Genetic diversity analysis of Saccharum spontaneum germplasm using SSR-SSCP and RAPD markers

Abstract

Saccharum spontaneum, the most important wild species used in the evolution of modern sugarcane varieties, imparts vigour, cold hardiness and tolerance towards biotic and abiotic stresses. Fourteen genotypes of S. spontaneum genotypes being maintained at Indian Institute of Sugarcane Research, Lucknow, were subjected to genetic diversity analysis using microsatellites and randomly amplified polymorphic DNA (RAPD) markers. Nine sugarcane specific flanking sequences of di and trinucleotide SSR (simple sequence repeat) motifs of EST (expressed sequence tags) and genomic DNA (Deoxyribonucleic acid) origin and 68 random operons were used for amplification. Single strand conformational polymorphism (SSCP) analysis of SSR amplicons yielded 128 conformers and, through RAPD 961 bands were amplified. Use of two types of markers amplifying different regions of the genome, allowed better analysis of genetic diversity; extensive molecular variability corroborated by the wide range of Dice similarity coefficients (0.04 to 0.48 in SSR-SSCP and 0.09 to 0.60 in RAPD) was observed. UPGMA (unweighed pair group method of arithmetic average) of similarity coefficients separated the genotypes in two main clusters. Identification of genetically distant genotypes of S. spontaneum would augment sugarcane breeding through the use of diverse parents facilitating the selection of hybrids with maximum genetic diversity and hybrid vigour.