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<p>Comprehensive maps of functional variation at transcription factor (TF) binding sites (<i>cis</i>-elements) are crucial for elucidating how genotype shapes phenotype. Here, we report the construction of a pan-cistrome of the maize leaf under well-watered and drought conditions. We quantified haplotype-specific TF footprints across a pan-genome of 25 maize hybrids and mapped over 200,000 variants, genetic, epigenetic, or both (termed binding quantitative trait loci (bQTL)), linked to <i>cis</i>-element occupancy. Three lines of evidence support the functional significance of bQTL: (1) coincidence with causative loci that regulate traits, including <i>vgt1</i>, <i>ZmTRE1</i> and the MITE transposon near <i>ZmNAC111</i> under drought; (2) bQTL allelic bias is shared between inbred parents and matches chromatin immunoprecipitation sequencing results; and (3) partitioning genetic variation across genomic regions demonstrates that bQTL capture the majority of heritable trait variation across ~72% of 143 phenotypes. Our study provides an auspicious approach to make functional <i>cis</i>-variation accessible at scale for genetic studies and targeted engineering of complex traits.</p>

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Genetic variation at transcription factor binding sites largely explains phenotypic heritability in maize

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2025年8月11日

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  • Julia Engelhorn,
  • Samantha J. Snodgrass,
  • Amelie Kok,
  • Arun S. Seetharam,
  • Michael Schneider,
  • Tatjana Kiwit,
  • Ayush Singh,
  • Michael Banf,
  • Duong Thi Hai Doan,
  • Merritt Khaipho-Burch,
  • Daniel E. Runcie,
  • Victor A. Sánchez-Camargo,
  • Rechien Bader,
  • J. Vladimir Torres-Rodriguez,
  • Guangchao Sun,
  • Maike Stam,
  • Fabio Fiorani,
  • Sebastian Beier,
  • James C. Schnable,
  • Hank W. Bass,
  • Matthew B. Hufford,
  • Benjamin Stich,
  • Wolf B. Frommer,
  • Jeffrey Ross-Ibarra,
  • Thomas Hartwig

摘要

Comprehensive maps of functional variation at transcription factor (TF) binding sites (cis-elements) are crucial for elucidating how genotype shapes phenotype. Here, we report the construction of a pan-cistrome of the maize leaf under well-watered and drought conditions. We quantified haplotype-specific TF footprints across a pan-genome of 25 maize hybrids and mapped over 200,000 variants, genetic, epigenetic, or both (termed binding quantitative trait loci (bQTL)), linked to cis-element occupancy. Three lines of evidence support the functional significance of bQTL: (1) coincidence with causative loci that regulate traits, including vgt1, ZmTRE1 and the MITE transposon near ZmNAC111 under drought; (2) bQTL allelic bias is shared between inbred parents and matches chromatin immunoprecipitation sequencing results; and (3) partitioning genetic variation across genomic regions demonstrates that bQTL capture the majority of heritable trait variation across ~72% of 143 phenotypes. Our study provides an auspicious approach to make functional cis-variation accessible at scale for genetic studies and targeted engineering of complex traits.