Abstract

Plant epigenomics and single-cell genomics are transformative tools for studying cis-regulatory variation in plant genomes. We are using these technologies to identify cis-regulatory elements, characterize their cell-type-specific activity, and uncover how genetic variants influence their activity. In this talk, I’ll explore how cutting-edge tools like epigenomics and single-cell genomics are rapidly advancing our understanding of plant biology by pinpointing the location of “cis-regulatory elements”, the non-coding regions of DNA that play a crucial role in gene expression control. Using maize (corn) as a model, we’re uncovering how these regulatory elements vary between plants and how those differences have influenced key traits during domestication and adaptation. While genome-wide association studies (GWAS) have helped connect genetic variation to important traits in crops, they often struggle to identify the precise variants responsible—especially because most trait-linked DNA changes lie outside of genes. By profiling over 700,000 individual cells across 172 genetically diverse maize lines, we’ve mapped the locations and activity of regulatory elements at unprecedented resolution. Our work reveals how mobile DNA elements (transposons) helped rewire gene regulation, how specific transcription factor binding sites influence chromatin accessibility, and how natural variation in these regions contributes to flowering time and other critical traits. These discoveries offer new insights into the molecular drivers of crop diversity and hold promise for improving agriculture through targeted genome editing.