Genetic diversity analysis of industrial Saccharomyces cerevisiae strains

Sugarcane molasses serves as a vital non-food feedstock for ethanol fermentation, and its efficient utilisation depends on breeding of excellent microbial strains. Therefore, identification of industrial strains for ethanol fermentation are central to improving fermentation efficiency. To identify high-efficiency ethanol-fermenting strains, we developed a method for preparing high-throughput polymerase chain reaction (PCR) templates within 3 min using seven industrial Saccharomyces cerevisiae strains, integrating single-cell morphology and phenotypic variations in ethanol fermentation. Method specificity was confirmed by amplifying and sequencing the internal transcribed spacer region, and the efficiency was validated by extracting genomic DNA using cetyltrimethylammonium bromide. Subsequent genetic diversity analysis using random amplified polymorphic DNA (RAPD) with eight effective primers screened from twenty-two random primers revealed genetic similarity coefficients ranging between 0.47–0.96. The high-yield strains 1015-04-01 and 1002-03-03 showed the highest similarity (0.96), whereas strain 1015-04-01 and the low-yield strain 1415 exhibited the lowest similarity (0.47). Unweighted pair group method with arithmetic mean cluster analysis demonstrated that the high-yield strain 1016-02-04, and strains 1415 and 1313 formed a major cluster, and the low-yield strains 1415 and 1313 formed a distinct subcluster; four other high-yield strains constituted a separate cluster, indicating significant genetic differentiation between the high- and low-yield strains. The RAPD results showed substantial concordance with variations in ethanol yield and single-cell morphological differences, providing a molecular basis for rapid identification, breeding, and development of high-performance strains for sugarcane molasse-based ethanol fermentation.