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<p>Auxin response factors (ARFs) play a pivotal role in regulating plant growth and development; yet, their evolutionary dynamics and functional divergence remain poorly understood in barley (<i>Hordeum vulgare</i> L.) In this study, we conducted a comprehensive genome-wide analysis of the ARF gene family across a 76-accession barley pan-genome. By integrating gene presence/absence variation (PAV) and copy number variation (CNV), phylogeny, expression profiling, transposable element (TE)-mediated regulation, and selection signatures, we characterized 1,911 ARF-coding genes and their structural, transcriptional, and functional variation at the population level. Phylogenetic analysis revealed lineage-specific expansion and dynamic duplications, particularly within the HvARF13 clade. Co-expression networks and tissue-resolved transcriptomes showed that many <i>HvARFs</i> are preferentially expressed in inflorescence and meristematic tissues. Selective sweep and haplotype analyses identified <i>HvARF3</i> as a candidate gene under selection during European barley breeding. A favorable haplotype of <i>HvARF3</i>, enriched in European cultivars, was significantly associated with increased grain size and weight, demonstrating the utility of pan-genome-enabled frameworks for accelerating gene-trait association and candidate gene discovery. This study highlights the power of multi-omics integration in decoding gene family complexity and provides valuable insights for functional genomics and trait improvement in cereal crops.</p>

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Pan-genome analysis reveals hidden diversity and selection signatures of auxin response factors (ARFs) associated with breeding in barley

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2026年4月20日

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  • Kenan Tan,
  • Zhenru Guo,
  • Thorsten Schnurbusch

摘要

Auxin response factors (ARFs) play a pivotal role in regulating plant growth and development; yet, their evolutionary dynamics and functional divergence remain poorly understood in barley (Hordeum vulgare L.) In this study, we conducted a comprehensive genome-wide analysis of the ARF gene family across a 76-accession barley pan-genome. By integrating gene presence/absence variation (PAV) and copy number variation (CNV), phylogeny, expression profiling, transposable element (TE)-mediated regulation, and selection signatures, we characterized 1,911 ARF-coding genes and their structural, transcriptional, and functional variation at the population level. Phylogenetic analysis revealed lineage-specific expansion and dynamic duplications, particularly within the HvARF13 clade. Co-expression networks and tissue-resolved transcriptomes showed that many HvARFs are preferentially expressed in inflorescence and meristematic tissues. Selective sweep and haplotype analyses identified HvARF3 as a candidate gene under selection during European barley breeding. A favorable haplotype of HvARF3, enriched in European cultivars, was significantly associated with increased grain size and weight, demonstrating the utility of pan-genome-enabled frameworks for accelerating gene-trait association and candidate gene discovery. This study highlights the power of multi-omics integration in decoding gene family complexity and provides valuable insights for functional genomics and trait improvement in cereal crops.