Isolation of microsatellites in striped bass Morone saxatilis (Teleostei) and their preliminary use in population identification

Atlantic Coastwide Population Structure of Striped Bass Morone saxatilis Using Microsatellite DNA Analysis

Striped bass Morone saxatilis support one of the most popular and important inshore recreational and commercial fisheries along the Atlantic Coast of North America. Populations at both extremes of its distribution are largely resident while those in the center of its range (Hudson River, New York, to Roanoke River, North Carolina) are seasonally migratory, ranging from the Bay of Fundy, Canada, to the Outer Banks of North Carolina. Historically, population abundances of striped bass fluctuated widely, sometimes resulting in the imposition of severe management measures to restrict their harvest. Detailed knowledge of its rangewide population structure would aid in more effective management; however, most genetic studies addressing the structure of the migratory coastal stock have largely failed to achieve this goal. To address this need, we used multi-loci microsatellite DNA analysis. We identified six genetically distinct populations across the species' distribution, including the Miramichi, Shubenacadie, Hudson, Delaware-Chesapeake, Roanoke, and Santee-Cooper rivers. We also report significant genetic differentiation between the Nanticoke and Choptank rivers along the eastern shore of the Chesapeake Bay and collections from tributaries along the western shore of the Bay. The Annapolis and Saint John rivers, tributaries of the Bay of Fundy, historically hosted striped bass aggregations that were extirpated, or nearly so, by anthropogenic stressors in the late 20th century. No specimens with unique genotypes were found in collections from either river; instead the vast majority were admixed with genotypes of Shubenacadie River, Hudson River, Chesapeake Bay, and Roanoke River lineage. Finally, we show in simulations that these genetic markers should be informative in quantifying the contributions of the Hudson River, Chesapeake Bay-Delaware, and Roanoke River to mixed-stock harvests that occur within the range of the coastal migratory stock.

A microsatellite linkage map of striped bass (Morone saxatilis) reveals conserved synteny with the three-spined stickleback (Gasterosteus aculeatus)

The striped bass (Morone saxatilis) and its relatives (genus Morone) are of great importance to fisheries and aquaculture in North America. As part of a collaborative effort to employ molecular genetics technologies in striped bass breeding programs, we previously developed nearly 500 microsatellite markers. The objectives of this study were to construct a microsatellite linkage map of striped bass and to examine conserved synteny between striped bass and three-spined stickleback (Gasterosteus aculeatus). Of 480 microsatellite markers screened for polymorphism, 289 informative markers were identified and used to genotype two half-sib mapping families. Twenty-six linkage groups were assembled, and only two markers remain unlinked. The sex-averaged map spans 1,623.8 cM with an average marker density of 5.78 cM per marker. Among 287 striped bass microsatellite markers assigned to linkage groups, 169 (58.9%) showed homology to sequences on stickleback chromosomes or scaffolds. Comparison between the stickleback genome and the striped bass linkage map revealed conserved synteny between these two species. This is the first linkage map for any of the Morone species. This map will be useful for molecular mapping and marker-assisted selection of genes of interest in striped bass breeding programs. The conserved synteny between striped bass and stickleback will facilitate fine mapping of genome regions of interest and will serve as a new resource for comparative mapping with other Perciform fishes such as European sea bass (Dicentrarchus labrax), gilthead sea bream (Sparus aurata), and tilapia (Oreochromis ssp.).

Sibship reconstruction demonstrates the extremely low effective population size of striped bass Morone saxatilis in the Santee-Cooper system, South Carolina, USA

For organisms with great fecundity and high mortality in early life stages, such as shellfish or fishes, the need to match reproductive activity with environmental conditions conducive to spawning, fertilization, larval development and recruitment may result in extreme variance in reproductive success among individuals. The main objective of this study was to investigate evidence of large variance in the reproductive success of the striped bass Morone saxatilis in the Santee-Cooper system, South Carolina, USA. Seven microsatellite loci were analysed in 603 recruits representing three yearly cohorts from 1992 to 1994, and a group analysis was performed to identify full-sib families. Large variance in reproductive success was detected, with a few large, full-sib families contributing disproportionately to each of the cohorts. The severity of sweepstakes reproductive success varied among cohorts depending on environmentally imposed mortality. Estimations of the effective number of breeders in these long-lived fish ranged from 24 in 1992 to 44 in 1994. Furthermore, the estimated genetic effective population size (N(e) = 93) is approximately four orders of magnitude lower than estimates of adult census size (N = 362 000). Furthermore, the presence of large full-sib families indicates that striped bass engage in pair mating in the wild. Heterogeneity in genetic composition was also observed among cohorts, suggesting that genetically different adults contribute to different cohorts and that chance rather than fitness variation determines reproductive success.

Evaluation of DNA pooling for the estimation of microsatellite allele frequencies: a case study using striped bass (Morone saxatilis)

Using striped bass (Morone saxatilis) and six multiplexed microsatellite markers, we evaluated procedures for estimating allele frequencies by pooling DNA from multiple individuals, a method suggested as cost-effective relative to individual genotyping. Using moment-based estimators, we estimated allele frequencies in experimental DNA pools and found that the three primary laboratory steps, DNA quantitation and pooling, PCR amplification, and electrophoresis, accounted for 23, 48, and 29%, respectively, of the technical variance of estimates in pools containing DNA from 2-24 individuals. Exact allele-frequency estimates could be made for pools of sizes 2-8, depending on the locus, by using an integer-valued estimator. Larger pools of size 12 and 24 tended to yield biased estimates; however, replicates of these estimates detected allele frequency differences among pools with different allelic compositions. We also derive an unbiased estimator of Hardy-Weinberg disequilibrium coefficients that uses multiple DNA pools and analyze the cost-efficiency of DNA pooling. DNA pooling yields the most potential cost savings when a large number of loci are employed using a large number of individuals, a situation becoming increasingly common as microsatellite loci are developed in increasing numbers of taxa.

Reconciling nuclear microsatellite and mitochondrial marker estimates of population structure: breeding population structure of Chesapeake Bay striped bass (Morone saxatilis)

Comparative analyses of nuclear and organelle genetic markers may help delineate evolutionarily significant units or management units, although population differentiation estimates from multiple genomes can also conflict. Striped bass (Morone saxatilis) are long-lived, highly migratory anadromous fish recently recovered from a severe decline in population size. Previous studies with protein, nuclear DNA and mitochondrial DNA (mtDNA) markers produced discordant results, and it remains uncertain if the multiple tributaries within Chesapeake Bay constitute distinct management units. Here, 196 young-of-the-year (YOY) striped bass were sampled from Maryland's Choptank, Potomac and Nanticoke Rivers and the north end of Chesapeake Bay in 1999 and from Virginia's Mataponi and Rappahannock Rivers in 2001. A total of 10 microsatellite loci exhibited between two and 27 alleles per locus with observed heterozygosities between 0.255 and 0.893. The 10-locus estimate of R(ST) among the six tributaries was -0.0065 (95% confidence interval -0.0198 to 0.0018). All R(ST) and all but one theta estimates for pairs of populations were not significantly different from zero. Reanalysis of Chesapeake Bay striped bass mtDNA data from two previous studies estimated population differentiation between theta=-0.002 and 0.160, values generally similar to mtDNA population differentiation predicted from microsatellite R(ST) after adjusting for reduced effective population size and uniparental inheritance in organelle genomes. Based on mtDNA differentiation, breeding sex ratios or gene flow may have been slightly male biased in some years. The results reconcile conflicting past studies based on different types of genetic markers, supporting a single Chesapeake Bay management unit encompassing a panmictic striped bass breeding population.

The impact of microsatellite electromorph size homoplasy on multilocus population structure estimates in a tropical tree (Corythophora alta) and an anadromous fish (Morone saxatilis)

Microsatellite allelic states are determined by electrophoretic sizing of polymerase chain reaction fragments to define electromorphs. Numerous studies have documented that identical microsatellite electromorphs are potentially heterogeneous at the DNA sequence level, a phenomenon called electromorph size homoplasy. Few studies have examined the impact of electromorph size homoplasy on estimates of population genetic parameters. We investigated the frequency of microsatellite electromorph size homoplasy for 12 loci in the tropical tree Corythophora alta and 11 loci in the anadromous fish Morone saxatilis by sequencing 14-23 homozygotes per locus sampled from multiple populations for a total of 453 sequences. Sequencing revealed no homoplasy for M. saxatilis loci. Seven C. alta loci exhibited homoplasy, including single and compound repeat motifs both with and without interruptions. Between 12.5 and 42.9% of electromorphs sampled per locus showed size homoplasy. Two methods of correction for homoplasy in C. alta generally produced little or no change in single-locus estimates of RST, except for two loci in which some additional differentiation among populations was revealed. Twelve-locus estimates of RST (including the seven loci corrected for homoplasy) were slightly greater than estimates from uncorrected data, although the 95% confidence intervals overlapped. The frequency of methodological errors such as clerical mistakes or sample mislabelling per genotype scored was estimated at 5.4 and 7.3% for C. alta and M. saxatilis, respectively. Simulations showed that the increase in RST produced by homoplasy correction was only slightly larger than variation in RST estimates expected to be caused by methodological errors.

Characterization of rainbow trout cell lines using microsatellite DNA profiling

Ten microsatellite loci (Omy27DU,Omy325(A3)UoG, OmyFGT5TUF,OmyFGT14TUF, OmyFGT15TUF,OmyFGT23TUF, Omy77DU,Ssa20.19NUIG, Ots1BML, andOne18ASC) were amplified using the polymerase chain reaction to create genetic profiles for nine cell lines (RTG-2, RTH-149,RTL-W1,RTgill-W1, RTS-11, RTS-34st, RTP-2, RTP-91E and RTP-91F) from rainbow trout(Oncorhynchus mykiss) and one cell line (CHSE-214) from Chinook salmon (O. tschawytscha). A cell line (PHL) from anon-salmonid, the Pacific herring (Clupea harengus pallasi), was included as a control. The ten loci clearly revealed the uniqueness of each cell line, except for two cell lines (RTP-91E andRTP-91F) from the same fish. RTP-91E and RTP-91F were identical at all loci except Ssa20.19NUIG. The most useful locus for demonstrating uniqueness was Ots1BML. The information was used to demonstrate that an uncharacterized rainbow trout cell line (Clone 1A)was in fact CHSE-214, illustrating the usefulness of multiplexed microsatellites for the creation of genetic profiles for salmonid cell lines and for the testing of cell line cross-contamination.