Identification of elite Indian sugarcane varieties through DNA fingerprinting using genic microsatellite markers

Sugarcane is one of the important crops for sustainable economy and global energy security with high phenotypic polymorphism. Precise identification and characterization of plant genetic resources is one of the most essential aspects for breeding programs. Sugarcane popular hybrid varieties and genetic stocks routinely being used as a parent in hybridization program were included in the study. Molecular cataloguing was accomplished using a set of 70 primer pairs, of which ~ 39% were found to be robust polymorphic and unique in all the genotypes used. The number of DNA bands amplified by expressed sequenced tags derived simple sequence repeat (EST-SSR) primers ranged from 1 to 10 with an average of 5 bands per primer pair and their fragment size ranged between 50 and 1690 bp. Polymorphism information content (PIC) values were ranged from 0.17 to 1.00 with an average of 0.58. Unique DNA fingerprints of thirteen elite sugarcane varieties were generated with 27 polymorphic sugarcane specific EST-SSR markers. Analyses of DNA profiles produced by microsatellite markers showed the unique bands specific for individual variety. Generated DNA profiles would facilitate accurate variety identification in the perspective of protection of the breeder’s intellectual property rights, farmer’s rights and their purity testing. In addition, developed reliable DNA fingerprinting system will be able to track a potent parent genotype for breeding programs. The identified genotype specific and unique EST-SSR markers will be valuable for conservation and management of sugarcane genetic resources.