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<p>Regulatory elements are essential components of plant genomes that have shaped the domestication and improvement of modern crops. However, their identity, function and diversity remain poorly characterized, limiting our ability to harness their full power for agricultural advances using induced or natural variation. Here we mapped transcription factor (TF) binding for 200 TFs from 30 families in two distinct maize inbred lines historically used in maize breeding. TF binding comparison revealed widespread differences between inbreds, driven largely by structural variation, that correlated with gene expression changes and explained complex quantitative trait loci such as <i>Vgt1</i>, an important determinant of flowering time, and <i>DICE</i>, an herbivore resistance enhancer. CRISPR–Cas9 editing of TF binding regions validated the function and structure of regulatory regions at various loci controlling plant architecture and biotic resistance. Our maize TF binding catalogue identifies functional regulatory regions and enables collective and comparative analysis, highlighting its value for agricultural improvement.</p>

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Transcription factor binding divergence drives transcriptional and phenotypic variation in maize

  • 期刊论文

  • 发表日期：

    2025年6月12日

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  • Mary Galli,
  • Zongliang Chen,
  • Tara Ghandour,
  • Amina Chaudhry,
  • Jason Gregory,
  • Fan Feng,
  • Miaomiao Li,
  • Nathaniel Schleif,
  • Xuan Zhang,
  • Yinxin Dong,
  • Gaoyuan Song,
  • Justin W. Walley,
  • George Chuck,
  • Clinton Whipple,
  • Heidi F. Kaeppler,
  • Shao-shan Carol Huang,
  • Andrea Gallavotti

摘要

Regulatory elements are essential components of plant genomes that have shaped the domestication and improvement of modern crops. However, their identity, function and diversity remain poorly characterized, limiting our ability to harness their full power for agricultural advances using induced or natural variation. Here we mapped transcription factor (TF) binding for 200 TFs from 30 families in two distinct maize inbred lines historically used in maize breeding. TF binding comparison revealed widespread differences between inbreds, driven largely by structural variation, that correlated with gene expression changes and explained complex quantitative trait loci such as Vgt1, an important determinant of flowering time, and DICE, an herbivore resistance enhancer. CRISPR–Cas9 editing of TF binding regions validated the function and structure of regulatory regions at various loci controlling plant architecture and biotic resistance. Our maize TF binding catalogue identifies functional regulatory regions and enables collective and comparative analysis, highlighting its value for agricultural improvement.