ArticleTAG. Theoretical and applied genetics. Theoretische und angewandte Genetik2026
Pan-genome analysis reveals hidden diversity and selection signatures of auxin response factors (ARFs) associated with breeding in barley.
Article in TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
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Abstract
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.
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