Characterization of 18 new microsatellite loci in Atlantic cod (Gadus morhua L.)

Eighteen new microsatellite loci consisting of 10 di‐, 5 tri‐, 2 tetra‐ and 1 heptanucleotide repeats are introduced for the Atlantic cod (Gadus morhua L.). All loci were co‐amplified in two polymerase chain reactions (plus two previously published microsatellites) and all products were typed clearly. The number of alleles per locus ranged from six (PGmo130) to 45 (PGmo76) and the observed heterozygosity ranged from 0.356 (PGmo130) to 0.957 (PGmo95). All loci except one followed Hardy–Weinberg expectations. Genetic linkage disequilibrium analysis between all pairs of loci did not yield any significant values.     

Identification and characterisation of nine new gene-associated microsatellite markers for Atlantic cod (<Emphasis Type="Italic">Gadus morhua</Emphasis> L.)

Nine polymorphic microsatellite markers were identified by screening of 2464 ESTs derived from a cDNA library of Atlantic cod (Gadus morhua L.). About 35 novel microsatellite loci were selected and characterised in 96 individual cod. Nine markers were successfully amplified with number of alleles from 3 to 18 per locus and the average heterozygosity was 0.57 in the panel examined (range 0.29–0.86). All loci followed the Hardy–Weinberg expectation and no significant linkage disequilibrium was found in a test including all pairwise combinations. The gene identity was determined at four of the loci, confirming the associated microsatellites as Type I markers.     

Development of 10 microsatellite loci in the ling (Molva molva)

We developed primers for two dinucleotide and eight tetranucleotide microsatellite loci in a marine fish, the ling (Molva molva). All markers were obtained from partial genomic DNA libraries and characterized in 55 unrelated individuals from one putative population. The number of alleles ranged from five to 24 (average 10.5) per locus, and the observed heterozygosity ranged from 0.218 to 0.981 (average 0.643). No loci amplified in two other gadoid species tested, the Atlantic cod (Gadus morhua) and the tusk (Brosme brosme).     

Eight new microsatellite markers in Atlantic cod (Gadus morhua L.) derived from an enriched genomic library

One hundred and fifty random clones from an enriched genomic library of Atlantic cod were sequenced. Primer pairs were designed for 15 microsatellites containing perfect di‐, tri‐, tetra‐ and hexanucleotide repeats and characterized in 96 unrelated fish. Eight markers were successfully amplified, with the number of alleles ranging from two to nine per locus and observed heterozygosity ranging from 0.341 to 0.977. Loci Gmo‐G13 and Gmo‐G14 had a significant excess of homozygotes. All loci conformed to the Hardy–Weinberg equilibrium. Genetic linkage disequilibrium analysis between all pairs of the loci showed no significant departure from the null hypothesis between any of the loci.     

Development of microsatellite loci for population studies of the pink ling,Genypterus blacodes (Teleostei: Ophidiidae)

Fifteen microsatellite loci were developed for pink ling (Genypterus blacodes), a fish of significant commercial importance to Australasia. Nine loci were examined in samples from five regions of Australia’s South East Fishery. All nine were highly polymorphic; numbers of alleles per locus ranged from 11 to 52 in total samples of 270–306 individuals. The average observed heterozygosity per locus per sample (0.823) was a little lower than the average Hardy–Weinberg expected heterozygosity per sample (0.895), perhaps reflecting the possible presence of null alleles at two loci. There was no significant evidence of genetic stock heterogeneity.     

Development and characterization of polymorphic microsatellite DNA loci for the endangered dusky gopher frog,Rana sevosa,and two closely related species,Rana capito and Rana areolata

A microsatellite library was developed using genomic DNA of the endangered dusky gopher frog, Rana sevosa. Polymerase chain reaction (PCR) primers and conditions are presented for R. sevosa (eight loci) and two sister taxa — other gopher frogs, Rana capito (seven loci) and crawfish frogs, Rana areolata (three loci). Polymorphism of each microsatellite locus was evaluated for each species. All loci have moderate to high genetic variation in terms of allelic richness (four to 10 alleles per locus), observed heterozygosity (0.595–0.946), and expected heterozygosity (0.531–0.856).     

Characterization of microsatellite DNA markers for a mahseer species,Tor tambroides (Cyprinidae) and cross‐amplification in four congeners

This study reports the isolation and characterization of microsatellite DNA markers in a mahseer species, Tor tambroides (Pisces, Cyprinidae). Of a total of 14 loci evaluated, 10 were polymorphic in T. tambroides samples, with an average of 2.86 alleles per locus. Deviations from Hardy–Weinberg equilibrium were observed at one locus and there was no indication of linkage disequilibrium among loci. A high level of cross‐amplification among four congeners was achieved, with 12 loci successfully amplifying and 11 loci showing polymorphism in at least one other species. These markers will be a useful resource for population genetic studies and broodstock management of closely related mahseer species.     

Polymorphic tetranucleotide microsatellite markers in the Caribbean spiny lobster,Panulirus argus

Ten tetranucleotide microsatellite loci are described for the Caribbean spiny lobster Panulirus argus. Loci were polymorphic (4–15 alleles per locus) and exhibited high levels of expected (0.553–0.921) and observed heterozygosity (0.469–0.906) from samples caught off Belize and Puerto Rico coasts. No significant departure from Hardy–Weinberg equilibrium conditions were observed for any locus. All microsatellite loci should be useful for assessing population discrimination for this valuable marine animal currently subjected to excessive fishing efforts.     

On genetic differentiation of the Pacific cod <Emphasis Type="Italic">Gadus macrocephalus</Emphasis> tilesius, 1810 (Gadiformes: Gadidae)

The variability of the Gmo3, Gmo34, Gmo35, and Pgmo32 DNA microsatellite loci in Pacific cod Gadus macrocephalus samples from different areas of the North Pacific was analyzed. The data obtained show that Pacific cod from the southern Kuril Islands significantly differs from the populations of the Bering Sea, the Sea of Okhotsk, and the coastal waters of Canada (the microsatellite loci Gmo3 and Pgmo32 bear the highest differentiating capacity). Despite the significant geographical remoteness of these areas from one another, the above three Pacific cod populations exhibit a high degree of similarity (I = 0.997–0.999).     

Polymorphic microsatellite DNA markers for Banksia hookeriana (Proteaceae)

We developed 11 polymorphic microsatellite DNA markers for an Australian native shrub Banksia hookeriana (Proteaceae). The number of alleles per locus in 37 individuals varied from three to 17, observed and expected heterozygosities ranged from 0.297 to 0.838 and from 0.279 to 0.900, respectively. Two loci (BH‐B5 and BH‐B107) showed significant deviation from Hardy–Weinberg equilibrium (P < 0.05), and null alleles may be present at these two loci. All loci showed independent inheritance.     

Development and cross-species testing of western bluebird (Sialia mexicana) microsatellite primers

Western and eastern bluebirds (Sialia mexicana and S. sialis) are socially monogamous passerines that engage in extra‐pair copulations. We obtained microsatellites from S. mexicana and optimized and characterized 15 microsatellite DNA loci in 60 individuals of this species. Primer pairs yielded an average of 13 alleles per locus in western bluebirds (range 3–35 alleles) with an average observed heterozygosity of 0.68 (range 0.27–0.88). All 15 loci also successfully amplified in S. sialis (n = 24), with an average of 11.5 alleles per locus (range 4–26) and an average observed heterozygosity of 0.59 (range 0.22–0.90).     

PERMANENT GENETIC RESOURCES: Identification and characterization of 14 polymorphic microsatellite loci in the argasid tick Ornithodoros coriaceus

Fourteen polymorphic microsatellite loci (di, tetra and di‐tetra complexes) were developed for the argasid tick Ornithodoros coriaceus. Polymorphism was assessed for 56 individuals from two populations separated by ~95 km. All loci were polymorphic (X = 7, range 3–17 alleles). All loci were in Hardy–Weinberg equilibrium except for one locus (OrC 8) in a single population (P < 0.00119, after Bonferroni correction for multiple tests).     

Stock composition in North Atlantic populations of whiting using microsatellite markers

A size-selected library constructed from DNA of the whiting Merlangius merlangus was screened. From about 3200 recombinant clones, 43 microsatellite loci were detected. Thirteen were sequenced in full. Primers were designed from the sequence of the flanking regions for six loci and used to test the allelic variability at these loci using the polymerase chain reaction (PCR). In addition, five primer pairs developed for the stickleback and another seven for cod were tested. Only six primer pairs revealed at least three alleles per locus. The three useful loci Gmo2, Mmer- UEAW01 and Mmer- UEAW02, had 14–23 alleles per locus in 370 samples. Estimates of genetic structure (φ) were not statistically significant. However, estimates of genetic differentiation ( F _st) were significantly different from zero. Heterogeneity χ²-analysis of allele frequencies among populations suggested relatively low levels of differentiation among samples. Significantly different allele frequency distributions were found for Borgensfjord and northern and southern North Sea samples for at least one locus, and between the latter samples for Mmer -UEAW02 and Gmo2 . There were significant excesses of homozygotes in all samples, over expectation for randomly mating populations in Hardy-Weinberg equilibrium. The estimated frequencies of null alleles were 14.3%, for Mmer -UEAW01, 10.2% for Mmer- UEAW02 and 11.6% for Gmo2 . This result calls for a careful interpretation of the significance of these microsatellite data.     

Polymorphic microsatellite DNA markers for Banksia attenuata (Proteaceae)

We developed 11 polymorphic microsatellite DNA markers for an Australian native shrub Banksia attenuata. The number of alleles per locus in 50 individuals varied from five to 18, observed and expected heterozygosities ranged from 0.300 to 0.740 and from 0.537 to 0.918, respectively. Six loci showed no significant deviation from Hardy–Weinberg equilibrium (P > 0.05), and null alleles appear to exist at locus BA‐B1. All loci showed independent inheritance.     

Microsatellite markers for northern red oak (Fagaceae: Quercus rubra)

We provide primer sequences for 14 (GA) _n microsatellite loci developed from northern red oak, an important timber species. We screened loci using two sets of samples. A parent–offspring set included DNA from seven acorns collected from one mother tree along with maternal DNA, to determine that all progeny carried a maternal allele at each locus. The other set was comprised of 10 adult trees sampled from Indiana old‐growth forest, providing a measure of diversity revealed by each locus.     

Isolation and characterization of microsatellite loci in the deep-sea marine fish, the roundnose grenadier (Coryphaenoides rupestris)

We developed polymerase chain reaction primers for eight dinucleotide microsatellite loci in the marine deep sea fish, roundnose grenadier (Coryphaenoides rupestris). All markers were obtained from a partial genomic DNA library, and characterized in 90 unrelated individuals from one putative population sampled on the Mid-Atlantic Ridge. The number of alleles ranged from two to 61 with an average of 21 per locus. The observed heterozygosity levels ranged from 0.301 to 0.987 with an average of 0.672. Several of the markers amplified multiple alleles from either the Atlantic cod (Gadus morhua) or the deep-sea fish roughhead grenadier (Macrourus berglax).     

Isolation and characterization of microsatellite loci in the flat‐headed bat (Tylonycteris pachypus)

Microsatellite loci were developed in the flat‐headed bat (Tylonycteris pachypus) from genomic DNA using an enriched library method. Nine loci were tested on 48 individuals sampled from Guangxi Province, China. The mean number of observed alleles per locus was 6.4 (range 4–12). Observed and expected heterozygosity values ranged from 0.24 to 0.83 and from 0.30 to 0.89, respectively. One locus revealed significant departure from Hardy–Weinberg equilibrium and no significant linkage disequilibrium was detected between loci pairs. These markers will be used to examine genetic structure and parentage analysis in this species.     

Isolation of highly polymorphic microsatellite markers from the intertidal barnacle Chthamalus montagui Southward

This study reports the isolation and characterization of seven highly polymorphic microsatellite loci in Chthamalus montagui (Crustacea, Cirripedia). The loci were isolated from a library constructed from genomic DNA enriched for CA repeats. The markers yielded three to 43 alleles per locus (mean 16.7) in samples averaging 49 individuals. Observed heterozygosity ranged from 0.08 to 0.58 (mean 0.39). These microsatellite loci will be valuable tools for population genetic studies of this species.     

Identification and characterization of nine polymorphic microsatellite loci in the North American pika,Ochotona princeps

Nine polymorphic microsatellite loci were developed for the North American pika (Ochotona princeps) from di‐ and tetranucleotide repeat‐enriched genomic libraries. Polymorphism was assessed for 165 individuals from eight geographical locations in the western United States. All loci were polymorphic. The number of alleles per locus ranged from three to 14, with observed heterozygosity between 0.189 and 0.822. All loci were in Hardy–Weinberg equilibrium (< 0.05). Regional differences were evident with unique alleles at multiple loci in six of eight populations.     

Polymorphic microsatellite loci in the European subterranean termite,Reticulitermes santonensis Feytaud

We report on the identification and characterization of two dinucleotide, two trinucleotide and eight tetranucleotide microsatellite DNA loci isolated from the European subterranean termite Reticulitermes santonensis. We tested the loci on 51–92 individuals from 46 colonies from different regions of France. Eleven loci were polymorphic with 2–8 alleles per locus and low observed heterozygosities (0.10–0.48). We also tested the loci on 17–20 individuals from 10 colonies in the closely related North American species R. flavipes and found significantly more alleles (2–9 alleles per locus) and higher observed heterozygosities (0.15–0.80) than in R. santonensis. The lower observed heterozygosities in R. santonensis are consistent with higher levels of inbreeding in these colonies due to the presence of numerous inbred replacement reproductives.