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Labeo rohita (Rohu) is naturally occurring fish in the rivers of Pakistan, Bangladesh, India, Terai region, Nepal, Burma, Sri-Lanka, Thailand, Vietnam and Laos etc. Despite its wide distribution and status genetic data of Pakistani population is not available in the literature. Genetic measurement of a species is not only significant for specific administration but also for understanding its genetic variations. Various genetic and molecular methods are available for the complete genetic analysis and phylogenetic relationships of species. This study involves simple sequence repeat markers for the determination of genetic variation between various samples of Labeo rohita specie, which were collected from Head Muhammad Wala, Muzaffargarh and Khangarh regions of river Chenab, Pakistan. DNA was extracted from the muscles of fish by (phenol:chloroform:isoamylalcohol) extraction method. PCR was performed for the amplification of microsatellite regions. Through Polyacrylamide gel electrophoresis (PAGE), scoring of bands for alleles was performed for the generation of genotypic data which was then used for various indications of genetic diversity. Mean value of polymorphism for all markers was 78.63%. Out of 543 loci detected 427 were found polymorphic in all samples. Allele number fluctuated from 2 ? 7 with average 3.58 values and allelic frequency was from 0.3333 to 1.0000 with average 0.6389. Gene diversity found was from 0.0000--0.7901 with average 0.5624 and PIC value was 0.0994 -- 0.7618 with average. 0.4988. Mostly values of Nei?s genetic distance among different populations of different areas of river Chenab were 0.6667, 0.7500, while values of Jaccard?s similarity coefficient were 0.7500 and 0.9167.These values indicate that genetic makeup of L. rohita individuals of different areas of river Chenab differ from each others. This difference may be due to anthropogenic interventions, reproductive isolations and environmental factors. Phylogenetic tree on the base of UPGMA divided all samples into three clusters. C1 xv contains all samples of Khangarh region, C2 contains samples of Head Muhammad Wala and C3 contains all the samples of Muzaffargarh region. Cluster analysis shows that samples of one region show similar genetic information but genetic differences are more with the fish of other regions. It means that geographic isolation and different aquatic conditions have effect on genetics of organisms.
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