Related Experiment Video
Updated: May 26, 2026
A Bioinformatics Pipeline to Accurately and Efficiently Analyze the MicroRNA Transcriptomes in Plants
Published on: January 21, 2020
Natural variation in biogenesis efficiency of individual Arabidopsis thaliana microRNAs
Marco Todesco1, Sureshkumar Balasubramanian, Jun Cao
1Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany.
Abstract:
Like protein-coding genes, loci that produce microRNAs (miRNAs) are generally considered to be under purifying selection, consistent with miRNA polymorphisms being able to cause disease. Nevertheless, it has been hypothesized that variation in miRNA genes may contribute to phenotypic diversity. Here we demonstrate that a naturally occurring polymorphism in the MIR164A gene affects leaf shape and shoot architecture in Arabidopsis thaliana, with the effects being modified by additional loci in the genome. A single base pair substitution in the miRNA complementary sequence alters the predicted stability of the miRNA:miRNA(∗) duplex. It thereby greatly reduces miRNA accumulation, probably because it interferes with precursor processing. We demonstrate that this is not a rare exception and that natural strains of Arabidopsis thaliana harbor dozens of similar polymorphisms that affect processing of a wide range of miRNA precursors. Our results suggest that natural variation in miRNA biogenesis resulting from cis mutations is a common contributor to phenotypic variation in plants.
Insights
Natural variation in microRNA (miRNA) genes influences plant traits. A specific MIR164A gene change impacts leaf shape and plant architecture by altering miRNA processing and accumulation.
Area of Science:
- Plant molecular biology
- Genetics
- Developmental biology
Background:
- MicroRNAs (miRNAs) are typically under purifying selection, with polymorphisms potentially causing disease.
- Variation in miRNA genes has been hypothesized to contribute to phenotypic diversity.
- Understanding miRNA gene variation is crucial for plant breeding and evolution.
Purpose of the Study:
- To investigate the role of natural polymorphisms in miRNA genes on plant phenotypes.
- To determine if variation in miRNA biogenesis contributes to phenotypic variation in Arabidopsis thaliana.
- To identify specific genetic mechanisms linking miRNA polymorphisms to observable traits.
Main Methods:
- Analysis of a naturally occurring polymorphism in the MIR164A gene in Arabidopsis thaliana.
- Assessment of the impact of the polymorphism on leaf shape and shoot architecture.
- Investigation of the molecular effects on miRNA:miRNA(∗) duplex stability and miRNA accumulation.
- Bioinformatic screening for similar polymorphisms across natural strains of Arabidopsis thaliana.
Main Results:
- A single base pair substitution in MIR164A alters miRNA:miRNA(∗) duplex stability, reducing miRNA accumulation.
- This polymorphism significantly affects leaf shape and shoot architecture in Arabidopsis thaliana.
- The effects of the MIR164A polymorphism are modulated by other genetic loci.
- Dozens of similar polymorphisms affecting miRNA precursor processing were identified in natural Arabidopsis strains.
Conclusions:
- Natural variation in miRNA biogenesis, driven by cis-acting mutations, is a common source of phenotypic variation in plants.
- Polymorphisms in miRNA genes can lead to significant, heritable changes in plant morphology.
- This finding broadens the understanding of genetic variation and its impact on plant evolution and development.
Related Concept Videos
01:22MicroRNAs
01:22MicroRNAs
01:22MicroRNAs