ArticleRice (New York, N.Y.)2013
Genome-wide identification and analysis of miRNA-related single nucleotide polymorphisms (SNPs) in rice.
Article in Rice (New York, N.Y.), 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
17 citing papers in PubMed, 38 citations in OpenAlex.
- Development of miRNA-SSR and target-SSR markers from yield-associate genes and their applicability in the assessment of genetic diversity and association mapping in rice (Molecular breeding : new strategies in plant improvement · 2024Article
- A microRNA-microRNA crosstalk network inferred from genome-wide single nucleotide polymorphism variants in natural populations ofFrontiers in plant science · 2022Article
- Article
- Genome-wide development of miRNA-based SSR markers in Cleistogenes songorica and analysis of their transferability to Gramineae/non-Gramineae species.Journal of applied genetics · 2020Article
- Genome-Wide Analysis of MicroRNA-related Single Nucleotide Polymorphisms (SNPs) in Mouse Genome.Scientific reports · 2020Article
- Integrated Analysis of Large-Scale Omics Data Revealed Relationship Between Tissue Specificity and Evolutionary Dynamics of Small RNAs in Maize (Frontiers in genetics · 2020Article
- RNAseq analysis reveals drought-responsive molecular pathways with candidate genes and putative molecular markers in root tissue of wheat.Scientific reports · 2019Article
- Development of transcriptome based web genomic resources of yellow mosaic disease inPhysiology and molecular biology of plants : an international journal of functional plant biology · 2017Article
- Comprehensive survey and evolutionary analysis of genome-wide miRNA genes from ten diploid Oryza species.BMC genomics · 2017Article
- Abiotic Stress Responsive miRNA-Target Network and Related Markers (SNP, SSR) inFrontiers in plant science · 2017Article
- Expression Variations of miRNAs and mRNAs in Rice (Oryza sativa).Genome biology and evolution · 2016Article
- Dissection of allelic interactions among Pto-miR257 and its targets and their effects on growth and wood properties in Populus.Heredity · 2016Article
- Association genetics in Populus reveals the interactions between Pto-miR160a and its target Pto-ARF16.Molecular genetics and genomics : MGG · 2016Article
- Association genetics in Populus reveals the interactions between Pt-miR397a and its target genes.Scientific reports · 2015Article
- Comparative analysis of the Dicer-like gene family reveals loss of miR162 target site in SmDCL1 from Salvia miltiorrhiza.Scientific reports · 2015Article
- Genome-wide identification and evolutionary analysis of positively selected miRNA genes in domesticated rice.Molecular genetics and genomics : MGG · 2015Article
- Identification and analysis of genetic variations in pri-miRNAs expressed specifically or at a high level in sheep skeletal muscle.PloS one · 2015Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundMiRNAs are key regulators in the miRNA-mediated regulatory networks. Single nucleotide polymorphisms (SNPs) that occur at miRNA-related regions may cause serious phenotype changes. To gain new insights into the evolution of miRNAs after SNP variation, we performed a genome-wide scan of miRNA-related SNPs, and analyzed their effects on the stability of miRNAs structure and the alteration of target spectrum in rice.
resultsWe find that the SNP density in pre-miRNAs is significantly higher than that in the flanking regions, owing to the rapid evolution of a large number of species-specific miRNAs in rice. In contrast, it is obvious that deeply conserved miRNAs are under strong purifying selection during evolution. In most cases, the SNPs in stem regions may result in the miRNA hairpin structures changing from stable to unstable status; And SNPs in mature miRNAs have great potential to have either newly created or disrupted the miRNA-target interactions. However, the total number of gained targets is over 2.5 times greater than that are lost after mutation. Notably, 12 putative domestication-related miRNAs have been identified, where the SNP density is significantly lower.
conclusionsThe present study provides the first outline of SNP variations occurred in rice pre-miRNAs at the whole genome-wide level. These analyses may deepen our understanding on the effects of SNPs on the evolution of miRNAs in the rice genome.
Identifiers
What OpenQuestion holds
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.