DOI: 10.5061/dryad.nk98sf82v
title: The genetic architecture of cell-type-specific cis-regulation in maize

description: 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
 &gt;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.
description: # 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 number of raw reads * Rows: Cell barcodes **Dryad_Data*_*S3 = TWAS results** * Columns: Measured maize phenotypes derived from [https://www.panzea.org/phenotypes](https://www.panzea.org/phenotypes) and [https://doi.org/10.1038/ncomms9974](https://doi.org/10.1038/ncomms9974)   * Rows: Z-score estimates for each gene across 49 phenotypes from TWAS **Dryad_Data*_*S4 = CAWAS results** * Columns: Measured maize phenotypes derived from [https://www.panzea.org/phenotypes](https://www.panzea.org/phenotypes) and [https://doi.org/10.1038/ncomms9974](https://doi.org/10.1038/ncomms9974)   * Rows: Z-score estimates for each ACR ID across 49 phenotypes from CAWAS **Dryad_Data*_*S5 = PVE results (fine mapped caQTL)** *tab1 (Mean_PVE)* * Columns: Measured maize phenotypes derived from [https://www.panzea.org/phenotypes](https://www.panzea.org/phenotypes) and [https://doi.org/10.1038/ncomms9974](https://doi.org/10.1038/ncomms9974)   * Rows: Cell type IDs * Values: Mean percent variance explained by cell type-specific caQTL *tab2 (Z-score_PVE)* * Columns: Measured maize phenotypes derived from [https://www.panzea.org/phenotypes](https://www.panzea.org/phenotypes) and [https://doi.org/10.1038/ncomms9974](https://doi.org/10.1038/ncomms9974)   * Rows: Cell type IDs * Values: Z-score of mean percent variance explained by cell type-specific caQTL versus null permutations (x1000) *tab3 (P-valuePVE*_empirical*)* * Columns: Measured maize phenotypes derived from [https://www.panzea.org/phenotypes](https://www.panzea.org/phenotypes) and [https://doi.org/10.1038/ncomms9974](https://doi.org/10.1038/ncomms9974)   * Rows: Cell type IDs * Values: Empirical P-value of mean percent variance explained by cell type-specific caQTL versus null permutations (x1000) **Dryad_Data*_*S6 = PVE results (single-cell specific and bulk caQTL)** *tab1 (Mean_PVE)* * Columns: Measured maize phenotypes derived from [https://www.panzea.org/phenotypes](https://www.panzea.org/phenotypes) and [https://doi.org/10.1038/ncomms9974](https://doi.org/10.1038/ncomms9974)   * Rows: Cell type IDs * Values: Mean percent variance explained by single-cell only and bulk caQTL *tab2 (Z-score_PVE)* * Columns: Measured maize phenotypes derived from [https://www.panzea.org/phenotypes](https://www.panzea.org/phenotypes) and [https://doi.org/10.1038/ncomms9974](https://doi.org/10.1038/ncomms9974)   * Rows: Cell context IDs * Values: Z-score of mean percent variance explained by single-cell only and bulk caQTL versus null permutations (x1000) *tab3 (P-valuePVE*_empirical*)* * Columns: Measured maize phenotypes derived from [https://www.panzea.org/phenotypes](https://www.panzea.org/phenotypes) and [https://doi.org/10.1038/ncomms9974](https://doi.org/10.1038/ncomms9974)   * Rows: Cell type IDs * Values: Empirical P-value of mean percent variance explained by single-cell only and bulk caQTL versus null permutations (x1000) ## Code/software Excel