Sunandar, Dadan
Pusat Penelitian dan Pengembangan Perikanan, Badan Penelitian dan Pengembangan Kelautan da

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THE APPLICATION OF RAPD FINGERPRINTING TO ASSESS INBREEDING LEVELS IN THE CULTURED POPULATIONS OF GIANT FRESHWATER PRAWN, Macrobrachium rosenbergii Imron, Imron; Sunandar, Dadan; Suprapto, Rommy; Listyowati, Nunuk
Indonesian Aquaculture Journal Vol 5, No 1 (2010): (June 2010)
Publisher : Pusat Penelitian dan Pengembangan Perikanan, Badan Penelitian dan Pengembangan Kelautan da

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (117.146 KB) | DOI: 10.15578/iaj.5.1.2010.73-82

Abstract

Inbreeding has been one of central issues with regard to genetic quality of aquaculture species, including giant fresh water prawn (GFP). Conventional methods for the estimation of inbreeding level are available, such as pedigree analyses which requires a good pedigree record which, unfortunately, is rarely available. Likewise, microsatellite molecular markers commonly applied to obtain the coefficient inbreeding estimates are both laborious and expensive. Hence, an alternative method of inbreeding assessment which is relatively easy but reliable is in need. This study was aimed to explore the applicability of RAPD fingerprinting, which is known to be simple and affordable, to estimate inbreeding level of GFP population. Three GFP populations namely inbred, outbred, and farm populations with inbreeding level of 25%, 0%, and unknown, respectively, were genotyped using five polymorphic RAPD primers. The inbreeding levels mentioned within the first two populations were determined using pedigree analysis. RAPD banding patterns were then used to calculate band sharing index (BSI) and inbreeding coefficient (F). Assessment of the applicability of inbreeding level estimates obtained by RAPD markers was performed by comparing them to those estimated by pedigree analysis. Results show that RAPD fingerprinting was capable of delineating populations differing in their inbreeding coefficients. The pattern resulted from molecular inbreeding coefficient within the inbred and outbred groups, was congruent with that shown by pedigree analysis, while the farm population showed closeness to the inbred group. While the accuracy of the estimate needs to be verified further, this study suggests that RAPD fingerprinting is applicable to estimate population inbreeding level, particularly due to its technical simplicity and cost affordability.
RANDOMLY AMPLIFIED POLYMORPHIC DNA (RAPD) FINGERPRINTING OF SIX INDONESIAN POPULATIONS OF GIANT FRESHWATER PRAWN, Macrobrachium rosenbergii Imron, Imron; Sunandar, Dadan; Susilowati, Rini; Suprapto, Rommy; Khasani, Ikhsan
Indonesian Aquaculture Journal Vol 4, No 2 (2009): (December 2009)
Publisher : Pusat Penelitian dan Pengembangan Perikanan, Badan Penelitian dan Pengembangan Kelautan da

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (373.592 KB) | DOI: 10.15578/iaj.4.2.2009.93-100

Abstract

Indonesia is rich of giant fresh water prawn (GFP) germ plasms. Best utilization of these resources for the purpose of either aquaculture development or conservation of genetic resources requires some information on the structure and levels of their genetic diversity. This study was aimed to characterize those GFP genetic resources by applying RAPD genetic markers. Six Indonesian populations of GFP from Asahan, Barito, Ciasem, Ogan, GImacro and Papua were collected and analyzed for their genetic variation using five RAPD primers. The results showed the diversity within the populations, as revealed by the level of polymorphism, ranged from 29% to 76% while genetic divergence between populations as shown by genetic distance ranged from 0.04 to 0.50. In terms of genetic divergence, two genetically distinct groups of GFP, namely the Papua GFP in one group and the remaining five GFP populations in the other, were identified. The results also showed the presence of specific population markers that are useful for genetic identification of GFP populations. Implication of these finding with regard to breed development is discussed.
MICROSATELLITE GENETIC VARIATION IN CULTURED POPULATIONS OF AFRICAN CATFISH (Clarias gariepinus) IN INDONESIA Imron, Imron; Sunandar, Dadan; Tahapari, Evi
Indonesian Aquaculture Journal Vol 6, No 1 (2011): (June 2011)
Publisher : Pusat Penelitian dan Pengembangan Perikanan, Badan Penelitian dan Pengembangan Kelautan da

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (120.77 KB) | DOI: 10.15578/iaj.6.1.2011.1-10

Abstract

African catfish, Clarias gariepinus, is one of economically important farmed species in Indonesia. To support the development of aquaculture industry, high genetic quality of both broodstock and seeds is required and breeding program is considered as viable option. Information on genetic variation of the populations being considered to form a base population may give insight toward the appropriate strategy to be implemented in breeding program. This study was aimed to assess genetic variation in farmed populations of catfish in Indonesia using microsatellite markers with special emphasis on their use to develop breeding program. Three populations of farmed catfish, namely Dumbo, Paiton, and Sangkuriang were collected. Fifteen individuals representing each population were screened for microsatellite variability using seven primer sets (cga01, cga02, cga03, cga05, cga06, cga09, cga10). Results found that with exception of two loci (cga01 and cg02) which had a slight increase, the other four loci showed reduction in the number of alleles ranging from 35% to 80% depending on loci. Farmed populations also showed heterozygote deficient and inbreeding level, being the highest was found in Sangkuriang and the least was observed in Dumbo population. Individuals within populations contributed most (95%) while interpopulation variation accounted for only 5% of the total genetic variation. Populations of Dumbo and Sangkuriang were genetically similar while populations of Paiton were genetically different from both Dumbo and Sangkuriang. Viewed from genetic perspective, by combining all information emerging from this study, the best possible strategy to establish a base population with broad genetic base and less inbreeding would be to combine all the populations into a synthetic base population.