ArticlePloS one2019
RNA-seq reveals differentially expressed genes in rice (Oryza sativa) roots during interactions with plant-growth promoting bacteria, Azospirillum brasilense.
Article in PloS one, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers, 2 of them syntheses that pooled it.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
32 citing papers in PubMed, 2 syntheses or guidelines pooled it, 67 citations in OpenAlex.
- Integrative meta-analysis of RNA-Seq data reveals conserved orthologous gene modules and pathways in wheat and rice in response to plant growth-promoting bacteria.Functional & integrative genomics · 2026Pooled it
- Modulation of plant transcription factors and priming of stress tolerance by plant growth-promoting bacteria: a systematic review.Annals of botany · 2025Pooled it
- Comparative transcriptomic analysis reveals distinct responses of beneficial bacterial endophytes to wild and cultivated rice root exudates.Plant cell reports · 2026Article
- A century ofPlant signaling & behavior · 2025Review
- Transcriptome-guided discovery of novel plant-associated genes in a rhizosphere Pseudomonas.Microbiome · 2025Article
- Recent Advances on the Individual Roles and Emerging Synergistic Effects of Plant Growth-Promoting Rhizobacteria and Silicon Nanoparticles in Mitigating Salinity Stress.Plants (Basel, Switzerland) · 2025Review
- Characterization of transcriptional and metabolic responses to a complex plant growth-promoting soil inoculum.Plant biology (Stuttgart, Germany) · 2025Article
- The impact of Bisphenol A on the endophytic bacterial community and transcriptome of soybean seedlings.iScience · 2025Article
- Ethylene signals through an ethylene receptor to modulate biofilm formation and root colonization in a beneficial plant-associated bacterium.PLoS genetics · 2025Article
- Nature's pre-installed helpers: diverse seed endophytes enhance rice nitrogen use efficiency.Frontiers in plant science · 2025Article
- Article
- Biosynthesis of Phenolic Compounds ofInternational journal of molecular sciences · 2024Article
- From trade-off to synergy: microbial insights into enhancing plant growth and immunity.Plant biotechnology journal · 2024Review
- Fine-Tuning ofPlants (Basel, Switzerland) · 2024Article
- Associative Bacteria and Arbuscular Mycorrhizal Fungus Increase Drought Tolerance in Maize (Plants (Basel, Switzerland) · 2024Article
- A comprehensive review onFrontiers in genetics · 2024Review
- Paired growth of cultivated and halophytic wild rice under salt stress induces bacterial endophytes and gene expression responses.Frontiers in plant science · 2023Article
- Article
- Flavonoids Are Intra- and Inter-Kingdom Modulator Signals.Microorganisms · 2022Review
- The Impact of Non-Nodulating Diazotrophic Bacteria in Agriculture: Understanding the Molecular Mechanisms That Benefit Crops.International journal of molecular sciences · 2022Review
Corrections and comments
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Authors and funding
8 authors at 2 institutions in 1 country.
Funding
Abstract
Major non-legume crops can form beneficial associations with nitrogen-fixing bacteria like Azospirillum brasilense. Our current understanding of the molecular aspects and signaling that occur between important crops like rice and these nitrogen-fixing bacteria is limited. In this study, we used an experimental system where the bacteria could colonize the plant roots and promote plant growth in wild type rice and symbiotic mutants (dmi3 and pollux) in rice. Our data suggest that plant growth promotion and root penetration is not dependent on these genes. We then used this colonization model to identify regulation of gene expression at two different time points during this interaction: at 1day post inoculation (dpi), we identified 1622 differentially expressed genes (DEGs) in rice roots, and at 14dpi, we identified 1995 DEGs. We performed a comprehensive data mining to classify the DEGs into the categories of transcription factors (TFs), protein kinases (PKs), and transporters (TRs). Several of these DEGs encode proteins that are involved in the flavonoid biosynthetic pathway, defense, and hormone signaling pathways. We identified genes that are involved in nitrate and sugar transport and are also implicated to play a role in other plant-microbe interactions. Overall, findings from this study will serve as an excellent resource to characterize the host genetic pathway controlling the interactions between non-legumes and beneficial bacteria which can have long-term implications towards sustainably improving agriculture.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.