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 netwo..., , , # The genetic architecture of cell-type-specific cis-regulation in maize

[https://doi.org/10.5061/dryad.nk98sf82v](https://doi.org/10.5061/dryad.nk98sf82v)

## Description of the data and file structure

Single-cell genomics on 172 maize genotypes

**Dryad_Data*_*S1 = Differentially accessible genes among clusters**

* Columns: log2 fold-change, log counts per million, F statistic, P-value, false discovery rate, cluster_id, geneID, gene description, computation description. 

- Rows: Genes

**Dryad_Data*_*S2 = Cell meta data**

* Columns: cellID, total read counts, number of reads mapping to TSS, number of reads mapping to ACRs, number of accessible ACRs, log10 transformed number of accessible ACRs, libraryID, genotype ID, umap1 coordinate, umap2 coordinate, reference ID, louvain cluster ID, Leiden cluster ID, cell type ID, full cell type name, cell cycle stage (G1 stage [G1], G1/Synthesis stage [G1/S], G2/Metaphase stage [G2/M], Metaphase [M] stage, and Synthesis stage [S]), total num...