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Cirrhinus mrigala (Family Cyprinidae) have vast presence in different studied rivers of Pakistan. Present study was designed to formulate the genetic diversity of desired sites in Cirrhinus mrigala populations using nine Random amplified polymorphic DNA markers. Total hundred individuals were used to conduct this study and were collected from three distinct rivers (River Indus, Chenab and Ravi) with four specified sites with wild of Pakistan were used to study. A random Amplified Polymorphic DNA primer analyzes various bands of polymorphic loci. Mean genetic diversity within and between populations found 81.53% and 2.27% respectively by using analysis of molecular variance. Fixation index was found variably and Pairwise Fst analysis showed significant difference between different sites of studied populations. Genetic divergence information would mark essential in order to improve genetic programming its management and conservation of natural inhabitation. In order to quantify the study of population divergence by using these molecular markers is an efficient way to pin point the genetic diversity within and among population.
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