Evaluation of smut resistance in selected sugarcane genotypes and their molecular characterization using SCoT, ISSR, and RAPD analysis

Sporisorium scitamineum causes sugarcane smut, which is a global problem that seriously reduces yield and quality. The disease is most effectively managed through the use of resistant cultivars. Molecular markers can support breeding programs by helping to identify resistant genotypes at early stages. In this study, three sugarcane varieties G.2003-47 (G3), G.2004-27 (G4), and the commercial cultivar G.T.54-9 (C9) were evaluated for whip smut response under artificial inoculation and characterized using Start codon Targeted (SCoT), inter simple sequence repeats (ISSR), and random amplified polymorphic DNA (RAPD) markers. Disease incidence was lowest in G.2004-27 (4%), while G.2003-47 and G.T.54-9 showed higher infection levels (13.34% and 12.88%, respectively). SCoT primers generated 25 bands with 55.33% polymorphism, whereas ISSR and RAPD produced 37 and 32 bands with polymorphism levels of 46.3% and 49%, respectively. Several primers across the three marker systems distinguished the relatively resistant variety G.2004-27 from the more susceptible genotypes. These findings indicate that SCoT, ISSR, and RAPD markers can complement phenotypic screening and assist in the preliminary identification of whip smut–resistant sugarcane clones for further field evaluation. Consequently, the variety G.2004-27 is recommended as a promising source of resistance for Egyptian sugarcane breeding programs. Additionally, SCoT markers proved to be more informative than RAPD and ISSR in discriminating among the tested genotypes.