ArticleGenome biology and evolution2016
Expression Variations of miRNAs and mRNAs in Rice (Oryza sativa).
Article in Genome biology and evolution, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- Photoperiodic patterns in miRNA-mRNA pairs and tRNA fragments revealed by time-course co-sequencing in Arabidopsis.PLoS genetics · 2026Article
- ComparativeFrontiers in plant science · 2026Article
- Review
- Inferring the Regulatory Network of miRNAs on Terpene Trilactone Biosynthesis Affected by Environmental Conditions.International journal of molecular sciences · 2023Article
- ZmEREB92 plays a negative role in seed germination by regulating ethylene signaling and starch mobilization in maize.PLoS genetics · 2023Article
- An Insight Into Pentatricopeptide-Mediated Chloroplast NecrosisFrontiers in genetics · 2022Article
- microRNA 166: an evolutionarily conserved stress biomarker in land plants targeting HD-ZIP family.Physiology and molecular biology of plants : an international journal of functional plant biology · 2021Review
- RNA-Sequencing Reveals Differentially Expressed Rice Genes Functionally Associated with Defense against BPH and WBPH in RILs Derived from a Cross between RP2068 and TN1.Rice (New York, N.Y.) · 2021Article
- Global mRNA and microRNA expression dynamics in response to anthracnose infection in sorghum.BMC genomics · 2020Article
- An inferred fitness consequence map of the rice genome.Nature plants · 2020Article
- Drought Response in Rice: The miRNA Story.International journal of molecular sciences · 2019Review
- Expression profiling across wild and cultivated tomatoes supports the relevance of early miR482/2118 suppression forProceedings. Biological sciences · 2018Article
- Integration of the Pokeweed miRNA and mRNA Transcriptomes Reveals Targeting of Jasmonic Acid-Responsive Genes.Frontiers in plant science · 2018Article
- Integrated analysis of mRNA and miRNA expression profiling in rice backcrossed progenies (BC2F12) with different plant height.PloS one · 2017Article
- Novel Insights into miRNA Regulation of Storage Protein Biosynthesis during Wheat Caryopsis Development under Drought Stress.Frontiers in plant science · 2017Article
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Authors and funding
6 authors.
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Abstract
Differences in expression levels are an important source of phenotypic variation within and between populations. MicroRNAs (miRNAs) are key players in post-transcriptional gene regulation that are important for plant development and stress responses. We surveyed expression variation of miRNAs and mRNAs of six accessions from two rice subspecies Oryza sativa L. ssp. indica and Oryza sativa L. ssp. japonica using deep sequencing. While more than half (53.7%) of the mature miRNAs exhibit differential expression between grains and seedlings of rice, only 11.0% show expression differences between subspecies, with an additional 2.2% differentiated for the development-by-subspecies interaction. Expression variation is greater for lowly conserved miRNAs than highly conserved miRNAs, whereas the latter show stronger negative correlation with their targets in expression changes between subspecies. Using a permutation test, we identified 51 miRNA-mRNA pairs that correlate negatively or positively in expression level among cultivated rice. Genes involved in various metabolic processes and stress responses are enriched in the differentially expressed genes between rice indica and japonica subspecies. Our results indicate that stabilizing selection is the major force governing miRNA expression in cultivated rice, albeit positive selection may be responsible for much of the between-subspecies expression divergence.
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