Quantitative Trait Loci Mapping in Winemaking Yeast

Abstract

Deciphering the genetic basis of fermentation traits of the yeast Saccharomyces cerevisiae remains a challenge. In this project, a new yeast resource is introduced for the study of yeast genetics in a winemaking context. A cross between two winemaking yeast strains was constructed and applied to: (a) the analysis of recombination; (b) de novo genome assembly; and (c) the identi cation of genes a ecting oenologically relevant traits. Two commercial winemaking yeasts, M2 and F15, were crossed and 96 recombinant F2 progeny were dissected from the F1 generation. All strains were sequenced using 2nd generation sequencing platforms. The genome of M2 was assembled against a reference genome sequence as well as de novo. Sequence variants sites were identi ed between M2 and F15 on both assemblies and the 96 recombinant progeny were genotyped at these loci. The genotyped reference assembly was used to detect copy number variation between the parents, to quantify crossover interference, to identify recombination hotspots in the genome, and to map quantitative trait loci (QTL). The genotyped de novo contigs were used to assemble a complete genome assembly. First, linkage data within contigs was used to detect wrongly assembled contigs. Next, linkage data between contigs was used to to concatenate them into sca olds and, eventually, whole chromosomes. This method represents an alternative and complementary approach to nishing genomes and may be particularly useful for assembling genomic sequences of natural fungal isolates without a reference genome. The genotyped reference assembly was annotated and used for mapping QTL. The 96 F2 progeny were phenotyped for many traits related to winemaking including: fermentation and sugar consumption performance, production of volatile aroma compounds, hydrogen sul de (H2S) and wine metabolites in Sauvignon blanc (S. blanc) wine, and growth in experimental formulations of model wine media. One and two-dimensional genome scans revealed QTL linked to many of the studied traits. Two QTL in uenced the production of H2S in wine. The F15 alleles of MET2 and MET5 both increased H2S production. Other strong QTL were found that a ected production of volatile aroma compounds, acidity in wine and fermentation rate. The relative contribution of each QTL to the traits and their interaction with other QTL were measured and will be useful for breeding of superior commercial wine yeast.