Antonie van Leeuwenhoek

, 100:569 | Cite as

Geographical markers for Saccharomyces cerevisiae strains with similar technological origins domesticated for rice-based ethnic fermented beverages production in North East India

  • Kumaraswamy Jeyaram
  • Jyoti Prakash Tamang
  • Angela Capece
  • Patrizia Romano
Original Paper


Autochthonous strains of Saccharomyces cerevisiae from traditional starters used for the production of rice-based ethnic fermented beverage in North East India were examined for their genetic polymorphism using mitochondrial DNA-RFLP and electrophoretic karyotyping. Mitochondrial DNA-RFLP analysis of S. cerevisiae strains with similar technological origins from hamei starter of Manipur and marcha starter of Sikkim revealed widely separated clusters based on their geographical origin. Electrophoretic karyotyping showed high polymorphism amongst the hamei strains within similar mitochondrial DNA-RFLP cluster and one unique karyotype of marcha strain was widely distributed in the Sikkim-Himalayan region. We conceptualized the possibility of separate domestication events for hamei strains in Manipur (located in the Indo-Burma biodiversity hotspot) and marcha strains in Sikkim (located in Himalayan biodiversity hotspot), as a consequence of less homogeneity in the genomic structure between these two groups, their clear separation being based on geographical origin, but not on technological origin and low strain level diversity within each group. The molecular markers developed based on HinfI-mtDNA-RFLP profile and the chromosomal doublets in chromosome VIII position of Sikkim-Himalayan strains could be effectively used as geographical markers for authenticating the above starter strains and differentiating them from other commercial strains.


Domestication Hamei Marcha mtDNA-RFLP Karyotyping 



This research was supported by the Department of Science and Technology (DST), Govt. of India-sponsored Indo-Italian Programme of Cooperation in Science and Technology 2005–2007 (BS-8).

Supplementary material

10482_2011_9612_MOESM1_ESM.doc (349 kb)
Fig. S1 Location of two geographical regions (Manipur and Sikkim) of North East India selected for studying genetic polymorphism of S. cerevisiae strains with similar technological origin. Grey area Indo-Burma biodiversity hotspot, dark area Himalayan biodiversity hotspot. The Brahmaputra River flow separating Manipur and Sikkim is highlighted with green color line. (DOC 349 kb)


  1. Aertsen A, Michiels CW (2005) Diversity or die: generation of diversity in response to stress. Crit Rev Microbiol 31:69–78PubMedCrossRefGoogle Scholar
  2. Blanco P, Ramilo A, Cerdeira M, Orriois I (2006) Genetic diversity of wine Saccharomyces cerevisiae strains in an experimental winery from Galicia (NW Spain). Antonie van Leeuwenhoek 89:351–357PubMedCrossRefGoogle Scholar
  3. Carro D, Pia B (2001) Genetic analysis of the karyotype instability in natural wine yeast strains. Yeast 18:1457–1470PubMedCrossRefGoogle Scholar
  4. Codón AC, Benítez T, Korhola M (1997) Chromosomal reorganization during meiosis of Saccharomyces cerevisiae baker’s yeasts. Curr Genet 32:247–259PubMedCrossRefGoogle Scholar
  5. Diamond J (2002) Evolution, consequences and future of plant and animal domestication. Nature 418:700–707PubMedCrossRefGoogle Scholar
  6. Drake JW (1991) A constant rate of spontaneous mutation in DNA based microbes. Proc Natl Acad Sci USA 88:7160–7164PubMedCrossRefGoogle Scholar
  7. Esteve-Zarzoso B, Manzanares P, Ramön D, Querol A (1998) The role of non-Saccharomyces yeasts in industrial winemaking. Int Microbiol 1:143–148PubMedGoogle Scholar
  8. Ezeronye OU, Legras JL (2009) Genetic analysis of Saccharomyces cerevisiae strains isolated from palm wine in eastern Nigeria, comparison with other African strains. J Appl Microbiol 106:1569–1578PubMedCrossRefGoogle Scholar
  9. Fay JC, Benavides JA (2005) Evidence for domesticated and wild populations of Saccharomyces cerevisiae. PLoS Genet 1(1):e5CrossRefGoogle Scholar
  10. Fernandez-Espinar MT, Esteve-zarzoso B, Querol A, Barrio E (2000) RFLP analysis of the internal transcribed spacers and the 5.8S rRNA gene region of the genus Saccharomyces: a fast method for species identification and the differentiation of flour yeasts. Antonie van Leeuwenhoek 78:87–97CrossRefGoogle Scholar
  11. Fernandez-Espinar MT, Lopez V, Ramon D, Bartra E, Querol A (2001) Study of the authenticity of commercial wine yeast strains by molecular techniques. Int J Food Microbiol 70:1–10PubMedCrossRefGoogle Scholar
  12. Fernandez-Espinar TM, Barrio E, Querol A (2003) Analysis of the genetic variability in the species of the Saccharomyces sensu stricto complex. Yeast 20:1213–1226CrossRefGoogle Scholar
  13. Fischer G, James SA, Roberts IN, Oliver SG, Louis EJ (2000) Chromosomal evolution in Saccharomyces. Nature 405:451–454PubMedCrossRefGoogle Scholar
  14. Granchi L, Bosco M, Messini A, Vincenzini M (1999) Rapid detection and quantification of yeast species during spontaneous wine fermentation by PCR-RFLP analysis of the rDNA ITS region. J Appl Microbiol 87:949–956PubMedCrossRefGoogle Scholar
  15. Guillamon JM, Barrio E, Querol A (1996) Characterization of wine yeast strains of the Saccharomyces genus on the basis of molecular markers: relationships between genetic distance and geographic or ecological origin. Syst Appl Microbiol 19:122–132Google Scholar
  16. Iranzo JFU, Perez AIB, Canar PMI (1998) Study of the oenological characteristics and enzymatic activities of wine yeasts. Food Microbiol 15:399–406CrossRefGoogle Scholar
  17. Jeyaram K, Singh MW, Capece A, Romano P (2008) Molecular identification of yeast species associated with ‘Hamei’—a traditional starter used for rice wine production in Manipur, India. Int J Food Microbiol 124:115–125PubMedCrossRefGoogle Scholar
  18. Jeyaram K, Singh TA, Romi W, Devi AR, Singh WM, Dayanidhi H, Singh NR, Tamang JP (2009) Traditional fermented foods of Manipur. Indian J Tradit Knowl 8(1):115–121Google Scholar
  19. Kreger-Van Rij NJW (1984) The yeasts a taxonomic study. Elsevier Science Publishers, AmsterdamGoogle Scholar
  20. Kurtzman CP, Robnett CJ (1998) Identification and phylogeny of ascomycetous yeasts from analysis of nuclear large subunit (26S) ribosomal DNA partial sequences. Antonie van Leeuwenhoek 73:331–371PubMedCrossRefGoogle Scholar
  21. Legras J, Merdinoglu D, Cornuet J, Karst F (2007) Bread, beer and wine: Saccharomyces cerevisiae diversity reflects human history. Mol Ecol 16:2091–2102PubMedCrossRefGoogle Scholar
  22. Liti G, Carter DM, Moses AM et al (2009) Population genomics of domestic and wild yeasts. Nature 458:337–341PubMedCrossRefGoogle Scholar
  23. Longo E, Vezinhet F (1993) Chromosomal rearrangements during vegetative growth of a wild strain of Saccharomyces cerevisiae. Appl Environ Microbiol 59:322–326PubMedGoogle Scholar
  24. Lopes M, Cotta-Ramusino C, Pellicioli A, Liberi G, Plevani P, Muzi-Falconi M, Newlon CS, Foiani M (2001) The DNA replication checkpoint response stabilizes stalled replication forks. Nature 412:557–561PubMedCrossRefGoogle Scholar
  25. 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 93:608–615PubMedCrossRefGoogle Scholar
  26. Lopes CA, Lavalle TL, Querol A, Caballero AC (2006) Combined use of killer biotype and mtDNA-RFLP patterns in a Patagonian wine Saccharomyces cerevisiae diversity study. Antonie van Leeuwenhoek 89:147–156PubMedCrossRefGoogle Scholar
  27. Martinez C, Gac S, Lavin A, Gangal M (2004) Genomic characterization of Saccharomyces cereviseae strains isolated from wine-producing areas in South America. J Appl Microbiol 96:1161–1168PubMedCrossRefGoogle Scholar
  28. Martinez C, Cosgaya P, Vasquez C, Gac S, Ganga A (2007) High degree of correlation between molecular polymorphism and geographic origin of wine yeast strains. J Appl Microbiol 103:2185–2195PubMedCrossRefGoogle Scholar
  29. McGovern PE, Zhang J, Tang J, Zhang Z, Hall GR, Moreau RA, Nunez A, Butrym ED, Richards MP, Wang CS, Cheng G, Zhao Z, Wang C (2004) Fermented beverages of pre- and proto-historic China. Proc Natl Acad Sci USA 101:17593–17598PubMedCrossRefGoogle Scholar
  30. Mortimer RK (2000) Evolution and variation of the yeast (Saccharomyces). Genome Res 10:403–409PubMedCrossRefGoogle Scholar
  31. Nakazato A, Kadokura T, Amoano M, Harayama T, Murakami Y, Takeda M, Ohkuma M, Kudo T, Kaneko T (1998) Comparison of the structural characteristics of chromosome VI in Saccharomyces sensu stricto: the divergence, species-dependent features and uniqueness of sake yeasts. Yeast 14:723–731PubMedCrossRefGoogle Scholar
  32. Pretorius IS (2000) Tailoring wine yeast for the new millennium: novel approaches to the ancient art of wine making. Yeast 16:675–729PubMedCrossRefGoogle Scholar
  33. Querol A, Barrio E, Ramon D (1992) A comparative study of different methods of yeast strain characterization. Syst Appl Microbiol 15:439–446Google Scholar
  34. Rachidi N, Barre P, Blondin B (1999) Multiple Ty-mediated chromosomal translocations lead to karyotype changes in a wine strain of Saccharomyces cerevisiae. Mol Gen Genet 261:841–850PubMedCrossRefGoogle Scholar
  35. Renfrew JW (1999) Palaeoethnobotany and the archaeology of wine. In: Robinson J (ed) The oxford companion to wine, 2nd edn. Oxford University Press, Oxford, pp 508–509Google Scholar
  36. Salinas F, Mandakovii D, Urzua U, Massera A, Miras S, Combina M, Ganga MA, Martinez C (2010) Genomic and phenotypic comparison of Saccharomyces cerevisiae from different geographical origins. J Appl Microbiol 108:1850–1858PubMedCrossRefGoogle Scholar
  37. Schacherer J, Shapiro JA, Ruderfer DM, Kruglyak L (2009) Comprehensive survey elucidates population structure of Saccharomyces cerevisiae. Nature 458:342–345PubMedCrossRefGoogle Scholar
  38. Schuller D, Pereira L, Alves H, Cambon B, Dequin S, Casal M (2007) Genetic characterization of commercial Saccharomyces cerevisiae isolates recovered from vineyard environment. Yeast 24:625–636PubMedCrossRefGoogle Scholar
  39. Schwartz DC, Cantor CR (1984) Separation of yeast chromosome-sized DNAs by pulsed field gradient gel electrophoresis. Cell 37:67–75PubMedCrossRefGoogle Scholar
  40. Sujaya IN, Antara NS, Sone T, Tamura Y, Aryanta WR, Yokota A, Asano K, Tomita F (2004) Identification and characterization of yeasts in brem, a traditional Balinese rice wine. World J Microbiol Biotechnol 20:143–150CrossRefGoogle Scholar
  41. Tamang JP (2010) Himalayan fermented foods: microbiology, nutrition, and ethnic values. CRC Press, Taylor and Francis Group, New YorkGoogle Scholar
  42. Tamang JP, Samuel D (2010) Dietary culture and antiquity of fermented foods and beverages. In: Tamang JP, Kailasapathy K (eds) Fermented foods and beverages of the world. CRC Press, Taylor and Francis Group, New YorkCrossRefGoogle Scholar
  43. Tamang JP, Thapa S (2006) Fermentation dynamics during production of bhaati jaanr, a traditional fermented rice beverage of the Eastern Himalayas. Food Biotechnol 20(3):251–261CrossRefGoogle Scholar
  44. Thapa S, Tamang JP (2004) Product characterization of kodo ko jaanr: fermented finger millet beverage of the Himalayas. Food Microbiol 21:617–622CrossRefGoogle Scholar
  45. Tsuyoshi N, Fudou R, Yamanaka S, Kozaki M, Tamang N, Thapa S, Tamang JP (2005) Identification of yeast strains isolated from marcha in Sikkim, a microbial starter for amylolytic fermentation. Int J Food Microbiol 99:135–146PubMedCrossRefGoogle Scholar
  46. Versavaud A, Coucoux P, Roulland C, Dulac L, Hallet J (1995) Genetic diversity and geographical distribution of wild Saccharomyces cerevisiae strains from the wine producing area of charentes, France. Appl Environ Microbiol 61:3521–3529PubMedGoogle Scholar

Copyright information

© Springer Science+Business Media B.V. 2011

Authors and Affiliations

  • Kumaraswamy Jeyaram
    • 1
  • Jyoti Prakash Tamang
    • 2
  • Angela Capece
    • 3
  • Patrizia Romano
    • 3
  1. 1.Microbial Resources DivisionInstitute of Bioresources and Sustainable Development (IBSD), Takyelpat Institutional AreaImphalIndia
  2. 2.Food Microbiology LaboratorySikkim UniversityTadong, GangtokIndia
  3. 3.Department of Biology, DBAFUniversity of BasilicataPotenzaItaly

Personalised recommendations