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.