Isolation and characterization of 23 polymorphic microsatellite markers for diversity and stock analysis in tiger shrimp (Penaeus monodon (original) (raw)
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Molecular Ecology Resources, 2009
Twenty-three polymorphic microsatellite markers were identified and characterized for Cyclura pinguis, a critically endangered species of lizard (Sauria: Iguanidae) native to Anegada Island in the British Virgin Islands. We examined variation at these loci for 39 C. pinguis, finding up to five alleles per locus and an average expected heterozygosity of 0.55. Allele frequency estimates for these microsatellite loci will be used to characterize genetic diversity of captive and wild C. pinguis populations and to estimate relatedness among adult iguanas at the San Diego Zoo that form the nucleus of a captive breeding programme for this critically endangered species.
Aquaculture, 2007
Despite large numbers of putative microsatellites currently listed in databases for Penaeus monodon, there are no publications on assessing these markers for multiplexed high throughput systems either for fingerprinting or population genetics study purposes in P. monodon. Accordingly, we started our investigation on the development of high throughput systems for P. monodon. Ninety publicly-available P. monodon microsatellite sequences were initially screened for suitability. They were assessed for the presence of tri-or tetra-nucleotide repeats, repeat number and type, suitability of flanking sequences for primer design and estimated size of product (100 to 350 bp). Nineteen sequences were chosen for preliminary assessment on a panel of 15 animals. Of the 19 tested, only 12 were suitable for further investigation. Therefore a 2-step enrichment library approach was adopted to develop additional microsatellites. Of 42 new unique microsatellite sequences obtained, eight sequences were assessed and seven showed polymorphism. Together, these 19 markers were examined further for their ease of amplification and reliability of allele calling for inclusion in high throughput systems. Thirteen polymorphic markers were incorporated into two multiplex systems (six and seven markers, respectively). These multiplexed systems were then used to evaluate the genetic diversity between two populations of P. monodon, one from the East Coast of Australia and a single pond containing farmed animals from Thailand. There were significant differences between the two populations. Three markers in system 1 showed Hardy-Weinberg disequilibrium in both populations, indicating their unsuitability as high throughput system markers. Using two systems and the UPGMA clustering methods revealed the existence of sub-populations within the Australian wild population. The results indicate the usefulness of the two multiplexed microsatellite systems in genetic diversity studies. Crown
New highly polymorphic microsatellite loci for the Galápagos marine iguana, Amblyrhynchus cristatus
Amphibia-Reptilia, 2012
We describe the development and characterisation of six new dinucleotide motif microsatellite loci for populations of marine iguanas (Amblyrhynchus cristatus), endemic to the Galápagos archipelago. Primers were based on microsatellitebearing sequences and initially developed using universally labelled primers. When analysed across 5 populations (representing 150 individuals), new loci displayed, on average, high levels of genetic diversity (range: 2-13 alleles, mean: 5.73) and values of heterozygosity (range: 0.0-0.906, mean: 0.605). No consistent deviations from Hardy-Weinberg equilibrium or significant linkage disequilibrium were observed, and all loci were shown to be free of common microsatellite errors. Utilising the 13 previously available microsatellite loci for this species, we describe here four multiplex combinations for the successful amplification of 19 microsatellite loci for marine iguanas. This powerful set of highly polymorphic markers will allow researchers to explore future questions regarding the ecology, evolution, and conservation of this unique species.
Aquaculture, 2008
Differences in genetic diversity between wild and domesticated Black Tiger shrimp (Penaeus monodon) were assessed in five stocks using molecular markers. These stocks represent an Australian wild population from a single location, and four populations of domesticated animals originating from the same location. Two established high-throughput genotyping systems with a total of 12 microsatellite markers were used to assess diversity of farmed stocks in comparison to wild-caught animals. Genetic diversity analyses showed a large decline in diversity from the wild-caught stocks to the domesticated stocks. Diversity shifts were noted in both allele numbers per locus corrected for sample size (allelic richness) and heterozygosity, declining from 14.2 to 4.6, and 0.77 to 0.61, respectively. The effective population size (N e ) of a commercial fourth generation domesticated strain, following multiple introductions of wild stocks was estimated at 10, highlighting the bottleneck effects possible within a few generations. Significant differences were noted between all pairs of stocks using F ST analysis (0.042 to 0.160, P b 0.05), with the greatest difference observed between wild animals and a fourth generation domesticated stock sampled from a commercial farm. This study illustrates the rapid loss of genetic diversity and reduction in effective population size that can occur during domestication when rigid genetic management of the stocks is not possible. This study also demonstrates the value of using molecular (microsatellite) marker systems in shrimp breeding programs to monitor genetic diversity and the effective population size.
Molecular Ecology Resources, 2008
We isolated and characterized 11 microsatellite loci in the Mona Island iguana (Cyclura cornuta stejnegeri). Eleven loci exhibit moderate to high allelic diversity (two to 12 alleles, mean = 4.5) and polymorphism (mean observed heterozygosity, 0.56; range, 0.26 to 0.78) in 41 adults. This marker set has low probability of identity and high parentage exclusion power and will be suitable for studies of paternity, social organization and relatedness in this species.
Molecular Ecology Notes, 2006
The Anolis roquet series of Caribbean lizards provides natural replicates with which to examine the role of historical contingency and ecological determinism in shaping evolutionary patterns. Here, we describe 10 polymorphic tetranucleotide microsatellites to facilitate studies on population differentiation and gene flow. All loci successfully amplified in several species from this series. Genotyping 96 individuals from two A. roquet populations demonstrated the markers’ suitability as population genetic markers: genetic diversity was high (9–22 alleles per locus); there were no instances of linkage disequilibrium; and, with one exception, all genotypic frequencies conformed to Hardy–Weinberg equilibrium expectations.
Aquaculture, 2001
Six microsatellites were used to study 1 the genetic diversity of wild Penaeus monodon Ž. shrimp from four geographic regions Palawan, Quezon, Capiz and Negros Occidental-W in the Ž. Philippines, and 2 its association with the status of mangroves and intensity of shrimp culture Ž. systems in these regions. Two cultured populations Negros Occidental-C and Antique were used for comparison. All six microsatellite loci were polymorphic. A total of 184 different alleles were found over all loci. The total number of alleles per locus ranged from 6 to 54, with allele size Ž. ranging from 159 base pairs bp to 400 bp. The observed heterozygosity of the six loci ranged from 0.47 to 1.00. The number of genotypes per locus ranged from 5 to 70. F values showed st
Electronic Journal of Biotechnology, 2013
Background: The objective of this study was to estimate the decline of genetic variability and the changes in effective population size in three shrimp populations. One was a wild population collected at several points in the Mexican Pacific Ocean. The other two populations were different generations (7 and 9) from a captive population selected for growth and survival. Microsatellite markers and pedigree were both used to assess genetic variability and effective population size. Results: Using 26 loci, both captive populations showed a decline in the expected heterozygosity (20%) and allelic diversity indices (48 to 91%) compared to the wild population (P < 0.05). The studied captive populations did not differ significantly from each other regarding their expected heterozygosity or allelic diversity indices (P > 0.05). Effective population size estimates based on microsatellites declined from 48.2 to 64.0% in cultured populations (P < 0.05) compared to the wild population. Conclusions: An important decline of genetic variability in the cultured selected population due to domestication, and evidence of a further smaller decline in effective population size across generations in the selected population were observed when analyzing pedigree (41%) and microsatellite data (37%). Pedigree keeping is required to prevent the decline of effective population size and maintain genetic variability in shrimp breeding programs, while microsatellites are useful to assess effective population size changes at the population level.
Molecular Ecology Notes, 2006
We describe here the cloning of 12 (7 dinucleotide, 1 trinucleotide and 4 tetranucleotide) microsatellite loci for the Galápagos marine iguana Amblyrhynchus cristatus . When tested for individuals from five different island populations on the Galápagos archipelago, high genetic diversities (9-20 alleles per locus) and heterozygosities (0.200-0.944) were observed. All loci showed no obvious deviations from Hardy-Weinberg equilibrium. The new set of microsatellite loci was able to assign individuals reliably to their island of origin, thus being able to discriminate between residents and migrants between islands.