Assessment of genetic diversity in old world and new world cotton cultivars using RAPD and ISSR markers

In the present investigation, 15 cotton cultivars (8 old world and 7 new world cotton) were used to assess genetic diversity through dominant PCR based markers (21 RAPD and 9 ISSR primers). RAPD (Random amplified polymorphic DNA) primers produced in total 245 bands, of which 241 were polymorphic with 98.36% polymorphism. While ISSR (Inter simple sequence repeats) primers gave 85 bands, of which 81 were polymorphic constituting 95.29% polymorphism. Dendrogram showed clear grouping between old world and new world cotton cultivars. Principle coordinate analysis (PCA) showed congruence with dendrogram pattern, while high bootstrap values at major nodes in both marker systems as well as in pooled data indicated robustness of cluster pattern in dendrogram construction. Analysis of molecular variance (AMOVA) indicated genetic variation within populations for RAPD and pooled data, while the ISSR marker system showed high variation among population. Mantel's test between similarity and cophenetic coefficient matrices in different combinations showed good to very good correlation between matrices except for ISSR cophenetic coefficient matrices showing slightly poor result. The present study indicates huge variation between old world and new world cotton, which can be utilized for conservation of important cultivars and development of future strategies for crop improvement programme.