ISSN: 1687-4285 Egyptian Journal of Aquatic Research, 2010, 36(3), 467-480 DNA fingerprinting of some tilapia fish in Suez Canal zone Mohamed E. Megahed 1* , Mahmoud M. Rifaat 2 , Mohamed A. EL Danasoury 1 , Safaa M. Sharaf 1 1 Department of Animal Production and Fish Resources, Faculty of Agriculture, Suez Canal University, Ismailia, 41522. 2 Department of Plant Genetics, Faculty of Agriculture, Suez Canal University, Ismailia, 41522. *Email: melsayedmam@yahoo.com Received 9 th December 2010, Accepted 3 rd March 2010 Abstract This study was conducted on samples collected from three wild environments with different salinities in the Suez Canal zone involving four species Oreochromis niloticus, Oreochromis aureus, Sarotherodon galilaeus and Tilapia zilli. Random Amplified Polymorphic DNA (RAPD PCR) using ten decamers primers was conducted on representative samples from the four species collected from the three different environments in the Suez Canal zone zilli fresh (ZF), zilli brakish (ZB), Zilli saline (ZS), niloticus fresh (NF), niloticus brakish (NB), aureus fresh (AF), aureus brakish (AB), galilaeus fresh (GF), and galilaeus brakish (GB). 340 bands were identified in the nine populations. The RAPD patterns generated by primers (OPA-03) and (OPA-19) were together sufficient to distinguish the nine tilapia populations. The discrimination indices of primers 1 and 6 were 0.89 and 0.83 respectively. The major components of variance for RAPD markers accounted for 72 % of the variance. The use of two ways clustering revealed that certain RAPD markers are associated with adaptation of the genomes to salinity or brackish water conditions. These markers will be useful in future experiments on MAS breeding for tolerance to salinity in Nile Tilapia. Keywords: DNA Fingerprinting, RAPD-PCR, Tilapia, salinity, Suez Canal. 1. Introduction Tilapias are the most popular and common cultivated fish in Egypt. Recently, attention has been paid to produce tilapia strains more tolerant to environmental conditions, especially salinity (such as red tilapia). In general, tilapias are mostly fresh water species but the production of tilapia strains in brackish or sea water is needed (Payne, 1983). A simple procedure based on Random Amplified Polymorphic DNA (RAPD) markers has been found useful for revealing the genetic differences within as well as among fish populations (Ali, 2003; Ali et al., 2004; Du et al., 2005). RAPD markers have found a wide range of applications in gene mapping, population genetics, molecular evolutionary genetics and plant and animal breeding (Bartish et al., 1999 & 2000). A main objective of management of tilapia species in the Suez Canal zone is the elucidation of the population structure and the preservation of the genetic resources within and between the populations. Management is rather simple to apply if the fish stocks are separated from each other, such as salmon. Salmon populations are separated according to spawning grounds. Many species of fish are separated by occupying separate inland bodies of waters. Stocks in these cases can be managed and harvested separately (Allendorf et al., 1987; and Koeller, 2003). Management becomes complicated if the stocks congregate in mixed populations. In such situations, identification of each contributing population should be accomplished first. Pella and Milner. (1987) and Kaewsanagk et al.: (2000) presented the procedure for this analysis, called "The stock composition analysis using genetic markers". By this procedure, the distribution of each contributing population within the mixed stocks can be estimated, and therefore, regulation of harvests to protect weaker populations can be made. In spite of the commercial importance and increasing demand of tilapia species, little is known about the genetic characteristics of wild and cultured populations of tilapia strains in Egypt. This study involves four tilapia (Oreochromis niloticus, Oreochromis aureus, Sarotherodon galilaeus and Tilapia zilli) species collected during geographical survey from wild environments in the Suez Canal zone, namely; Ismailia Fresh Water Canal, Western Lagoon and Lake Timsah. The aim of this study was to characterize at the DNA level, the differences among tilapia species collected from the three different wild environments from Suez Canal zone. EJAR