Linder, R. A. | bioRxiv Science

bioRxiv2020

Two synthetic 18-way outcrossed populations of diploid budding yeast with utility for complex trait dissection

Advanced generation multi-parent populations (MPPs) are a valuable tool for dissecting complex traits, having more power than GWAS to detect rare variants, and higher resolution than F2 linkage mapping. To extend the advantages of MPPs in budding yeast, we describe the creation and characterization of two outbred MPPs derived from eighteen genetically diverse founding strains. We carried out de novo assemblies of the genomes of the eighteen founder strains, such that virtually all variation segregating between these strains is known and represent those assemblies as Santa Cruz Genome Browser tracks. We discover complex patterns of structural variation segregating amongst the founders, including a large deletion within the vacuolar ATPase VMA1, several different deletions within the osmosensor MSB2, a series of deletions and insertions at PRM7 and the adjacent BSC1, as well as copy number variation at the dehydrogenase ALD2. Resequenced haploid recombinant clones from the two MPPs have a median unrecombined block size of 66kb, demonstrating the population are highly recombined. We pool sequenced the two MPPs to 3270X and 2226X coverage and demonstrate that we can accurately estimate local haplotype frequencies using pooled data. We further down-sampled the poolseq data to ~20-40X and show that local haplotype frequency estimates remain accurate, with median error rate 0.8% and 0.6% at 20X and 40X, respectively. Haplotypes frequencies are estimated much more accurately than SNP frequencies obtained directly from the same data. Deep sequencing of the two populations revealed that ten or more founders are present at a detectable frequency for over 98% of the genome, validating the utility of this resource for the exploration of the role of standing variation in the architecture of complex traits.

genetics↗

bioRxiv2017

The stress-inducible peroxidase TSA2 enables Chromosome IV duplication to be conditionally beneficial in Saccharomyces cerevisiae

Although chromosomal duplications are often deleterious, in some cases they enhance cells abilities to tolerate specific genetic or environmental challenges. Identifying the genes that cause particular chromosomal duplications to confer these conditionally beneficial effects can improve our understanding of the genetic and molecular mechanisms that enable certain aneuploidies to persist in cell populations and contribute to disease and evolution. Here, we perform a screen for spontaneous mutations that improve the tolerance of haploid Saccharomyces cerevisiae to hydrogen peroxide. Chromosome IV duplication is the most frequent mutation, as well as the only change in chromosomal copy number, seen in the screen. Using a genetic mapping strategy that involves systematically deleting segments of a duplicated chromosome, we show that the Chromosome IV duplications effect is largely due to the generation of a second copy of the stress-inducible cytoplasmic thioredoxin peroxidase TSA2. This finding is consistent with a growing literature indicating that the conditionally beneficial effects of chromosomal duplications tend to reflect the contributions of small numbers of genes that enhance tolerance to specific stresses when their copy number is increased.\n\nArticle summaryChanges in karyotype play an important role in evolution and health. Although these aneuploidization events are usually deleterious, in some instances they show conditionally beneficial effects by enabling cells to tolerate specific mutations or environmental stresses. The mechanisms underlying these protective effects of aneuploidization are not fully understood. To provide insights into this problem, we identify and characterize a conditionally beneficial chromosomal duplication that makes haploid yeast more tolerant to oxidative stress. We determine that the effect of the chromosomal duplication on oxidative stress tolerance is largely explained by duplication of a single stress-inducible gene.

genetics↗