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Breeding and hybridization strategies currently used with brewing yeasts

As discussed above, most ale and lager yeasts are not ‘pure' diploid organisms, but instead exhibit various levels of aneuploidy, polyploidy, and/or interspecific hybridization. This means that these strains are generally unable to proceed through meiosis to give viable haploid spores, probably due to problems with chromosome pairing during meiosis and/or other incompatibility issues that specifically arise as a result of interspecific hybridization (Greig et al., 2002; Greig, 2007; Lee et al., 2008; Kao et al., 2010; Hou et al., 2015). This makes it difficult or impossible to perform typical genetic analyses, and thus typical breeding strategies, with most brewing yeasts. Recently, however, various directed breeding techniques using brewing and other industrial yeasts have been carried out with success, potentially leading to useful ways to generate novel brewing yeasts.

Directed breeding, also called selective or controlled breeding or artificial selection (Darwin, 1859, 1868), is the process by which desired phenotypic characteristics from different lineages are combined by humans, through the controlled mating of selected individuals from these lineages. For millennia, despite lacking an understanding of the underlying genetic mechanisms, humans both intentionally and unintentionally domesticated a variety of different organisms, including plants, animals, and microorganisms, by continually selecting individuals that displayed the phenotypic characteristics of interest and allowing only those chosen individuals to reproduce. There is evidence from many regions across the world that humans have been interacting with yeasts for more than 9000 years, almost certainly at first as a way to transform fruits and grains into intoxicating beverages (McGovern, 2003), possibly aiding in societal development (McGovern, 2009; Kahn, 2015). These early humans were not only unintentionally selecting for yeast strains that would merely survive and thrive in the somewhat harsh conditions of fruit juices or soaked grains, but were also - most likely by transferring foam from only the ‘best' fermentations to subsequent batches - repeatedly enriching and selecting for those yeasts that made a pleasing flavour while still providing an intoxicating experience (McGovern, 2009), eventually selecting for different strains of yeasts specialized for various different types of fermentation (Legras et al., 2007). In fact virtually all of the yeast strains used in brewing today, possibly even including lambic and ‘wild' beers that are not deliberately inoculated and are fermented by organisms existing in the brewery environment (see Chapter 7), are found only in association with human activity, having become totally ‘domesticated’. On the other hand, some would say (albeit in semi-jest - or possibly not), that humans have been ‘domesticated' by yeasts to become their unwitting caretakers (Katz, 2010; Dawson, 2013).

However, after the concepts of natural selection (Darwin and Wallace, 1858) and genetic inheritance (Mendel, 1865) were introduced and understood, it became even easier to carry out directed breeding of organisms. In many cases, the inheritance patterns of different traits could be easily elucidated, leading to precise predictions of the phenotypes of offspring relative to the parents. These calculations are very simple if a trait is controlled by one or two genes, but the vast majority of traits are ‘quantitative', meaning that the particular trait is influenced by many genes, also called a polygenic' trait. The genes controlling such traits are called quantitative trait loci (QTL). However, statistical calculations can be used in these cases to accurately predict offspring phenotypes. Today, directed breeding is carried out in all areas of agriculture and animal husbandry.

Yeasts capable of sexually reproducing can also be bred through this process (see Fig. 5.3A and ‘Direct mating', below). However, as mentioned above, many brewing yeasts are essentially sterile, i.e. they do not produce viable spores. Although cases of successful ale and lager yeast breeding using rare viable spores have been reported and will be described in more detail below, in general both lager and ale yeasts are very difficult to selectively breed using traditional spore mating methodology. Furthermore, the rare surviving spores that arise after such defective meiotic events are, by definition, selected to carry traits correlated with spore survival, but in fact these traits may not be correlated (and may even be anti-correlated) with desired brewing traits.

Several methods have been adapted to overcome the sexual limitation of brewing yeasts, with most relying on the fusion of two parental strains (usually diploid, aneuploid, or polyploid) to form a higher ploidy hybrid line via ‘rare mating' events or ‘protoplast fusion' (described in more detail below). These methods avoid sporulation - and thus the chromosomal reduction step that occurs with meiosis - therefore sidestepping the problems of spore inviability and selection of rare viable spores that can occur with aneuploid or interspecific hybrid yeasts. The resulting higher ploidy organism (tetraploid in the case of two diploid parental strains) ideally combines the phenotypic characteristics ofboth parental strains, similar to the way that standard mating of haploid spores combines those characteristics in the diploid zygote. This hybrid line may even be more genetically tractable than the aneuploid parental strains, since its increased gene complement may prevent inviability upon meiosis (Morales and Dujon, 2012). An additional benefit of producing hybrids between already domesticated lines is increased fitness and vigour during fermentation (Plech et al., 2014; Steensels et al., 2014a). Conversely, strains resulting from forced interspecific hybridization have been shown to experience an increased rate of chromosome loss (Marinoni et al., 1999), although the magnitude of this effect is debated (Kumaran et al., 2013).

The following sections describe several different directed breeding techniques for yeast that are genetically tractable (i.e. undergo meiosis and produce viable spores), as well as techniques that circumvent the need for ‘genetically well-behaved strains' (Figs. 5.3 and 5.4). For comprehensive treatments of directed and other types of breeding methods in yeasts, see Chambers et al. (2009) and Steensels et al. (2014b).

 
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