Abstract
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.
| Original language | English |
|---|---|
| Pages (from-to) | 1205-1219 |
| Number of pages | 15 |
| Journal | Nature Plants |
| Volume | 11 |
| Issue number | 6 |
| DOIs | |
| State | Published - Jun 2025 |
Funding
We thank R. Macrae for helpful comments and suggestions on the manuscript and maizeGDB for data curation of informatics resources. We acknowledge the Office of Advanced Research Computing at Rutgers, the State University of New Jersey, for providing access to the Amarel cluster. This work was supported in part through the NYU IT High Performance Computing resources, services and staff expertise. This work was supported by NSF Plant Genome Research Project grant no. IOS-1916804 to A.G. and S.-s.C.H. and NIH award no. R35GM138143 to S.-s.C.H. A.C. is a Fulbright Scholar and recipient of a Meta Prevorsek Turner Fellowship. This material was also in part based on work supported by the Center for Bioenergy Innovation, US Department of Energy, Office of Science, Biological and Environmental Research Program under award no. ERKP886 and the Oak Ridge National Laboratory Director’s R&D Program (M.L.). Oak Ridge National Laboratory is managed by UT-Battelle, LLC, for the Office of Science of the US Department of Energy under contract no. DE-AC05-00OR22725.