| Summary: | The Giant freshwater prawn (GFP) Si Jawa population is a new population of GFP from Bengawan Solo domesticated by BPTPB Cangkringan. The good morphometric and genetic characteristics of Si Jawa have never been compared with those of Bengawan Solo, or with cross-breeding populations such as Siratu. This study was to compare the morphometric and polymorphic characteristics of the DNA of three populations. Sampling of GFP was carried out at UKBAP Samas. Characterization was carried out at the Laboratory of Molecular Biology, Universitas Ahmad Dahlan. Each population took three male and three female individuals as samples. DNA polymorphisms were determined using ISSR 5 and ISSR 8 primers. Data on interpopulation morphometric characters were compared with the Kruskal Wallis test. The results showed that for the characters Cephalothorax:abdomen and carapace:abdomen was highest in males of Si Jawa and the lowest respectively in males of Siratu and Bengawan Solo. Carapace:rostrum were not significantly different (P>0.05). DNA polymorphisms from highest to lowest was Bengawan Solo (75%), Si Jawa (71.43%) and Siratu (68.75%). The results showed that Si Jawa was a morphometrically and genetically good population.
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