Development of an RAPD-based SCAR marker for smut disease resistance in commercial sugarcane cultivars of Pakistan

A 300-bp RAPD-derived Sequence Characterized Amplified Region (SCAR) marker linked with resistance to sugarcane smut disease was developed. Bulked segregant analysis and RAPD were conducted using 480 random decamers in the initial screening of 12 sugarcane cultivars (two completely smut resistant, two completely smut susceptible, four moderately smut resistant, and four moderately smut susceptible). Eighty-four of these primers proved to be polymorphic while only one (B17) produced a reproducible polymorphic fragment, which appeared to co-segregate in repulsion with sugarcane smut resistance. A 300-bp B1SM-F/B1SM-R SCAR marker was designed based on the sequence alignment of the B17 products. Testing of this SCAR marker on these12 cultivars confirmed its specificity on two completely and four partially resistant cultivars. Further screening of this SCAR marker on seven additional sugarcane cultivars of Pakistan verified the earlier findings. Therefore, it was deduced that the B1SM-F/B1SM-R SCAR marker is linked with smut resistance trait in sugarcane. NCBI blast of the SCAR marker sequence showed no homology to any of the earlier identified sequences in GenBank. The newly discovered B1SM-F/B1SM-R SCAR marker for sugarcane smut resistance will facilitate sugarcane breeding programs since it can be used for marker-assisted selection in sugarcane.