Quantitative Trait Nucleotides Impacting the Technological Performances of Industrial Saccharomyces cerevisiae Strains.

Emilien Peltier,Anne Friedrich,Joseph Schacherer,Philippe Marullo

doi:10.3389/fgene.2019.00683

Abstract

The budding yeast Saccharomyces cerevisiae is certainly the prime industrial microorganism and is related to many biotechnological applications including food fermentations, biofuel production, green chemistry, and drug production. A noteworthy characteristic of this species is the existence of subgroups well adapted to specific processes with some individuals showing optimal technological traits. In the last 20 years, many studies have established a link between quantitative traits and single-nucleotide polymorphisms found in hundreds of genes. These natural variations constitute a pool of QTNs (quantitative trait nucleotides) that modulate yeast traits of economic interest for industry. By selecting a subset of genes functionally validated, a total of 284 QTNs were inventoried. Their distribution across pan and core genome and their frequency within the 1,011 Saccharomyces cerevisiae genomes were analyzed. We found that 150 of the 284 QTNs have a frequency lower than 5%, meaning that these variants would be undetectable by genome-wide association studies (GWAS). This analysis also suggests that most of the functional variants are private to a subpopulation, possibly due to their adaptive role to specific industrial environment. In this review, we provide a literature survey of their phenotypic impact and discuss the opportunities and the limits of their use for industrial strain selection.

Highlights

Between individuals of the same species, a broad palette of genetic variants is found, including large chromosomal rearrangements and punctual mutations (Griffiths et al, 2000)
With the relative ease of obtaining genome-wide SNPdata, their impact on complex trait can be tracked by either genome-wide association studies (GWAS) or quantitative trait loci mapping (QTL mapping) in medicine (Beck et al, 2014) or agronomy (Brachi et al, 2011; Sharma et al, 2015)
When they are statistically linked to a phenotype, these singlenucleotide polymorphisms (SNP) become quantitative trait nucleotides (QTN) and could be listed in large databases for research communities (Grant et al, 2010; Youens-Clark et al, 2011)

Summary

Introduction

Between individuals of the same species, a broad palette of genetic variants is found, including large chromosomal rearrangements (deletions, duplications, inversions, translocations, and introgressions) and punctual mutations (Griffiths et al, 2000). Traits were sorted in three main phenotypic classes: traits linked to metabolism (e.g., nitrogen, carbon, vitamin, and fermentation activity), traits linked to stress resistance (e.g., acidic and basic, temperature, osmotic, and ethanol), and traits impacting the organoleptic properties of the products (Figure 1A). 71% of these genes were identified in an industrial context since they concern media and/ or strains related to aroma production (1%), bioethanol (18%), or traditional fermented goods including wine (41%), sake (5%), bakery (3%), or beer (3%).

Results

Conclusion