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Epigenetic Switches in the Proximal 3' UTR Reprograms TaFAR1-L Temporal Expression in Wheat During Leaf Rust

Uzma Afreen1, Shailendra Kumar Jha2, Kunal Mukhopadhyay1

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Physiologia Plantarum
|October 19, 2025
PubMed
Summary

Wheat FAR-RED IMPAIRED RESPONSE1 (FAR1) gene regulation was studied in leaf rust. Demethylation in resistant wheat enhanced FAR1 expression, suggesting FAR1 aids rust tolerance and epigenetic marks can control its expression.

Keywords:
3′ UTRCpG methylationTaFAR1‐Lcis‐regulatory elementsleaf rustsORFswheat

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Area of Science:

  • Plant molecular biology
  • Epigenetics
  • Wheat genetics

Background:

  • Noncoding DNA regulatory roles are often underestimated.
  • FAR-RED IMPAIRED RESPONSE1 (FAR1) is a transcription factor vital for light signaling and defense.
  • Wheat FAR1 gene regulation, especially during pathogen attack, remains largely uncharacterized.

Purpose of the Study:

  • To investigate the regulatory role of the 3' UTR sequence and epigenetic modifications of wheat FAR1 (TaFAR1-L) genes.
  • To decipher the importance of TaFAR1-L during leaf rust pathogenesis in wheat.
  • To explore the potential of epigenetic modifications as regulatory markers for TaFAR1-L.

Main Methods:

  • Genome mining to identify TaFAR1-L homoeologs in wheat.
  • Identification and network analysis of leaf rust-responsive miRNAs targeting TaFAR1-L.
  • Phylogenetic analysis of TaFAR1-L with related species.
  • Analysis of CpG site methylation states in the 3' UTR of TaFAR1-L-15.

Main Results:

  • 19 TaFAR1-L homoeologs were identified across wheat subgenomes.
  • Leaf rust-responsive miRNAs targeting TaFAR1-L were identified.
  • Significant demethylation of 3' UTR CpG sites in resistant wheat post-inoculation.
  • Upregulated TaFAR1-L expression and downregulated TamiR-142 in resistant lines, contrasting with susceptible lines.

Conclusions:

  • TaFAR1-L likely acts as a positive regulator in wheat leaf rust tolerance.
  • Cytosine methylation in proximal 3' UTR cis-elements may control TaFAR1-L expression.
  • Epigenetic modifications in noncoding regions offer potential targets for crop improvement.