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

Abstract

<jats:title>Abstract</jats:title><jats:p>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 F<jats:sub>2</jats:sub> 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 <jats:italic>de novo</jats:italic> 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 <jats:italic>VMA1</jats:italic>, several different deletions within the osmosensor <jats:italic>MSB2</jats:italic>, a series of deletions and insertions at <jats:italic>PRM7</jats:italic> and the adjacent <jats:italic>BSC1</jats:italic>, as well as copy number variation at the dehydrogenase <jats:italic>ALD2</jats:italic>. 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.</jats:p>

Crossing design shapes patterns of genetic variation in synthetic recombinant populations ofSaccharomyces cerevisiae

“…For instance, we do find evidence that two specific regions of the genome exhibit similar dynamics in haplotype frequencies, compared to similar prior work; Burke et al 20 previously implicated these regions as potentially driving adaptation for frequent outcrossing. We also compared our results to those of Linder et al 23 which features synthetic populations constructed using the same founder strains present in this study. However, here we did not find it was the case that haplotypes most common in their populations on average are also the most common in our populations.…”

“…This particular haplotype caller was developed specifically to estimate haplotype frequencies in multiparent populations when founder haplotypes are known. A full description of the algorithm being used, and results of empirical validation can be found in Linder et al (2020).…”

“…In other words, if there is substantial variation in mating efficiencies among founding strains, this could lead to the over-representation of certain haplotypes belonging to strains that mate most efficiently. By contrast, the second approach for constructing synthetic populations is more complex and involves some level of pairwise crossing between founders [22][23][24][25]29 . While this approach is significantly more labor-intensive and time-consuming, it perhaps has advantages in terms of producing populations that have more equal founder haplotype representation and, consequently, higher levels of genetic variation.…”

Mouse Genetic Reference Populations: Cellular Platforms for Integrative Systems Genetics

“…With the use of large populations with segregating alleles, phenotypes can be mapped to genotypes. This approach has been particularly rewarding in yeast, where QTLs have been shown to explain over 70% of the narrow-sense heritability of traits [28][29][30][31][32][33]. However, these panels offer extreme under-sampling of the functional variation that could segregate in natural populations.…”

“…These individuals can also be inbred to create a panel of recombinant inbred (RI) lines that are homozygous, reproducible genetic mosaics of the founder strains. Such MPP panels have now been generated for in vitro studies in Saccharomyces cerevisiae using four and 18 fully sequenced founder strains [33,34] (Table 1).…”