Data for: Raw count data, transcribed variant count data, and reference genomic annotation files for Boocock et al. 2024

Expression quantitative trait loci (eQTLs) provide a key bridge between
noncoding DNA sequence variants and organismal traits. The effects of
eQTLs can differ among tissues, cell types, and cellular states, but these
differences are obscured by gene expression measurements in bulk
populations. We developed a one-pot approach to map eQTLs in Saccharomyces
cerevisiae by single-cell RNA sequencing (scRNA-seq) and applied it to
over 100,000 single cells from three crosses. We used scRNA-seq data to
genotype each cell, measure gene expression, and classify the cells by
cell-cycle stage. We mapped thousands of local and distant eQTLs and
identified interactions between eQTL effects and cell-cycle stages. We
took advantage of single-cell expression information to identify hundreds
of genes with allele-specific effects on expression noise. We used
cell-cycle stage classification to map 20 loci that influence cell-cycle
progression. One of these loci influenced the expression of genes involved
in the mating response. We showed that the effects of this locus arise
from a common variant (W82R) in the gene GPA1, which encodes a signaling
protein that negatively regulates the mating pathway. The 82R allele
increases mating efficiency at the cost of slower cell-cycle progression
and is associated with a higher rate of outcrossing in nature. Our results
provide a more granular picture of the effects of genetic variants on gene
expression and downstream traits.