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Genetic diversity was assessed in 48 popular varieties of tetraploid cotton from each cultivated zone of India using 68 SSR markers distributed across linkage groups. The markers produced a total of 144 alleles with an average of 2.19 per locus. The polymorphism information content (PIC) ranged from 0.04 to 0.57 with a mean of 0.23 indicating lesser diversity in the studied material. Jaccard’s similarity index based neighbourhood joining cluster analysis grouped the genotypes into three major clusters, each of which was further classified into sub-groups. Inconsistencies were observed between the clusters and known pedigree of the cultivars. A narrow genetic base was also revealed among the cotton cultivars. The SSR markers revealed a genetic similarity of 73% among the varieties studied. The DNA fingerprint developed using a selected set of 14 markers showed a probability of identical match of 2.47×10-3 with high goodness of fit (r2=0.86). The identified markers have great potential in DNA fingerprinting in cotton which in future could be integrated with DUS data descriptors for effective cultivar identification and differentiation.

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