Refining the resolution of the yeast genotype-phenotype map using single-cell RNA-sequencing

Genotype-phenotype mapping (GPM), or the association of trait variation to genetic variation, has been a long-lasting problem in biology. The existing approaches to this problem allowed researchers to partially understand within- and between-species variation as well as the emergence or evolution of phenotypes. However, traditional GPM methods typically ignore the transcriptome or have low statistical power due to challenges related to dataset scale. Thus, it is not clear to what extent selection modulates transcriptomes and whether cis- or trans-regulatory elements are more important. To overcome these challenges, we leveraged the cost efficiency and scalability of single-cell RNA sequencing (scRNA-seq) by collecting data from 18,233 yeast cells from 4489 F2 segregants derived from an F1 cross between the laboratory strain BY4741 and the vineyard strain RM11-1a. More precisely, we performed expression quantitative trait loci (eQTL) mapping with the scRNA-seq data to identify single-cell eQTL and transcriptome variation patterns associated with fitness variation inferred from the segregant bulk fitness assay. Due to the larger scale of our dataset and its multidimensionality, we could recapitulate results from decades of work in GPM from yeast bulk assays while revealing new associations between phenotypic and transcriptomic variations at a broad scale. We evaluated the strength of the association between phenotype variation and expression variation, revealed new hotspots of gene expression regulation associated with trait variation, revealed new gene functions with high expression heritability, and highlighted the larger aggregate effect of trans-regulation compared to cis-regulation. Altogether, these results suggest that integrating large-scale scRNA-seq data into GPM improves our understanding of trait variation in the context of transcriptomic regulation.