Fig. 2

Overview of the identified QTLs underlying 18 industrially relevant phenotypes. A Number of causal variants of each functional class identified for each phenotype. B Comparison of the fraction of QTN of each functional class between studies employing the same cross; “Intergenic” includes all single nucleotide polymorphisms at non-coding regions, e.g., promoters, terminators, 5’ and 3’ UTRs, etc. C Histograms of the number of strains within the 1011 Genome Project yeast collection carrying at least 1 copy of the RM11-1a allele (top) and YJM975α allele (bottom) at the identified QTN across all phenotypes. D Phenotypic effect (as normalized z-scores) of the parental allele for each candidate locus (N = 678) and their prevalence in the 1011 sequenced S. cerevisiae strains [37]. The origin of the variants is indicated in blue (RM11-1a) and yellow (YJM975α), and the size of the point represents the frequency of the variant genotype in the 1011 sequenced S. cerevisiae isolates. E Phylogenetic distribution of the top 5 QTLs with strongest average effect on each trait (boxes) by lineage across the 1011 Genome Project yeast collection (phylogenetic tree adapted from [37], mosaic strains were excluded). For each site a distinction is made between QTN (triangle 1nt resolution) and QTL (square from 1 to 1000nt). Size of the circles indicates the fraction of strains within each lineage carrying at least 1 copy of the RM11-1a (blue) and YJM975α (yellow) allele at the specific locus. Red stroke indicates the parental allele with stronger effect on the trait. Lineage assignment is based on [37] and the number of strains is indicated next to the lineage name. RM11-1a and YJM975α lineages are colored blue and yellow, respectively