The genetic architecture of cell-type-specific cis-regulation in maize
Data files
Dec 23, 2024 version files 232.20 MB
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Dryad_Data_S1.xlsx
87.60 MB
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Dryad_Data_S2.xlsx
88.61 MB
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Dryad_Data_S3.xlsx
13.96 MB
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Dryad_Data_S4.xlsx
41.95 MB
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Dryad_Data_S5.xlsx
42.28 KB
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Dryad_Data_S6.xlsx
44.14 KB
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README.md
3.96 KB
Abstract
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.
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 and 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 and 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 and 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 and 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 and 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 and 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 and 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 and 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