Fig. 1: Generating a large panel of diploid segregants with known genotypes that can be phenotyped as a pool.

a Overview of the experimental design. Parental haploids, BY and 3S, were mated and sporulated. The resulting MATα and MATa segregants were barcoded at a common genomic location and sequenced. Segregants were mated as pairs to generate a panel of ~200,000 double-barcoded diploid strains with known genotypes. All diploid strains originating from a single haploid parent are referred to as a ‘family’. b MATα and MATa barcodes were brought to the same genomic location by inducing recombination between homologous chromosomes via Cre-loxP. c Diploid strains were pooled and grown in competition for 12–15 generations. Barcode sequencing over the course of the competition was used to estimate the fitness of each strain. d Density plot of the raw fitness of double barcodes representing the same diploid strain in the same pooled growth condition (Glucose 1). e Density plot of the mean raw fitness of the same diploid strain measured in two replicate growth cultures (Glucose 1 and Glucose 2). f The mean broad-sense and narrow-sense heritability estimates for the 8 environments. The standard errors for both heritability estimates are shown as error bars for each point. g Violin plots of the fitnesses of diploid strains in 8 environments (n > 187,000 in each environment). Raw fitness estimates of BY/BY, BY/3S, 3S/BY, and 3S/3S diploid strains are shown as colored lines. Overlaid boxplots, here and in subsequent figures, indicate the median (white dots), interquartile range (IQR; black boxes), and lower and upper adjacent values (black lines extending from the black boxes), defined as first quartile − 1.5 IQR and third quartile + 1.5 IQR, respectively.