Yeast segregants datasets.

A) Reference panel from the barcoded bulk sequencing. The 99,995 yeast segregants in the reference panel come from a F1 cross between a laboratory strain of yeast (BY) and a natural vineyard strain (RM) (24). Thus, they only have 2 possible alleles at each of the 41,594 polymorphic sites. The lineages barcodes enabled fitness estimation from competition assays in 18 environments recapitulating the adaptation to temperature gradients, the ability to process different sources of carbon and the resistance to antifungal compounds. B) Pooled scRNA-seq dataset from a single batch. We performed scRNA-seq of the first batch of segregants (n=4,489) to obtain genotypes that are similar to the reference panel and single cell’s expression profiles. Non-covered sites, sequencing errors and the presence of reads in the wrong library (index swapping) are corrected for using the HMM described in Figure S1.

Single-cell RNA-seq data recapitulate bulk DNA and RNA assays results.

A) Effect of the HMM on the relatedness between single cell genotypes and their closest reference lineage. The single-cell original genotype represents the genotype of the cells before the correction with the HMM. The relatedness to the closest lineage in batch1 has been measured with the adjusted R2. To control for genotype uncertainty, only the 13,069 barcodes with a significant lineage assignment (lineage-barcode genotype correlation FDR<0.05) and a reference lineage with a lower uncertainty than the single cell HMM are selected, which represents 72.2% of the barcodes. We then rounded the genotypes to remove the uncertainty during the comparison. Wilcoxon signed test p-value is indicated above the violin plots. B) Narrow-sense heritability measured with non-multiplexed DNA sequencing and scRNA-seq. The grey bars represent the scRNA-seq estimates of narrow-sense heritability while the red dots represent the estimates from bulk DNA sequencing. The interval of confidence of the bulk DNA sequencing is indicated by the red line around the red dot and was obtained from genotype and phenotype measurement error in the BB-QTL paper (24). The 23C-37C represents the temperature for the competition assay in YPD media while the other phenotypes represent growth on YNB, molasses (mol), mannose (Mann) or raffinose (raff) and chemical resistance to copper sulfate (Cu), ethanol (eth), guanidinium chloride (gu), lithium acetate (Li), Sodium dodecyl sulfate (SDS) and suloctidil (suloc) (24).

Variance partitioning of the 30C phenotype from scRNA-seq data.

The percentages represent the proportion of fitness variance (whole rectangle area) explained by the components. The ellipse area represents the phenotype variance explained by genotype variation and the circle area represents the phenotype variance explained by expression variation. The black area of the rectangle represents the residual of the model while the other colored areas represent the shared and exclusive components explaining fitness variation.

eQTL features underlying trait variation across the BY/RM segregants.

A) Mapping of the 30C QTL in the eQTL hotspots. We represent the hotspots of expression regulation as genomic windows (25 kb) to acknowledge the uncertainty around the real position of the eQTL due to linkage disequilibrium. We annotated the 5 top eQTL hotspots and the eQTL hotspots in which the top additive QTL identified by the BB-QTL mapping of the 30C phenotype are located. In these regions, we represented the most affected trans-regulated genes in red, the most affect cis- regulated gene in blue and the genes of the top QTL in black. The double quotation characters represent the absence of such genes in the associated region. We also represented the rank of the QTL in the set of 159 QTL of the 30C phenotype. B) Partitioning of the expression heritability or explained variance (R2) among cis- and trans-eQTL. Each pair of points connected by a line represents a gene. Green lines represent the genes that are only have trans-eQTL and orange lines represent the genes that have both trans- and cis-eQTL. C) Comparison of the mean effect size between cis- and trans-eQTL. Each pair of points connected by a line represents a gene. The ratio of the average effect size between cis- and trans-eQTL is represented by the line color. The sample size of each eQTL category is represented in the x axis. This is the number of trans-eQTL and cis- eQTL used for calculating the average effect sizes per gene not the number of points per distribution.