Complex phenotypes are regulated by multiple interacting quantitative trait loci (QTLs). Dissection of the genetic mechanisms underlying the phenotypic variations remains a major conceptual and experimental challenge, due to the complex genetic architecture with many loci contributing to phenotypic effects, low penetrance, gene-gene and gene-environment interactions. Over the past years, the budding yeast Saccharomyces cerevisiae has become an important model. This success is partially due to its intrinsic biological features, such as its short sexual generation time, high meiotic recombination rate, and small genome size. Precise reverse genetics technologies offer the unique opportunity to experimentally measure the phenotypic effect of genetic variants. Furthermore, intensive efforts have provided the genome sequence of numerous S. cerevisiae isolates and related species allowing powerful comparative genomics and new perspectives for functional and evolutionary studies. So far, nearly all of the yeast QTL mapping studies have used classical F1 meiotic segregants but novel strategies to produce powerful mapping population is needed. This proposal provides an innovative approach to link complex yeast phenotypes with high-resolution mapping of the genetics factors. We will implement an innovative strategy, named return to growth (RTG) that is rapid and does not require classical crosses to generate a large mapping population. This method takes advantage of the natural capacity of S. cerevisiae, to reverse its meiotic progression and yield diploid cells. Most importantly, our preliminary data, based on Next Generation Sequencing (NGS) of a yeast polymorphic strain, demonstrate that the process of RTG gives rise to recombined diploid cells. The repair of the meiotic DSBs upon gene conversion or crossover resolution leads to the maintenance or loss of heterozygosity (LOH) in various ratios and locations. Cells derived from RTG are all genetically different, a resource for quantitative trait analyses and mapping. Our preliminary phenotypic analysis of few multi-factorial traits (colony morphology, sporulation efficiency, growth at high temperature) revealed quantitative variation, providing a proof of concept for using the RTG process in QTL mapping. To optimize and utilize this approach for laboratory and industrial yeast strains, we will collaborate to: (i) isolate, NGS and bioinformatically determine the allelic genotype of 96 RTG diploids of the S288c/SK1 hybrid strain as well as 96 strains derived from spores, (ii) perform high throughput phenotypic analyses of recombined strains for multiple traits, map and validate the QTLs and, (iii) develop a genetic system that allows one to follow the progress of the meiotic cycle and the frequency of LOH in a large variety of strains. We will generate several sets of diploid recombined strains for identifying QTLs of medical and biotechnological relevance. Importantly, we will test if RTG is able to produce recombinant hybrids between different reproductively isolated Saccharomyces species. These experiments will allow us to understand the contribution of RTG to genome structure evolution, where inter-specific introgressions are prevalent in the Saccharomyces species. We envisage that the RTG process is likely to have profound implications in terms of genome evolution, since yeasts have to survive in fluctuating environments where they must also undergo rapid diversification. This scenario offers an attractive alternative to the full meiotic cycle where sequence divergence and chromosomal rearrangements can impair the process, resulting in poor gamete viability and therefore reducing the individual fitness. This ambitious project will bring a new dimension to QTL mapping, strengthen budding yeast as a model organism for quantitative genetics and provide a GMO-free innovation to improve the performance of industrial yeast strains.

Sustaining a growing population while preserving nature is challenging, especially when climates are increasingly unpredictable. Wine is one of the main commodities of the French economy, accounting for 1.3% of total exports in 2012 (5.6 billion euros of wine exports). In the context of global change and a highly competitive international market, maintaining high production levels of fine wine while limiting chemical inputs will require biological innovations. Such breakthroughs are likely to arise from experimenting with the grape must’s microbial community, a neglected actor of winemaking which impacts many wine characteristics. Much has yet to be learned about the main wine yeast, Saccharomyces cerevisiae, which can still fail to carry out alcoholic fermentation to fruition, despite modern microbiological techniques aimed at controlling fermentations. Although there is evidence that S. cerevisiae carries specific adaptations for growing in grape must, its overall level of adaptation to grape must is unknown. This matter can only be resolved with selection experiments, which assess the effect of new genetic variation on adaptation. We propose to study the adaptive potential of S. cerevisiae in natural grape must, including their microbial communities. We will analyze the impact of i) different amount of standing genetic variation and ii) experimental horizontal gene transfers (HGT) on yeast adaptation to different biotic and abiotic environments. These two genetic mechanisms of adaptation (standing genetic variation and HGT) correspond to previously described modes of adaptation to grape must by S. cerevisiae. Specifically, adaptation in S. cerevisiae will be studied in a factorial selection experiment involving five microbial community treatments (T. delbrueckii, H. uvarum, both species, whole microbial community, or sterile grape must) and three recombinant populations of S. cerevisiae (wine strains alone, wine strains and closely related domesticated strains, or strains from all known S. cerevisiae sub-groups). The competitive fitness, fermentation traits, and genomics of adaptation will be studied in the evolved populations. The prevalence of HGT as a mechanism of adaptation to grape musts will be studied among non-Saccharomyces yeasts isolated from natural grape musts, as well as with experimental evolution in S. cerevisiae. Two strategies of experimental HGT will be implemented to test if new HGT can be beneficial for S. cerevisiae in grape must. Our findings will be applicable to oenological research because all experiments will be performed in natural grape must using species and strains isolated from that environment, instead of using single-clones with undefined evolutionary history in standard laboratory media (typical for microbial evolutionary experiments). This innovative approach will allow us to test if previous laboratory studies are transposable to complex natural environments. Our work can impact wine starter technologies by providing new alleles, allele combinations for improving wine technological traits (i.e. fermentation completion). Better knowledge of the ecological niche of wine yeasts, including the effect of biotic interactions on S. cerevisiae growth and evolution, will help stabilize alcoholic fermentations. Moreover, experimental horizontal gene transfer (eHGT) has never been studied as extensively as in our project. Our results will increase dramatically our knowledge of the prevalence and functions of horizontal gene transfers. Sequencing genomes from species isolated from grape must’s microbial communities will fill a major gap in our knowledge of these communities, including the importance of HGT. The project will benefit from our broad consortium of experts because it requires the integration of new challenging approaches (eHGT, experimental evolution in complex environments) and advanced tools (phenomics robotic platform, genomics).