SynthesisBMC genomics2024
Functional annotation and meta-analysis of maize transcriptomes reveal genes involved in biotic and abiotic stress.
Synthesis in BMC genomics, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers, 2 of them syntheses that pooled it.
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Who cites it
15 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- 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
- Unveiling crosstalk between abiotic and biotic stress responses in soybean (Glycine max) using integrative RNA-Seq meta-analysis.Molecular genetics and genomics : MGG · 2025Pooled it
- Artificial intelligence in plant salt stress research: from predictive models to multi-omics integration.Journal of experimental botany · 2026Review
- Genome-Wide Identification of the P-Type CaInternational journal of molecular sciences · 2026Article
- Integrative transcriptional regulatory networks governing cereal root responses to heavy metals and drought.Plant cell reports · 2026Review
- Genome-wide identification and expression analysis of YTH domain-containing RNA-binding protein family in maize reveals their potential role under abiotic stresses.Scientific reports · 2026Article
- MaizeGDB Phylostrata Tool: exploring evolutionary origins of maize proteins.Bioinformatics advances · 2026Article
- Article
- LcTprxII Overexpression Enhances Physiological and Biochemical Effects in Maize Under Alkaline (NaPlants (Basel, Switzerland) · 2025Article
- The resistance awakens: Diversity at the DNA, RNA, and protein levels informs engineering of plant immune receptors from Arabidopsis to crops.The Plant cell · 2025Review
- Predictive prioritization of genes significantly associated with biotic and abiotic stresses in maize using machine learning algorithms.Frontiers in plant science · 2025Article
- Gaining insights into genomic regions associated withFrontiers in genetics · 2025Article
- A Critical Review of Recent Advances in Maize Stress Molecular Biology.International journal of molecular sciences · 2024Review
- The Interplay of Nitric Oxide and Nitrosative Modifications in Maize: Implications for Aphid Herbivory and Drought Stress.International journal of molecular sciences · 2024Article
- Article
Corrections and comments
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Authors and funding
7 authors.
Funding
Abstract
backgroundEnvironmental stress factors, such as biotic and abiotic stress, are becoming more common due to climate variability, significantly affecting global maize yield. Transcriptome profiling studies provide insights into the molecular mechanisms underlying stress response in maize, though the functions of many genes are still unknown. To enhance the functional annotation of maize-specific genes, MaizeGDB has outlined a data-driven approach with an emphasis on identifying genes and traits related to biotic and abiotic stress.
resultsWe mapped high-quality RNA-Seq expression reads from 24 different publicly available datasets (17 abiotic and seven biotic studies) generated from the B73 cultivar to the recent version of the reference genome B73 (B73v5) and deduced stress-related functional annotation of maize gene models. We conducted a robust meta-analysis of the transcriptome profiles from the datasets to identify maize loci responsive to stress, identifying 3,230 differentially expressed genes (DEGs): 2,555 DEGs regulated in response to abiotic stress, 408 DEGs regulated during biotic stress, and 267 common DEGs (co-DEGs) that overlap between abiotic and biotic stress. We discovered hub genes from network analyses, and among the hub genes of the co-DEGs we identified a putative NAC domain transcription factor superfamily protein (Zm00001eb369060) IDP275, which previously responded to herbivory and drought stress. IDP275 was up-regulated in our analysis in response to eight different abiotic and four different biotic stresses. A gene set enrichment and pathway analysis of hub genes of the co-DEGs revealed hormone-mediated signaling processes and phenylpropanoid biosynthesis pathways, respectively. Using phylostratigraphic analysis, we also demonstrated how abiotic and biotic stress genes differentially evolve to adapt to changing environments.
conclusionsThese results will help facilitate the functional annotation of multiple stress response gene models and annotation in maize. Data can be accessed and downloaded at the Maize Genetics and Genomics Database (MaizeGDB).
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