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Understanding the pattern of diversity among the commercial sugarcane hybrids is highly useful to sugarcane breeders in planning and broadening the genetic base. Genetic analysis of 22 cultivated sugarcane hybrids representing all agro-eco climatic regions of tropical India was carried out using ten sequence tagged microsatellite sites (STMS) primers. A total of 127 markers were amplified, of which 78.74% were polymorphic with an average of 10 polymorphic products per STMS primer. Jaccard's similarity coefficient value estimated between closely related hybrids was 0.889 while the lowest coefficient value of 0.574 was detected with distantly related hybrids. The average genetic similarity among the hybrids was~84.8%. These results indicated the existence of low level of genetic diversity among the commercial hybrids under cultivation. Unweighted pair group method with arithmetic averages (UPGMA) cluster analysis detected five major clusters. Cluster II consisted of four varieties which had Co 775 as one of the parents. Variety CoC 671 and its somaclone Co 94012 were grouped into cluster IIa. Varieties grouped in the cluster III had either CoC 671 or Co 775 in their genealogy indicating the influence of parental genome contribution to clustering. Varieties developed for east coast zone were grouped in the clusters IIb, IIIb, IIIc and IVe which indicated the influence of adaptation of varieties to particular agro-climatic condition. The study also identified 12 unique markers which can be useful in varietal identification and rouging in seed plot.

Sugarcane is second most important industrial crop in India. In order to avoid genetic vulnerability of hybrids for new emerging pests or diseases and to design a new sugarcane breeding strategy, it is essential to know the genetic diversity in present commercial hybrids. Randomly Amplified Polymorphic DNA (RAPD) marker was used to detect the DNA polymorphism among 22 hybrids grown in Peninsular and East coast zones of tropical India. Of the 143 fragments generated by 16 RAPD primers, 69 were polymorphic with an average of 4.31 polymorphic fragments per primer. The level of polymorphism observed among these hybrids was 42.6%. Jaccard's similarity coefficient value recorded between closely related hybrids was 0.951 while lowest coefficient value of 0.727 was detected with distantly related hybrids. The average similarity coefficient among these hybrids was 0.831. Unweighted pair group method with arithmetic averages (UPGMA) cluster analysis divided all these hybrids into two major clusters based on adaptation to agro-climatic conditions. However, hybrids in these clusters divided into subclusters based on their pedigree. Genetic similarity obtained from the analysis could be useful for plant breeders to choose diverse parents for creating more variability and select elite varieties in breeding programmes.