at three distinct developmental stages.
The regulatory networks and metabolite variations during rhizome development in Drynaria roosii Nakaike · 2026 · DOIEarly postgermination growth is critical for uniform seedling emergence in direct-seeded rice; however, the underlying regulatory mechanisms remain unclear.
Prime editing of an RR26-responsive cis-element enhances DAHPS2 expression and submergence tolerance in rice through the shikimate pathway · 2026 · DOIAdditionally, we discuss potential regulatory models for RLK-PUB modules whose mechanisms remain unresolved and highlight key questions that warrant further investigation.
Crosstalk and reciprocal regulation of phosphorylation and ubiquitination mediated by receptor-like kinases and U-box E3 ligases during plant growth and environmental stress responses · 2026 · DOIIt is also crucial to investigate whether additional regulators from other pathways interact with BES1/BZR1 to modulate more cellular or developmental processes responsive to BR.
In-depth bioinformatics analysis of the DUF superfamily is essential for completing the functional annotation of plant genomes, - Further studies are needed to reveal novel regulatory mechanisms in plant systems, - Functional validation of candidate genes in maize development and abiotic stress responses…
Pan-Genome-Wide Identification, Evolutionary Analysis, and Stress-Responsive Expression Profiling of the Maize DUF668 Gene Family · 2026 · DOIInvestigate the contribution of the expanded PIN gene family to desert adaptation, - Examine the role of additional PIN transporters in regulating auxin distribution under desert conditions, - Directly investigate the function of PIN genes…
Genome-Wide Analysis of the PIN-FORMED Gene Family in Populus euphratica and Functional Characterization of PePIN1a Through Heterologous Expression in Arabidopsis thaliana · 2026 · DOIThe regulation of BR transport by sugar signals remains unreported, - Traditional studies have predominantly focused on transcriptional regulation, - The knowledge gap regarding the rapid regulation of metabolic flux by hormonal signals has been recently…
Further study of glycosyltransferase's function in Chrysanthemum - Research on CmbZIP3 and CmNAC1 as potential transcription factors regulating cold tolerance - Investigation of the role of flavonoid metabolism in response to low temperature…
Integrated Metabolomics and Transcriptomics Reveal the Key Role of Flavonoids in the Cold Tolerance of Chrysanthemum · 2024 · DOIThe devised approach is expected to be applicable to any other study-to-(key-of-interest) associations, - Further expansion of the range of MADS box members associated with plant organs and trait-linked…
Elucidate the unique regulatory mechanism miRNAs and lncRNAs in the formation of plant stress memory, - Further research is needed to elucidate the direct evidence elucidating the acetyl-CoA promoted histone acetylation in response to salt stress, - The precise mechanism by which histone variants mediate plant salt tolerance remains to be fully…
This review also offers a perspective on future research directions in peptide signaling…
Most-cited papers in Plant Molecular Biology Research
- Analysis of the genome sequence of the flowering plant Arabidopsis thaliana · Nature · 2000 · 7,468 citations
- Genome-Wide Insertional Mutagenesis of Arabidopsis thaliana · Science · 2003 · 4,334 citations
- Abscisic Acid Inhibits Type 2C Protein Phosphatases via the PYR/PYL Family of START Proteins · Science · 2009 · 2,579 citations
- Arabidopsis Transcription Factors: Genome-Wide Comparative Analysis Among Eukaryotes · Science · 2000 · 2,400 citations
- RNA silencing in plants · Nature · 2004 · 2,164 citations
- Regulators of PP2C Phosphatase Activity Function as Abscisic Acid Sensors · Science · 2009 · 2,133 citations
- A prion-like domain in ELF3 functions as a thermosensor in Arabidopsis · Nature · 2020 · 652 citations
- Reporters for sensitive and quantitative measurement of auxin response · Nature Methods · 2015 · 473 citations
- Enhanced sustainable green revolution yield via nitrogen-responsive chromatin modulation in rice · Science · 2020 · 459 citations
- Leaf senescence: progression, regulation, and application · Molecular Horticulture · 2021 · 403 citations
Most recent work
- Dynamic Coordination: How ERF Transcription Factors Coordinate Plant Development and Adaptive Stress Responses · Biomolecules · 2026
- Imputation integrates single-cell and spatial gene expression data to resolve transcriptional networks in barley shoot meristem development · Nature Plants · 2026
- Epigenetic modifications in plant abiotic stress adaptation: towards climate-resilient and sustainable crop improvement · Frontiers in Plant Science · 2026
- Guanylate cyclase activity of TIR1/AFB auxin receptors mediates rapid auxin responses · bioRxiv · 2026
- Turgor reduction triggers FERONIA nanodomain assembly for osmosensing in plants · Current Biology · 2026
- Sex‐specific ethylene responses drive floral sexual plasticity in Cannabis sativa · The Plant Journal · 2026
- Histone deacetylases and cell-cycle regulators orchestrate cell-identity transitions during Arabidopsis root regeneration · Molecular Plant · 2026
- SPL transcription factors in plants: a potential stress regulator · Horticultural Plant Journal · 2026
- Synthetic promoter design in plants: integration of computational and experimental approaches · Frontiers in Plant Science · 2026
- Plant cell surface receptors · The Plant Journal · 2026
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