The genetic basis of differential autodiploidization in evolving yeast populations

Abstract

Spontaneous whole-genome duplication, or autodiploidization, is a common route to adaptation in experimental evolution of haploid budding yeast populations. The rate at which autodiploids fix in these populations appears to vary across strain backgrounds, but the genetic basis of these differences remains poorly characterized. Here, we show that the frequency of autodiploidization differs dramatically between two closely related laboratory strains of Saccharomyces cerevisiae, BY4741 and W303. To investigate the genetic basis of this difference, we crossed these strains to generate hundreds of unique F1 segregants and tested the tendency of each segregant to autodiplodize across hundreds of generations of laboratory evolution. We find that variants in the SSD1 gene are the primary genetic determinant of differences in autodiploidization. We then used multiple laboratory and wild strains of S. cerevisiae to show that clonal populations of strains with a functional copy of SSD1 autodiploidize more frequently in evolution experiments, while knocking out this gene or replacing it with the W303 allele reduces autodiploidization propensity across all genetic backgrounds tested. These results suggest a potential strategy for modifying rates of spontaneous whole-genome duplications in laboratory evolution experiments in haploid budding yeast. They may also have relevance to other settings in which eukaryotic genome stability plays an important role, such as biomanufacturing and the treatment of pathogenic fungal diseases and cancers.

Keywords: Saccharomyces cerevisiae; QTL analysis; experimental evolution; ploidy evolution; whole-genome duplication.

Figure 1

Schematic diagram of the QTL mapping experiment. Parents with different autodiploidization propensities were crossed, and F1 segregants either dissected from tetrads (“tetrad spores”) or selected in bulk on selective media (“selected spores”). All spores were subject to 500 generations of evolution in rich media. At the conclusion of the evolution experiment, the ploidy of all populations was assayed via flow cytometry. All “tetrad spores” were genotyped individually via whole-genome sequencing, and the combined genetic and phenotypic data were used to detect QTLs. The “selected spores” were sequenced in pools and analyzed for enrichment of the identified QTL, SSD1.

Figure 2

QTL mapping identified a single locus driving variation in autodiploidization propensity. (A) Percentage of populations autodiploidized among the clonal replicates of the two parental strains (YAN463 and yGIL646) and their F1 segregants (tetrad spores) after evolving for 500 generations. The numbers inside square brackets denote the number of populations in each category. (B) Histogram of the number of autodiploidized spores out of four spores in a tetrad. The numbers in red denote the number of tetrads in each category. (C) LOD score for variation in autodiploidization is plotted against the genetic map. The red dashed line indicates a 5% LOD significance threshold computed from 10,000 permutations. The one statistically significant QTL contains a single SNP in the SSD1 gene. (D) Autodiploidization propensity conditional on BY (SSD1) and W303 (ssd1-d) alleles respectively across all tetrad spores.

Figure 3

Ploidy status of the “selected spores” after evolution, and enrichment of the BY allele of SSD1 in diploids. (A) Percentage of populations autodiploidized among the spores selected in SD –Ade –His +Can and SD –Ade –His –Ura –Trp +Can media after evolving for 500 generations. The numbers inside square brackets denote the number of populations in each category. Populations with ambiguous ploidy status are shown as haploids. (B) Percentage of sequencing reads at SSD1 locus matching BY allele in haploid and diploid pools of the “selected spores.” Here n denotes the total number of reads at SSD1 locus for each pool.

Figure 4

The effect of SSD1 on autodiploidization. A nonfunctional SSD1 gene reduced autodiploidization in W303 populations, while BY, RM, and other domesticated and wild strains expressing full length Ssd1 protein autodiploidized with high frequency. Knocking out SSD1 reduced autodiploidization in BY and RM, making their frequency similar to that of W303. Allele swap experiments showed that irrespective of the genetic background, presence of the allele expressing the full length Ssd1 protein led to increased autodiploidization, whereas the allele expressing truncated Ssd1 protein reduced it. The numbers in square brackets denote the total number of clonal replicates for each strain. The full genotype of each strain can be found in Table 1.