Yeast is arguably the most important industrial microorganism in the world, playing a critical role in the fermentation of food and beverage products, as well as cellular factory for production of biofuels, chemicals, and pharmaceuticals. In order to produce such a range of products efficiently and economically, specialized yeast must be optimized for each task. Current tools for yeast optimization are lacking, especially in the sectors of food, beverage, and feed, where consumers demand non-GMO yeast products.