Abstract

--- - Lager yeasts are limited to a few strains worldwide, imposing restrictions on flavour and aroma diversity and hindering our understanding of the complex evolutionary mechanisms during yeast domestication. The recent finding of diverse S. eubayanus lineages from Patagonia offers potential for generating new lager yeasts with different flavour profiles. Here, we leverage the natural genetic diversity of S. eubayanus and expand the lager yeast repertoire by including three distinct Patagonian S. eubayanus lineages. We used experimental evolution and selection on desirable traits to enhance the fermentation profiles of novel S. cerevisiae x S. eubayanus hybrids. Our analyses reveal an intricate interplay of pre-existing diversity, selection on species-specific mitochondria, de-novo mutations, and gene copy variations in sugar metabolism genes, resulting in high ethanol production and unique aroma profiles. Hybrids with S. eubayanus mitochondria exhibited greater evolutionary potential and superior fitness post-evolution, analogous to commercial lager hybrids. Using genome-wide screens of the parental subgenomes, we identified genetic changes in IRA2, IMA1, and MALX genes that influence maltose metabolism, and increase glycolytic flux and sugar consumption in the evolved hybrids. Functional validation and transcriptome analyses confirmed increased maltose-related gene expression, influencing greater maltotriose consumption in evolved hybrids. This study demonstrates the potential for generating industrially viable lager yeast hybrids from wild Patagonian strains. Our hybridization, evolution, and mitochondrial selection approach produced hybrids with high fermentation capacity and expands lager beer brewing options. - Lager beer dominates the global market, accounting for over 90% of commercial beer varieties. The main player in lager fermentation is the yeast Saccharomyces pastorianus, an interspecific hybrid between S. cerevisiae and S. eubayanus. Despite its popularity, the range of flavours and aromas found in lager beers is restricted by the low genetic diversity of available lager strains. Here, we explored if lager yeast profiles can be diversified by leveraging natural isolates of S. eubayanus from Chilean Patagonia. We generated de novo hybrids between S. cerevisiae and three distinct S. eubayanus Patagonian lineages. Through experimental evolution and selection on fermentation traits, we improved the fermentation profiles of the hybrids. We found that mutations in IRA2, IMA1, and MALX genes enhanced their maltose and maltotriose metabolism, resulting in higher ethanol production and unique aroma profiles. Our results also confirm that S. eubayanus mitochondria confer a greater evolutionary potential than S. cerevisiae mitochondria. The current study encourages the use of wild yeast strains to develop new brewing applications to expand the repertoire of de novo lager yeasts.