RAPD fingerprinting of snakehead fish (Channa striata) in brantas watershed, East Java, Indonesia

Information about the genetic structure of Channa striata in their habitat is very important for sustainable aquaculture and genetic-based conservation relating to the use and management of their habitat. The aim of this study is to identify the genetic distance, genetic diversity, and genetic differentiation between three different populations from Brantas Watershed. One population from Bengawan Solo Watershed was used as an out-group. Random Amplified Polymorphic DNA (RAPD) was used as a marker to evaluate the genetic structure. After initial PCR screening, three primers, OPA 1, OPA 8 and OPA 9, were able to produce clear and well separated bands. The amplification using these primers resulted in fragment length between one hundred to more than one thousand base pair assigned to 33 loci from all population. Estimates of average expected heterozygosity (He) or Nei’s genetic diversity values range between 0.0750 – 0.2085, in which population from Porong has the highest genetic diversity. The estimates values of Gst is 0.3914, showed that genetic variaton among population is lower than within population. The values of Nei’s unbiased genetic distance (D) range between 0.0750 – 0.2085. Among the three population in Brantas watershed, the highest genetic distance is between population form Karangkates and Surabaya. The dendogram constructed using UPGMA revealed very close genetic relationship between population from Porong and Surabaya. The values of genetic distance estimated in this study is directly proportional to the geographical distance. This result indicates that the genetic differentiation between populations was mainly caused by geographical isolation.