Computational models for prediction of yeast strain potential for winemaking from phenotypic profiles

Ines Mendes (1) , Ricardo Franco-Duarte (1) , Lan Umek (2, 3) , Elza Fonseca (1) , Joao Drumonde-Neves (1, 4) , Sylvie Dequin (5) , Blaz Zupan (3) , Dorit Schuller (1)

1 Dept Biol, CBMA Ctr Mol & Environm Biol
2 Fac Adm
3 Fac Comp & Informat Sci
4 Dept Agr Sci, Res Ctr Agr Technol
5 SPO - Sciences Pour l'Oenologie

Saccharomyces cerevisiae strains from diverse natural habitats harbour a vast amount of phenotypic diversity, driven by interactions between yeast and the respective environment. In grape juice fermentations, strains are exposed to a wide array of biotic and abiotic stressors, which may lead to strain selection and generate naturally arising strain diversity. Certain phenotypes are of particular interest for the winemaking industry and could be identified by screening of large number of different strains. The objective of the present work was to use data mining approaches to identify those phenotypic tests that are most useful to predict a strain's potential for winemaking. We have constituted a S. cerevisiae collection comprising 172 strains of worldwide geographical origins or technological applications. Their phenotype was screened by considering 30 physiological traits that are important from an oenological point of view. Growth in the presence of potassium bisulphite, growth at 40 degrees C, and resistance to ethanol were mostly contributing to strain variability, as shown by the principal component analysis. In the hierarchical clustering of phenotypic profiles the strains isolated from the same wines and vineyards were scattered throughout all clusters, whereas commercial winemaking strains tended to co-cluster. Mann-Whitney test revealed significant associations between phenotypic results and strain's technological application or origin. Naive Bayesian classifier identified 3 of the 30 phenotypic tests of growth in iprodion (0.05 mg/mL), cycloheximide (0.1 mu g/mL) and potassium bisulphite (150 mg/mL) that provided most information for the assignment of a strain to the group of commercial strains. The probability of a strain to be assigned to this group was 27% using the entire phenotypic profile and increased to 95%, when only results from the three tests were considered. Results show the usefulness of computational approaches to simplify strain selection procedures.

Domaines: Sciences du Vivant [q-bio]

Ines Mendes, Ricardo Franco-Duarte, Lan Umek, Elza Fonseca, Joao Drumonde-Neves, et al.. Computational models for prediction of yeast strain potential for winemaking from phenotypic profiles. PLoS ONE, 2013, 8 (7), ⟨10.1371/journal.pone.0066523⟩. ⟨hal-01837687⟩