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Background <p>The epidermal patterning factor/epidermal patterning factor-like (EPF/EPFL) proteins are pivotal regulators of stomatal development and responses to abiotic stress. However, their functions in wheat (<i>Triticum aestivum L.</i>) remain underexplored despite their critical roles in water-use efficiency and drought adaptation.</p> Result <p>This pan-genomic identification study investigated a diverse panel of 13 wheat accessions, including wild relatives and modern cultivars, to analyze the genomic diversity, evolutionary history, and functional characterization of the <i>EPF</i>/<i>EPFL</i> family. A total of 365 non-redundant <i>EPF</i>/<i>EPFL</i> genes were identified, revealing substantial structural and phylogenetic divergence between the EPF (24.9%) and EPFL (75.1%) clades. Comparative analyses demonstrated species-specific chromosomal distributions, conserved motif architectures (e.g., Stomagen domains in EPFL9 homologs), and widespread purifying selection (66% of duplicated pairs), indicating functional constraints. Promoter cis-element profiling revealed enrichment for motifs related to stress responses (ABRE, MBS) and hormonal signaling (auxin, jasmonate), consistent with their roles in drought adaptation. MicroRNA target prediction identified <i>Tae-miR530</i> and <i>Tae-miR408</i> as key post-transcriptional regulators of <i>EPF</i>/<i>EPFL</i> genes. Collinearity analyses across <i>Poaceae</i> species emphasized conserved synteny blocks, while RNA-seq and RT-qPCR validation in <i>T. aestivum</i> cv. Chinese Spring revealed tissue and stress-specific expression patterns, with <i>TaCSEPFL5</i>, <i>TaCSEPFL8</i>, and <i>TaCSEPFL9</i> homologs exhibiting significant upregulation in spikes, leaves, and roots under PEG-induced osmotic stress. Notably, <i>TaCSEPF1-1B</i> and <i>TaCSEPFL2-3&#xa0;A</i> displayed antagonistic regulatory dynamics, suggesting functional diversification.</p> Conclusion <p>This study provides a genomic atlas of the wheat <i>EPF</i>/<i>EPFL</i> gene family, elucidating their evolutionary trajectories, regulatory networks, and drought-responsive expression landscapes. These insights can benefit wheat breeding by enhancing climate resilience through targeted stomatal optimization and the development of stress-adaptive traits.</p>

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Pan-genomic diversity of the EPF/EPFL gene family across wild and modern wheat species

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2026年1月31日

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  • Jazib Javed,
  • Guorui Wang,
  • Shijun Sun,
  • Huma Saleem,
  • Faheem Shehzad Baloch,
  • Xueyi Xue,
  • Jin-Ying Gou

摘要

Background

The epidermal patterning factor/epidermal patterning factor-like (EPF/EPFL) proteins are pivotal regulators of stomatal development and responses to abiotic stress. However, their functions in wheat (Triticum aestivum L.) remain underexplored despite their critical roles in water-use efficiency and drought adaptation.

Result

This pan-genomic identification study investigated a diverse panel of 13 wheat accessions, including wild relatives and modern cultivars, to analyze the genomic diversity, evolutionary history, and functional characterization of the EPF/EPFL family. A total of 365 non-redundant EPF/EPFL genes were identified, revealing substantial structural and phylogenetic divergence between the EPF (24.9%) and EPFL (75.1%) clades. Comparative analyses demonstrated species-specific chromosomal distributions, conserved motif architectures (e.g., Stomagen domains in EPFL9 homologs), and widespread purifying selection (66% of duplicated pairs), indicating functional constraints. Promoter cis-element profiling revealed enrichment for motifs related to stress responses (ABRE, MBS) and hormonal signaling (auxin, jasmonate), consistent with their roles in drought adaptation. MicroRNA target prediction identified Tae-miR530 and Tae-miR408 as key post-transcriptional regulators of EPF/EPFL genes. Collinearity analyses across Poaceae species emphasized conserved synteny blocks, while RNA-seq and RT-qPCR validation in T. aestivum cv. Chinese Spring revealed tissue and stress-specific expression patterns, with TaCSEPFL5, TaCSEPFL8, and TaCSEPFL9 homologs exhibiting significant upregulation in spikes, leaves, and roots under PEG-induced osmotic stress. Notably, TaCSEPF1-1B and TaCSEPFL2-3 A displayed antagonistic regulatory dynamics, suggesting functional diversification.

Conclusion

This study provides a genomic atlas of the wheat EPF/EPFL gene family, elucidating their evolutionary trajectories, regulatory networks, and drought-responsive expression landscapes. These insights can benefit wheat breeding by enhancing climate resilience through targeted stomatal optimization and the development of stress-adaptive traits.