Use of RAPD markers to characterize commercially grown rust resistant cultivars of sugarcane.

The brown leaf rust caused by Puccinia melanaocephala (Syd. & P. Syd.) is a major cause of reduction in sugar production and withdrawal of sugarcane cultivars from growing fields. In The present study, the eight commercially grown sugarcane cultivar was characterized under natural inoculation and divided into two discrete groups i.e. four rust resistant and four rust susceptible. The extracted genomic DNA was subjected against RAPD (Random Amplified Polymorphic DNA) markers. After screening of decamers, 7 were picked for further analysis on the basis of polymorphism, which is the most important application of DNA markers. These decamers generated 21 trackable loci with the range of 400-2500 bp and 100% polymorphic loci were recorded genomic DNA of eight sugarcane cultivars. From 7 primers, 3 generated 5 specific loci in 4 sugarcane cultivars, which is a potential use of RAPD-PCR for identifying Saccharum spp. hybrids and clones. Primer G-06 generated only one locus 1200 bp in the rust susceptible cultivar NSG-59 while J-05 had produced two loci i.e. 400 bp and 1100 bp in rust resistant cultivars NSG-555 and CP-77-400 respectively. Primer L-18 generated 700 bp and 1400 bp loci in rust susceptible cultivar CoJS-84. The homology tree was constructed using DNAMAN software based on binary data set. During cluster analysis, we found two major groups of cultivars with different minor groups. This study will be useful to characterize rust resistance in sugarcane and could be extended for the development of SCAR (Sequence Characterized Amplified Region) marker, which is specific, reliable and reproducible marker.