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MicroRNAs01:22

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MicroRNA (miRNA) are short, regulatory RNA transcribed from introns (non-coding regions of a gene) or intergenic regions (stretches of DNA present between genes). Several processing steps are required to form biologically active, mature miRNA. The initial transcript, called primary miRNA (pri-mRNA), base-pairs with itself, forming a stem-loop structure. Within the nucleus, an endonuclease enzyme, called Drosha, shortens the stem-loop structure into hairpin-shaped pre-miRNA. After the pre-miRNA...
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RNA interference (RNAi) is a cellular mechanism that inhibits gene expression by suppressing its transcription or activating the RNA degradation process. The mechanism was discovered by Andrew Fire and Craig Mello in 1998 in plants. Today, it is observed in almost all eukaryotes, including protozoa, flies, nematodes, insects, parasites, and mammals. This precise cellular mechanism of gene silencing has been developed into a technique that provides an efficient way to identify and determine the...
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Updated: Jun 4, 2025

RNA Blot Analysis for the Detection and Quantification of Plant MicroRNAs
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Genome-Wide Dissection of Selection on microRNA Target Genes Involved in Rice Flower Development.

Fen Zhang1, Li-Zhen Ling2, Li-Zhi Gao1,2

  • 1Engineering Research Center for Selecting and Breeding New Tropical Crop Varieties, Ministry of Education, Tropical Biodiversity and Genomics Research Center, Hainan University, Haikou 570228, China.

Plants (Basel, Switzerland)
|December 17, 2024
PubMed
Summary

Rice flower development involves distinct selection pressures on microRNA (miRNA) targets. Conserved miRNA binding sites show purifying selection, while non-conserved sites exhibit population-specific variations, suggesting roles in phenotypic diversity.

Keywords:
Oryza sativaflower developmentmicroRNA binding sitemolecular evolutionsequence polymorphism

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Area of Science:

  • Plant genetics and genomics
  • Evolutionary biology
  • Molecular biology

Background:

  • Genome-wide studies have identified regions under selection in domesticated species.
  • Characterizing selection regimes on microRNA (miRNA)-associated motifs in specific biological processes remains underexplored.

Purpose of the Study:

  • To perform a genome-wide analysis of nucleotide variation and selection on miRNA targets related to rice flower development.
  • To characterize the distinct selection pressures acting on these targets across diverse rice populations.

Main Methods:

  • Resequencing of 26 miRNA targets from globally diverse Asian cultivated rice and wild relatives.
  • Analysis of nucleotide variation and selection patterns at conserved and non-conserved miRNA binding sites.

Main Results:

  • Purifying selection has reduced genetic variation at conserved miRNA binding sites, maintaining sequence integrity.
  • Non-neutral evolution, including positive and/or artificial selection, has driven elevated variation at non-conserved binding sites in a population-specific manner.
  • These variations may contribute to phenotypic diversity in rice flower development.

Conclusions:

  • MiRNA targets involved in rice flower development are subjected to distinct evolutionary selection regimes.
  • Conserved binding sites are maintained by purifying selection, while non-conserved sites show adaptive variation influencing phenotypes.