Genetic diversity in farmed Asian Nile and red hybrid tilapia stocks evaluated from microsatellite and mitochondrial DNA analysis
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We analyzed microsatellite and mitochondrial DNA restriction fragment length polymorphism (mtDNA-RFLP) in two domesticated (NIFI and Israel) and four genetically improved (GIFT, GMT, FAC-selected and SEAFDEC-selected) Nile tilapia (Oreochromis niloticus) as well as five red hybrid tilapia (Oreochromis mossambicus × O. niloticus) stocks (BFS, FACred, NIFIred, HL, and PF) farmed in Asia. Microsatellite variation at five loci (UNH216, UNH172, UNH123, UNH147, UNH222) was more informative in characterizing stock differences than the mtDNA-RFLP markers that were based only on 14 restriction morphs. Contemporary microsatellite data showed that GIFT Nile tilapia had the highest mean expected heterozygosity (H>e=0.813), while GMT had the lowest (He=0.666). The unselected NIFI stock and SEAFDEC-selected were genetically similar, while GMT differed significantly from the other Nile tilapia stocks. Among the red tilapias, NIFIred had the highest He (0.715), while BFS had the lowest variability (He=0.567). The Taiwanese red tilapia HL and Thai NIFIred were genetically similar. Except for NIFI, most of the Nile and red tilapia stocks exhibited remarkably significant homozygote excess relative to Hardy–Weinberg Equilibrium (HWE), suggesting some degree of inbreeding. Asian Nile tilapias were more genetically diverse (pooled He=0.791; mtDNA nucleotide divergence value dA=0.009) than the red tilapias (pooled He=0.697; mean dA=0.004). This slight divergence between the Nile and red tilapias was also seen in the analysis of molecular variance (AMOVA; FCT=0.0018) and in genetic distance and nucleotide divergence dendrograms. However, the AMOVA revealed that the greater percentage of variation (99.33%) in the total genetic diversity of the surveyed stocks is principally due to differences at the individual level and not between nor within groups. The significance of these results is that they reflect and lead to new inferences regarding the selective breeding and culture methods used in managing these farmed stocks.
CitationRomana-Eguia, M. R. R., Ikeda, M., Basiao, Z. U., & Taniguchi, N. (2004). Genetic diversity in farmed Asian Nile and red hybrid tilapia stocks evaluated from microsatellite and mitochondrial DNA analysis.
The authors would like to thank Drs. Tereso A. Abella, Remedios Bolivar and Jose Abucay of FAC-CLSU, Mr. Basilio Rodriguez Jr. and his staff at GIFT Foundation International and PhilFishGen for allowing the collection of fin-clip samples from their tilapia breeding stocks. The assistance of Ruel V. Eguia, Adelaida L. Arago, Bienvenido Banaag and Federico Reyes of SEAFDEC/AQD is likewise appreciated. M.R.R. Eguia is grateful to the Philippine Department of Science and Technology for their support and to the Japan Society for the Promotion of Science for providing research funds for this study.
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Conference paperMRR Romana-Eguia - In JH Primavera, ET Quinitio & MR Eguia (Eds.), Proceedings of the Regional Technical Consultation on Stock Enhancement for Threatened Species of International Concern, Iloilo City, Philippines, 13-15 July 2005, 2006 - Aquaculture Department, Southeast Asian Fisheries Development CenterAquaculture and fisheries management require tools for identifying individuals or groups of aquatic organisms for the purpose of monitoring performance (growth, survival and behavior) and stock structure. In aquaculture research, commercially important traits of tagged individuals are assessed to generate supportive data for selective breeding, genetic improvement and commercial-scale fish farming. Fisheries management employs identification systems for the evaluation of stock abundance, population dynamics and documentation of wild and hatchery-bred stocks. Stock structure analysis is useful in the planning and implementation of sound stock management and more importantly, in stock enhancement programs. Blankenship and Leber (1995) underscored the inclusion of tagging/marking strategies for released hatchery stocks in the guidelines for responsible marine stock enhancement. Identifying and keeping track of introduced stocks in release habitats allows an assessment of their adaptability in the wild (Allendorf et al., 1988) and the success of the reseeding and/or restocking effort. Although often used interchangeably, the terms ‘tags’ and ‘markers’ differ by definition. Tags are artificial or synthetic materials that are attached to the aquatic organism to allow individual or group identification while markers are traits or characters either applied or inherent to the organism (Thorsteinsson, 2002). Tags/markers are essential in evaluating resource distribution patterns, behavior, migration and movement of stocks, dynamics of exploited aquatic populations and evolutionary processes, all of which comprise baseline information for any stock management, enhancement and conservation program in aquaculture and fisheries (Allendorf et al 1988, Mulvey et al., 1998).
Genetic diversity and stock delineation of Philippine populations of the orange mud crab, Scylla olivacea FJM Paran & RJ Ravago-Gotanco - In ET Quinitio, FD Parado-Estepa & RM Coloso (Eds.), Philippines : In the forefront of the mud crab industry development : proceedings of the 1st National Mud Crab Congress, 16-18 November 2015, Iloilo City, Philippines, 2017 - Aquaculture Department, Southeast Asian Fisheries Development CenterThe orange mud crab, Scylla olivacea, is regarded as an important fishery resource due to high demand and high market value. However, mud crab populations are threatened by over exploitation and habitat degradation, and would benefit from resource management interventions. The study examined patterns of genetic diversity and connectivity of orange mud crab populations across the Philippines, with the aim of identifying putative management units. A total of 387 Scylla olivacea were collected from ten localities across the Philippine archipelago. Phylogenetic analysis of mitochondrial control region (mtDNA-CR) DNA sequences revealed cryptic diversity among Scylla olivacea specimens with four mitochondrial lineages recovered. Analysis of molecular variance revealed that Philippine populations do not constitute a single genetic stock (0ST=0.00262; P=0.00015). Thirteen microsatellite loci were also utilized as additional markers to infer population structure and estimate genetic variation. Overall, S. olivacea populations exhibit high haplotype diversity (mean h=0.9803) and nucleotide diversity (mean ~p3.46%), which may be indicative of a large, stable population within Philippine archipelagic waters. This study provides information on genetic diversity and population structure of S. olivacea, which will be useful towards developing management and conservation strategies for sustainable development of natural S. olivacea populations in the Philippines.
magazineArticleDetermining changes in the genetic diversity of selected hatchery stocks through DNA-level polymorphisms analysis provides aquaculturists with a means to monitor inbreeding, control loss of genetic diversity, and achieve sustainable levels of genetic gain in the development of improved stocks. Tests with selected and domesticated tilapia stocks in the Philippines revealed variability between marker system results.