Computational approaches for the genetic and phenotypic characterization of a Saccharomyces cerevisiae wine yeast collection

Yeast

Volumn 26, Issue 12, 2009, Pages 675-692

  Franco Duarte, R ^a   Umek, L ^b   Zupan, B ^b,c   Schuller, D ^a  

^a UNIVERSITY OF MINHO   (Portugal)

^b UNIVERSITY OF LJUBLJANA   (Slovenia)

^c BAYLOR COLLEGE OF MEDICINE   (United States)

Author keywords

Bayesian classifier; Ethanol resistance; Genotype; Indigenous yeast; Microsatellite; Phenotype; Saccharomyces cerevisiae; Strain collection; Winemaking

Indexed keywords

AREA UNDER THE CURVE; ARTICLE; FUNGAL STRAIN; FUNGUS CULTURE; FUNGUS GROWTH; FUNGUS IDENTIFICATION; GENETIC SIMILARITY; GENETIC VARIABILITY; GENOTYPE PHENOTYPE CORRELATION; GEOGRAPHIC DISTRIBUTION; GROWTH INHIBITION; NONHUMAN; PHENOTYPE; PRIORITY JOURNAL; SACCHAROMYCES CEREVISIAE; TAXONOMIC RANK; TEMPERATURE;

ALLELES; BASE SEQUENCE; BAYES THEOREM; COMPUTATIONAL BIOLOGY; DNA PRIMERS; DNA, FUNGAL; GENETIC ASSOCIATION STUDIES; GENETIC VARIATION; GENOTYPE; MICROSATELLITE REPEATS; MODELS, GENETIC; PHENOTYPE; SACCHAROMYCES CEREVISIAE; VITIS; WINE;

SACCHAROMYCES CEREVISIAE;

EID: 73649090813     PISSN: 0749503X     EISSN: 10970061     Source Type: Journal    
DOI: 10.1002/yea.1728     Document Type: Article

References (54)

1. Agnolucci M, Scarano S, Santoro S, et al. 2007. Genetic and phenotypic diversity of autochthonous Saccharomyces spp. strains associated to natural fermentation of 'Malvasia delle Lipari'. Lett Appl Microbiol 45: 657-662.
2. Aires-de-Sousa J, Aires-de-Sousa L. 2003. Representation of DNA sequences with virtual potentials and their processing by (SEQREP) Kohonen self-organizing maps. Bioinformatics 19: 30-36.
3. Ashida S, Eiji I, Suginami K, Imayasu S. 1987. Isolation and application of mutants producing sufficient isoamyl acetate, a sake flavor component. Agric Biol Chem 51: 2061-2065.
4. Barnett JA, Payne RW, Yarrow D. 2000. Yeasts: Characterization and Identification, 2nd edn. Cambridge University Press: Cambridge.
5. Bely M, Sablayrolles J-M, Barre P. 1990. Automatic detection of assimilable nitrogen deficiencies during alcoholic fermentation in enological conditions. J Ferment Bioeng 70: 246-252.
6. Bisson LF. 1999. Stuck and sluggish fermentations. Am J Enol Viticult 50: 107-119.
7. Briones AI, Ubeda JF, Cabezudo MD, et al. 1995. Selection of spontaneous strains of Saccharomyces cerevisiae as starters in their viticultural area. In Food Flavours: Generation, Analysis and Process Influence. Elsevier Science: Amsterdam; 1597-1622.
8. Caridi A, Cufari JA, Ramondino D. 2002. Isolation and clonal preselection of enological Saccharomyces. J Gen Appl Microbiol 48: 261-267.
9. Carrasco P, Querol A, del Olmo M. 2001. Analysis of the stress resistance of commercial wine yeast strains. Arch Microbiol 175: 450-457.
10. Comi G, Maifreni M, Manzano M, et al. 2000. Mitochondrial DNA restriction enzyme analysis and evaluation of the enological characteristics of Saccharomyces cerevisiae strains isolated from grapes of the wine-producing area of Collio (Italy). Int J Food Microbiol 58: 117-121.
11. Curk T, Demsar J, Xu Q, et al. 2005. Microarray data mining with visual programming. Bioinformatics 21: 396-398.
12. Demsar J, Zupan B, Leban G. 2004. Orange: from experimental machine learning to interactive data mining. White paper, Faculty of Computer and Information Science, University of Ljubljana: www.ailab.si/orange.
13. Esteve-Zarzoso B, Gostíncar A, Bobet R, et al. 2000. Selection and molecular characterization of wine yeasts isolated from the 'El Pened̀es' area (Spain). Food Microbiol 17: 553-562.
14. Field D, Wills C. 1998. Abundant microsatellite polymorphism in Saccharomyces cerevisiae, and the different distributions of microsatellites in eight prokaryotes and S. cerevisiae, result from strong mutation pressures and a variety of selective forces. Proc Natl Acad Sci USA 95: 1647-1652.
15. Frezier V, Dubourdieu D. 1992. Ecology of yeast strains Saccharomyces cerevisiae during spontaneous fermentation in Bordeaux winery. Am J Enol Viticult 43: 375-380.
16. Gallego FJ, Perez MA, Martinez I, Hidalgo P. 1998. Microsatellites obtained from database sequences are useful to characterize Saccharomyces cerevisiae strains. Am J Enol Viticult 49: 350-351.
17. González Techera A, Jubany S, Carray FM, Gaggero C. 2001. Differentiation of industrial wine yeast strains using microsatellite markers. Lett Appl Microbiol 33: 71-75.
18. Guerra E, Mannazzu I, Sordi G, et al. 1999. Characterization of indigenous Saccharomyces cerevisiae from the Italian region of Marche: hunting for new strains for local wine quality improvement. Ann Microbiol Enzimol 49: 79-88.
19. Hanley JA, McNeil BJ. 1982. The meaning and use of the area under a receiver operating characteristic (ROC) curve. Radiology 143: 29-36.
20. Hennequin C, Thierry A, Richard GF, et al. 2001. Microsatellite typing as a new tool for identification of Saccharomyces cerevisiae strains. J Clin Microbiol 39: 551-559.
21. 2S-producing potential of Saccharomyces cerevisiae wine yeasts under enological conditions Am J Enol Vitic 46: 269-273.
22. Kohonen T. 2001. Self-organizing Maps. Springer: Berlin.
23. Kononenko I, Simec E, Robnik-Sikonja M. 1997. Overcoming the myopia of inductive learning algorithms with ReliefF. Appl Intel 7: 39-55.
24. Kvitek DJ, Will JL, Gasch AP. 2008. Variations in stress sensitivity and genomic expression in diverse S. cerevisiae isolates. PLoS Genet 4: e1000223.
25. Legras JL, Merdinoglu D, Cornuet J-M, Karst F. 2007. Bread, beer, and wine: Saccharomyces cerevisiae diversity reflects human history. Mol Ecol 16: 2091-2102.
26. Legras JL, Ruh O, Merdinoglu D, Karst F. 2005. Selection of hypervariable microsatellite loci for the characterization of Saccharomyces cerevisiae strains. Int J Food Microbiol 102: 73-83.
27. Lopes CA, Rodriguez ME, Sangorrin M, et al. 2007. Patagonian wines: the selection of an indigenous yeast starter. J Ind Microbiol Biotechnol 34: 539-546.
28. Lopes CA, Van Broock M, Querol A, Caballero AC. 2002. Saccharomyces cerevisiae wine yeast populations in a cold region in Argentinean Patagonia. A study at different fermentation scales. J Appl Microbiol 93: 608-615.
29. Lopez V, Querol A, Ramon D, Fernandez-Espinar MT. 2001. A simplified procedure to analyse mitochondrial DNA from industrial yeasts. Int J Food Microbiol 68: 75-81.
30. Maifreni M, Comi G, Rondinini G. 1999. Selection and oenological characterisation of Saccharomyces cerevisiae strains isolated from Tocai, Pinot and Malvasia grapes and musts of the Collio area. Ann Microbiol Enzimol 49: 33-43.
31. Mannazzu I, Angelozzi D, Belviso S, et al. 2008. Behaviour of Saccharomyces cerevisiae wine strains during adaptation to unfavourable conditions of fermentation on synthetic medium: cell lipid composition, membrane integrity, viability and fermentative activity. Int J Food Microbiol 121: 84-91.
32. Mannazzu I, Clementi F, Ciani M. 2002. Strategies and criteria for the isolation and selection of autochthonous starter. In Biodiversity and Biotechnology of Wine Yeasts, Ciani M (ed.). Research Signpost: Trivanduram, India.
33. Martínez-Rodríguez AJ, Carrascosa AV, Barcenilla JM, et al. 2001. Autolytic capacity and foam analysis as additional criteria for the selection of yeast strains for sparkling wine production. Food Microbiol 18: 183-191.
34. Mendes-Ferreira A, Mendes-Faia A, Leao C. 2002. Survey of hydrogen sulphide production by wine yeasts. J Food Prot 65: 1033-1037.
35. Monteiro FF, Bisson LF. 1991. Amino acid utilization and urea formation during vinification fermentations Am Soc Enol Viticult 42: 199-208.
36. Oliveira VA, Vicente MA, Fietto LG, et al. 2008. Biochemical and molecular characterization of Saccharomyces cerevisiae strains obtained from sugar-cane juice fermentations and their impact in cachaca production. Appl Environ Microbiol 74: 693-701.
37. Ough CS. 1976. Ethyl carbamate in fermented beverages and foods. Part I: Naturally occurring ethyl carbamate. J Agric Food Chem 24: 323-328.
38. Pérez-Coello MS, Pérez AIB, Iranzo JFU, Alvarez PJM. 1999. Characteristics of wines fermented with different Saccharomyces cerevisiae strains isolated from the La Mancha region. Food Microbiol 16: 563-573.
39. Perez MA, Gallego FJ, Hidalgo P. 2001a. Evaluation of molecular techniques for the genetic characterization of Saccharomyces cerevisiae strains. FEMS Microbiol Lett 205: 375-378.
40. Perez MA, Gallego FJ, Martinez I, Hidalgo P. 2001b. Detection, distribution and selection of microsatellites (SSRs) in the genome of the yeast Saccharomyces cerevisiae as molecular markers. Lett Appl Microbiol 33: 461-466.
41. Rainieri S, Pretorius IS. 2000. Selection and improvement of wine yeasts. Ann Microbiol 50: 15-31.
42. Regodon JA, Perez F, Valdes ME, et al. 1997. A simple and effective procedure for selection of wine yeast strains. Food Microbiol 14: 247-254.
43. Romesburg HC. 1984. Cluster Analysis for Researchers. Lifetime Learning: Belmont, CA.
44. Sabate J, Cano J, Querol A, Guillamon JM. 1998. Diversity of Saccharomyces strains in wine fermentations: analysis for two consecutive years. Lett Appl Microbiol 26: 452-455.
45. Schneider S, Roessli D, Excoffier L. 1997. Arlequin Version 2.000: A Software for Population Genetics Data Analysis. Genetics and Biometry Laboratory, Department of Anthropology and Ecology, University of Geneva: Geneva, Switzerland.
46. Schuller D, Alves H, Dequin S, Casal M. 2005. Ecological survey of Saccharomyces cerevisiae strains from vineyards in the Vinho Verde Region of Portugal. FEMS Microbiol Ecol 51: 167-177.
47. Schuller D, Casal M. 2007. The genetic structure of fermentative vineyard-associated Saccharomyces cerevisiae populations revealed by microsatellite analysis. Antonie Van Leeuwenhoek 91: 137-150.
48. Schuller D, Valero E, Dequin S, Casal M. 2004. Survey of molecular methods for the typing of wine yeast strains. FEMS Microbiol Lett 231: 19-26.
49. Tan P, Steinbach M, Kumar V. 2006. Introduction to Data Mining. Pearson Addison Wesley: Boston, MA.
50. Techera AG, Jubany S, Carrau FM, Gaggero C. 2001. Differentiation of industrial wine yeast strains using microsatellite markers. Lett Appl Microbiol 33: 71-75.
51. Valero E, Cambon B, Schuller D, et al. 2007. Biodiversity of Saccharomyces yeast strains from grape berries of wine-producing areas using starter commercial yeasts. FEMS Yeast Res 7: 317-329.
52. Viana F, Gil JV, Genoves S, et al. 2008. Rational selection of non-Saccharomyces wine yeasts for mixed starters based on ester formation and enological traits. Food Microbiol 25: 778-785.
53. Whitney PA, Cooper TG. 1972. Urea carboxylase and allophanate hydrolase. Two components of adenosine triphosphate: urea amido-lyase in Saccharomyces cerevisiae. J Biol Chem 247: 1349-1353.
54. Zuzuarregui A, del Olmo M. 2004. Analyses of stress resistance under laboratory conditions constitute a suitable criterion for wine yeast selection. Antonie van Leeuwenhoek 85: 271-280.