SHORT COMMUNICATION Development and application of RAPD-SCAR markers to identify intra-species hybrids of industrial Saccharomyces cerevisiae Pin-Mei Wang • Xue-Chang Wu • Xiao-Qin Chi • Yu-Dong Li • Dao-Qiong Zheng • Rui Ding • Hang Min Received: 19 January 2010 / Accepted: 28 April 2010 / Published online: 14 May 2010 Ó Springer Science+Business Media B.V. 2010 Abstract To overcome the drawbacks of protoplast fusion in industrial breeding, strain-specific molecular markers were applied to select hybrids of industrial Saccharomyces cerevisiae strains. Random Amplified Polymorphic DNA (RAPD) analysis was used to generate strain-specific RAPD markers for two industrial yeast strains, Z8 and Z9. For industrial and technical controls, two RAPD markers with non-coding regions were converted into stable Sequence Characterized Amplified Region (SCAR) markers. Hybrids of Z8 and Z9 were obtained by protoplast fusion in combi- nation with SCAR markers and were found to increase ethanol production by 4.3–8.1%. Results suggested that protoplast fusion could be combined with RAPD-SCAR molecular markers and applied in industrial breeding instead of auxotrophic markers. Keywords Industrial breeding Á Molecular marker Á Protoplast fusion Á Saccharomyces cerevisiae Introduction Ethanol, one of the most common renewable fuels in the market today, is conventionally produced from sugar or grain (starch) using industrial strains of the yeast Saccha- romyces cerevisiae. The characteristics of industrial S. cerevisiae strains are closely related to ethanol produc- tion. Protoplast fusion has the potential to generate improved hybrids possessing novel combinations of parent characteristics (Mukai et al. 2001). Practical application of yeast breeding by protoplast fusion, however, has been limited because many industrial yeast strains lack suitable genetic markers for screening potential hybrids (Urano et al. 2000). Although these genetic markers can be obtained through various mutations and genetic manipu- lation, they are usually costly, difficult to perform, and may bring about some unexpected changes, especially in industrial strains with low sporulation ability. Markers based on natural DNA polymorphisms can overcome these problems. To this end, Random Amplified Polymorphic DNA (RAPD) has been widely used to detect extensive polymorphisms because of its simplicity, rapidity, and lack of any requirement for radioisotope usage (Echeverrigaray et al. 2000; Zhao et al. 2009). However, the sensitivity of RAPD profiles to a number of reaction con- ditions, makes them less useful as markers for the analysis of industrial strains (Li et al. 2008). To overcome the drawbacks of RAPD application during industrial pro- cesses, a combination of RAPD specific marker and Sequence Characterized Amplified Region (SCAR) marker has proven to be more reproducible for the authentication and identification of genotypes (Li et al. 2008; Vidal et al. 2000). In this study, RAPD-SCAR molecular markers were applied to select hybrids obtained by protoplast fusion between industrial yeast strains with low sporulation ability. Pin-Mei Wang and Xue-Chang Wu contributed equally. P.-M. Wang Á X.-C. Wu (&) Á X.-Q. Chi Á Y.-D. Li Á D.-Q. Zheng Á R. Ding Á H. Min (&) College of Life Sciences, Zhejiang University, 310058 Hangzhou, Zhejiang, People’s Republic of China e-mail: mblab@163.com H. Min e-mail: mh_mgf@hotmail.com 123 World J Microbiol Biotechnol (2011) 27:185–188 DOI 10.1007/s11274-010-0430-7