The genetic architecture of cell-type-specific cis-regulation in maize

Gene expression and complex phenotypes are determined by the activity of
cis-regulatory elements. However, an understanding of how extant genetic
variants affect cis-regulation remains limited. Here, we investigated the
consequences of cis-regulatory diversity using single-cell genomics of
>0.7 million nuclei across 172 maize inbreds. Our analyses
pinpointed cis-regulatory elements distinct to domesticated maize and
revealed how historical transposon activity has rewired the regulatory
landscape. Leveraging principles of population genetics, we fine-mapped
~22,000chromatin accessibility-associated genetic variants with widespread
cell-type-specific effects. Variants in TEOSINTE
BRANCHED1/CYCLOIDEA/PROLIFERATING CELL FACTOR binding sites were the most
prevalent determinants of chromatin accessibility. Finally, integration of
chromatin accessibility-assocaited variants, organismal trait variation,
and population differentiation revealed how local adaptation has rewired
regulatory networks in unique cellular context to alter maize flowering
phenotypes.