BIODIVERSITAS ISSN: 1412-033X Volume 18, Number 1, January 2017 E-ISSN: 2085-4722 Pages: 609-618 DOI: 10.13057/biodiv/d180123 Inbreeding depression level of post-larvae freshwater prawn (Macrobrachium rosenbergii) from several hatcheries in Java, Indonesia ROBI BINUR 1,♥ , ADI PANCORO 2,♥♥ 1 Laboratory of Zoology, Department of Biology, Faculty of Mathematics and Natural Sciences, Universitas Papua. Jl. Gunung Salju Amban, Manokwari 98314, West Papua, Indonesia. ♥ email: robi.binur@yahoo.co.id 2 Laboratory of Genetics and Biomolecular, Department of Biotechnology, Labtex. IX, School of Life Sciences and Technology, Institut Teknologi Bandung. Jl. Ganesha 10 Bandung 40132, Indonesia. ♥♥ email: adi@sith.itb.ac.id. Manuscript received: 2 September 2016. Revision accepted: 21 March 2017. Abstract. Binur R, Pancoro A. 2017. Inbreeding depression level of post-larvae freshwater prawn (Macrobrachium rosenbergii) from several hatcheries in Java, Indonesia. Biodiversitas 18: 609-618. Inbreeding accumulation will tend to reduce genetic variation or depressed of the prawn fry produced. This problem has caused a decrease in production and quality of prawns culture in Indonesia. The purpose of this study is to measure the level of inbreeding depression prawn fry generated from several hatcheries in Java by microsatellite markers. There is four microsatellite locus to be used i.e Prk9A/T1, Prk4G/T1, TGFP16, and Mr8-88. The amplification of fourth locus using PCR with 6-carboxy-fluorescine (6-FAM) label. The number of alleles (Na) from fourth locus is Mr8-88 (11 alleles), TGFP16 (10 alleles), Prk4G/T1 (9 alleles), dan Prk9A/T1 (5 alleles), respectively. The level of polymorphism locus from highest to lowest is locus Prk4G/T1 (0.703), Prk9A/T1 (0.507), TGFP16 (0.410), and Mr8-88 (0.370), respectively. Inbreeding depression level of postlarvae (PL) M. rosenbergii tend to moderate with BBI Ciamis (He 0.444), BBUG Samas (He 0.514), LRPTBPAT Sukamandi (He 0.519), and UPBL Probolinggo (He 0.530), respectively. AMOVA analysis showed about 8.0% genetic variation among populations. From these results, it can be concluded that the PL produced indicated have been depressed. Post-larvae prawns produced from fourth hatcheries is not recommended to be a broodstock but can be used for cultivation for farmers. Keywords: Freshwater prawn, Macrobrachium rosenbergii, post-larvae, microsatellite, inbreeding depression, heterozygosity, genetic diversity INTRODUCTION Giant freshwater prawns Macrobrachium rosenbergii (De Man, 1879) is a native species freshwater prawn from Indonesia, which has the largest body size among other freshwater prawn species. The total body length of adult male up to 320 mm and female 250 mm with weight more than 300 grams (Holthuis and Ng 2010; Wowor and Ng 2007). Therefore, this shrimp has a high economic value and very liked by farmers. The high economic value of shrimp was not the increasing production of prawns in Indonesia. Most of the production of traditional catch prawns has declined every year. According to FAO (2012) Indonesia is the country with the largest natural catching is 5,460 tons/year. To reduce this catch, the government began improving prawns farming. Based on data FAO (1998-2007) Indonesian prawn culture production is relative low, approximately 688.83 tons/year or 0.43% of the average global production (161,666 tons/year) (New 2010). Though Indonesia has a very wide farming land involving marine and coastal area covers 5.8 million km 2 and 5.4 million hectares of inland waters are potential prawns culture (Saifuddin 2008). One major problem for farmers is not the availability of high- quality fries. The increasing market has causing increased demand for fries. To meet this demand then some hatchery in Java to make the breeding program. Its good program must be avoided is inbreeding depression (Gjerde 2005) because will be reducing genetic variation or heterozygosity of the prawn populations (Sonesson et al. 2005). Center of prawn culture in Indonesia mostly located in Java include West Java, Central Java, Yogyakarta and East Java. Outside Java prawns culture in Bali and Nusa Tenggara Barat (NTB). In Java, Yogyakarta has the highest production than other provinces. But Bali had the largest national production up to 742 tons in 2010. If compared with the extent of land culture in Java, this indicates that the production of prawns in Java is having problems. Good breeding programs should avoid the depression of fries produced. Genetically, this phenomenon is the main trigger of declining production and quality of shrimp produced. Inbreeding depression is an effect of the breeding accumulation conducted within the same population. This effect will reduce genetic variation or heterozygosity of fry produced, because for traits with dominant inheritance was expected heterozygotes to be equal or better than one or both of the homozygotes. Inbreeding depression leads primarily to a reduction of the mean phenotypic value shown by characters connected with reproductive capacity (fecundity, egg size, hatchability) or physiological efficiency (fry deformities, growth rate, survival) (Gjerde 2005; Sonesson et al. 2005). This phenomenon has been shown from the decrease in the weight of prawns produced by farmers in Indonesia within a certain period. Then, was 2012 by 80% of prawn