Asiatic cotton (G. arboreum) is one of the important cultivated species of cotton originated in Indian subcontinent. Owing to its climate resilience, Asiatic cotton in particular and desi cotton in general, constitutes valuable genetic resources for cotton improvement to achieve sustainable cotton production in India. In the present study, 24 popular Asiatic cotton varieties were profiled using 300 genome-wide SSR markers. Of these, 48 were identified as distinctly polymorphic which detected a total of 124 alleles ranging from 2 to 5 alleles per loci with an average of 2.58. The genetic dissimilarity among 24 G. arboreum varieties ranged from 0.27 to 0.53 with an average of 0.42 indicating presence of sufficient genetic diversity in Indian arboreum varieties. The dissimilarity based unweighted neighbor joining method of clustering grouped them into 6 distinct clusters. The clustering pattern was found to be inconsistent with their known source or pedigree. We propose a set of 8 informative SSR markers for variety identification in diploid cotton using those, DNA fingerprint of 24 Asiatic cotton varieties was developed. Very low probability of identical match (2.68 x 10(-6)) with goodness of fit of 0.65 indicated robustness and reliability of the developed DNA fingerprint. Information generated in the present study about pattern of diversity among popular Asiatic cotton varieties of India and identified polymorphic markers will be of immense utility in maintenance of valuable desi cotton varieties and marker assisted breeding.
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