Microsatellite DNA markers for kinship analysis and genetic mapping in red drum,Sciaenops ocellatus (Sciaenidae,Teleostei)

Thirty‐eight nuclear‐encoded microsatellites were isolated from the marine fish Sciaenops ocellatus (red drum). The species is of economic importance in the southeastern United States, and declines in abundance have led to augmentation of the ‘wild’ fishery with hatchery‐raised fingerlings. The microsatellites will be useful for studies designed to assess larval/juvenile recruitment of hatchery‐raised individuals at varying spatial and temporal scales and for assessment of genetic components contributing to variation in performance and survival of hatchery‐produced fingerlings in the wild. The microsatellites also will prove useful as ‘anchor’ loci in constructing a genetic map.     

Isolation and characterization of eight microsatellite loci from silver‐lipped pearl oyster Pinctada maxima

We have developed di‐ and tetra‐nucleotide microsatellite markers for the silver‐lipped pearl oyster Pinctada maxima. Screening of approximately 50 000 clones resulted in the identification of 74 microsatellites. Fluorescent PCR was optimized for eight polymorphic loci. In a sample of 1637 individuals, these eight loci possessed between 14 and 68 alleles (average 29.8), with observed and expected heterozygosity ranging from 0.479 to 0.891 and 0.872 to 0.972, respectively.     

Isolation and characterization of eight microsatellite loci for the vulnerable Hainan Eld’s deer (<Emphasis Type="Italic">Cervus eldi hainanus</Emphasis>) in China

We report on the isolation and characterization of eight microsatellite markers in the Hainan Eld’s deer (Cervus eldi hainanus) from genomic DNA-enriched libraries. Thirty-three microsatellites were screened from the libraries, and 8 of the screened microsatellites were polymorphic. The number of observed alleles for each locus in 47 individuals ranged from 2 to 9, and the expected and observed heterozygosity was 0.141–0.792 and 0.128–0.957, respectively. Three loci (CEH-2, CEH-6 and CEH-8) of eight deviated from Hardy-Weinberg expectation and no significant linkage association was found among all these loci. These microsatellite markers provide useful tool for population genetic studies of the Eld’s deer.     

Characterization of polymorphic microsatellite loci in a traditional Chinese medicinal plant,Gastrodia elata

Genetic characterization of germplasm resource is essential for the conservation and efficient utilization of a traditional Chinese medicinal plant, Gastrodia elata. Thirty‐two primer pairs flanking microsatellite repeats were designed and tested using 32 individuals from eight wild populations. A total of 13 microsatellite loci were found highly polymorphic, with three to 10 alleles per locus and gene diversity ranging from 0.400 to 0.841. These microsatellites have been directly applied to the ongoing population and conservation genetics studies.     

Characterization of 17 polymorphic microsatellite loci in the Anise swallowtail,Papilio zelicaon (Lepidoptera: Papilionidae), and their amplification in related species

Fifteen polymorphic dinucleotide and two trinucleotide microsatellite loci were identified in the Anise swallowtail, Papilio zelicaon, from DNA genomic libraries enriched for simple sequence repeats. Allele numbers varied from eight to 29, with an excess of homozygotes observed for nine loci. This homozygosity is a feature of other lepidopteran microsatellites and is probably due to null alleles. Sixteen markers were amplified successfully in other representatives of Papilio with 11 loci retaining polymorphism in at least one species. These results suggest that the microsatellites reported here may be appropriate for measuring population genetic structure in a number of Papilio species.     

Characteristics of single- and multi-copy microsatellites from Pinus radiata

 Dinucleotide microsatellites were isolated from Pinus radiata using both a standard genomic library and libraries enriched for microsatellites. Locus-specific primers were designed to amplify 43 unique microsatellites. Thirty two of these loci had interpretable PCR patterns, 11 of which were polymorphic in a screen of 19 P. radiata individuals; all 11 polymorphic loci contained at least 17 repeats in the sequenced plasmid. Six of the eleven primer pairs amplified multiple fragments per individual (3–8), suggesting that these loci were present in multiple copies in the genome. Genotyping a 48-tree P. radiata production population with seven of the most polymorphic microsatellites revealed an average of 17 bands per locus (the multi-copy microsatellites were treated as one locus). When tested on known pedigrees, both single and multi-copy microsatellites exhibited co-dominant inheritance and Mendelian segregation. Two loci had null alleles and one locus had a high frequency of non-parental alleles, suggesting a high mutation rate. Eight of these microsatellites, including five multi-copy loci, were placed on a partially constructed P. radiata genetic map. Four of the five multi-copy microsatellites had two or more sets of alleles that mapped to the same locus, and the fifth mapped to two unlinked loci. All seven tested primer pairs amplified PCR products from other species of hard pine, three amplified products from soft-pine species, and one amplified bands in other conifers. Received: 10 November 1997 / Accepted: 5 January 1998     

A multiplex set of microsatellite markers for the scarlet rosefinch (Carpodacus erythrinus)

Cardueline finches have become important models in studies of sexual selection and evolution of carotenoid‐based ornamentation. Here, we describe eight new polymorphic microsatellites isolated from the Scarlet rosefinch (Carpodacus erythrinus) and four from the House finch (Carpodacus mexicanus). Together with the cross‐species amplification of additional loci, originally published for two species of songbirds, we optimized a multiplex panel for C. erythrinus allowing genotyping of 22 polymorphic loci. Number of alleles and heterozygosity per locus in a sample of 34 individuals ranged from three to 38 and from 0.27 to 0.94, respectively.     

Isolation and characterization of microsatellite loci in the Amami rabbit (Pentalagus furnessi)

We report on the isolation and characterization of eight polymorphic and five monomorphic microsatellites in the Amami rabbit (Pentalagus furnessi). Microsatellite polymorphism was determined using 25 individuals. There were 2–11 alleles for each polymorphic locus with heterozygosity ranging between 0.08 and 0.76. Linkage disequilibrium was not suggested between any pairs among the eight polymorphic loci. We suggest that these primers be used in future studies to monitor population size, determine dispersal patterns, and genetic diversity within and between populations of this and related species.     

Isolation and characterization of microsatellite loci in Bemisia tabaci

Bemisia tabaci (Hemiptera: Aleyrodidae) is a haplo‐diploid species with a global distribution demonstrating strong geographical structure with eight recognizable genetic groups. Fifteen microsatellite loci (335 alleles, 6–44 alleles per locus) were derived from four of the eight groups and were then screened across 33 populations. These loci clearly differentiate the populations. The microsatellites amplified best in individuals from genetic groups rep‐resenting the Mediterranean, Middle East, Asia (three groups) and Australasia/Oceania and amplified less well with populations from sub‐Saharan Africa and the New World. This differential amplification pattern is a direct result of the relatedness to the microsatellite source material.     

Isolation and characterization of microsatellites in lane snapper (Lutjanus synagris), mutton snapper (Lutjanus analis), and yellowtail snapper (Ocyurus chrysurus)

Polymerase chain reaction primer pairs for a total of 25 nuclear‐encoded microsatellites (loci) were developed from genomic DNA libraries of lane snapper (Lutjanus synagris), mutton snapper (Lutjanus analis), and yellowtail snapper (Ocyurus chrysurus). The microsatellites include 24 perfect (21 dinucleotide and three trinucleotide) and one imperfect (combination tetranucleotide/tetranucleotide) repeat motifs. A total of 32 individuals of each species were assayed for allelic variation at all 25 microsatellites; reliable amplification products were generated for lane snapper (25 loci), mutton snapper (21 loci), and yellowtail snapper (24 loci). Significant deviations from Hardy–Weinberg expectations, following Bonferroni corrections, were found for one microsatellite in lane and yellowtail snappers, and for three microsatellites in mutton snapper. All pairwise comparisons of microsatellites (all three species) did not deviate significantly from genotypic equilibrium.     

Development of microsatellite markers in red-tide causative species Prorocentrum micans (Dinophyceae)

We isolated eight polymorphic microsatellites from the red-tide causing microalgae Prorocentrum micans. These loci provide a class of highly variable genetic markers, as the number of alleles ranged from two to six with an average of 3.9, and the estimate of gene diversity was from 0.15 to 0.55 with an average of 0.41 across the eight microsatellites. We consider that these loci have a potential to reveal the genetic structure and gene flow among P. micans populations.     

Isolation and multiplex analysis of six polymorphic microsatellites in the Antarctic notothenioid fish,Trematomus newnesi

Six polymorphic microsatellites were isolated from the dusky notothen, Trematomus newnesi (Boulenger 1902), using a microsatellite enrichment protocol and selective hybridization with di‐ tetra‐ and penta‐repeat probes. The loci were screened in 48 individuals captured in the Southern Ocean (coastal zone of Terre‐Adélie), revealing eight to 22 alleles per locus and an observed heterozygosity ranging from 0.70 to 0.92. These microsatellite markers provide a tool to study the relationship between the various morphs observed in this species and can be used for population genetic analysis and biodiversity studies.     

Isolation and characterization of microsatellite loci in Santalum insulare,Santalaceae

The forest tree Santalum insulare is endemic to the archipelagos of eastern Polynesia and is threatened by important anthropic pressures. In order to investigate the genetic diversity and structure of this species, we developed eight pairs of primers for nuclear microsatellites. One hundred and sixty‐two individuals distributed in 10 islands were analysed. These loci were all polymorphic and displayed three to 15 alleles per locus. Significant Hardy–Weinberg deviation was detected and interpreted as a result of Wahlund effect. These markers constitute an efficient tool in investigating the genetic patterns of S. insulare populations.     

Isolation and characterization of microsatellite loci in the flour mite Acarus siro

Thirteen microsatellites with dinucleotide repeats were isolated from genomic DNA in solution by hybridization capture. Eleven were evaluated against Acarus siro using a multiple‐tube approach to assess polymorphism and reliability of the results. The multiple‐tube method demonstrated the presence of null alleles due to low levels of DNA. Seven of the 11 microsatellite loci were polymorphic and six produced reliable amplification products, if results only from individuals that scored at all six loci were used in the analysis. These were evaluated in eight strains of A. siro. Two of the samples showed some genetic divergence using F_ST values.     

Characterization of 23 Tri‐ and tetranucleotide Microsatellite Loci in the Brown Tiger Prawn,Penaeus esculentus

Twenty‐three unique tri and tetra‐nucleotide microsatellites were isolated and characterized from the genome of the brown tiger prawn Penaeus esculentus. Nine of the 23 microsatellite loci were found to be polymorphic and were tested across a sample of wild caught Penaeus esculentus. Good fits to Hardy–Weinberg expectations were observed for six of the markers when tested in a population of at least 180 individuals. The total number of alleles for these six markers ranged from eight to 19, with an average total of 13. These values will make them useful for future stock identification and population genetics studies.     

Isolation and characterization of microsatellites in the columnar cactus: Polaskia chichipe and cross‐species amplification within the Tribe Pachycereeae (Cactaceae)

Microsatellite markers were developed for the columnar cactus Polaskia chichipe from central Mexico. After an enrichment procedure and three screening steps 87% of colonies contained microsatellites. A pair of primers for 10 loci (seven polymorphic) were developed, tested and used to estimate variation in samples of 18–45 individuals from the Tehuacan Valley, Mexico. Alleles per locus ranged from two to eight (mean 5.28; SD 2.5). Range of expected heterozygosity values was 0.188–0.797 (mean 0.502; SD 0.25). These loci are particularly useful for more precise evolutionary studies, such as gene flow and breeding systems, for this cactus species.     

Characterization and isolation of novel microsatellites from the Drosophila dunni subgroup

We have isolated and characterized 77 novel microsatellites from two species, Drosophila dunni and Drosophila nigrodunni, which are closely related Caribbean-island endemics from the Drosophila cardini species group. These species are very distantly related to all other Drosophila from which microsatellites have previously been characterized. We find that the average length of microsatellites isolated in these species is quite small, with an overall mean length of 9.8 repeat units for dinucleotide microsatellites in the two study species. The nucleotide composition of dinucleotides differs between the two species: D. nigrodunni has a predominance of (AC/GT)n repeats, whereas D. dunni has equal numbers of (AC/GT)n and (AG/CT)n repeats. Tri- and tetranucleotide repeats are not abundant in either species. We assayed the variability of eight microsatellites in a closely related third species, Drosophila arawakana, using wild-caught individuals from the island of Guadeloupe. We found the microsatellites to be extremely variable in this population, with observed heterozygosities ranging from 0.541 to 0.889. DNA amplification trials suggest that these eight microsatellites are widely conserved across the D. cardini group, with five of the eight producing amplification products in every species tested. However, the loci are very poorly conserved over greater phylogenetic distances. DNA amplification of the microsatellite loci was unreliable in members of the closely related Drosophila quinaria, Drosophila calloptera, Drosophila guarani and Drosophila tripunctata species groups. Furthermore, these microsatellites could not be detected in the genome of Drosophila melanogaster, despite the conservation of microsatellite flanking regions at some loci. These data indicate that Drosophila microsatellite loci are quite short lived over evolutionary timescales relative to many other taxa.     

Polymorphic tetranucleotide microsatellite loci in the Hwamei (Garrulax canorus canorus) (Timaliidae)

Eight polymorphic tetrarepeat (GATA)_n, microsatellite loci were isolated from a babbler, Hwamei (Garrulax canorus canorus). We evaluated the polymorphism of these microsatellite loci by genotyping 36–48 individuals from the Asian mainland. The number of alleles for each locus ranged from eight to 29. The heterozygosity was between 0.587 and 0.978. Except for one locus, genotype frequencies of these microsatellites did not significantly deviate from the Hardy–Weinberg expectation. These markers should be useful for monitoring potential hybridization between different Hwamei subspecies and provide new insights into the mating system and geographical differentiation of these birds.     

Genetic introgression between an introduced babbler, the Chinese hwamei Leucodioptron c. canorum, and the endemic Taiwan hwamei L. taewanus: a multiple marker systems analysis

Identification of interspecific hybrids is often a subject of primary concern in the development of conservation strategies. Here we performed a genetic analysis combining mitochondrial DNA (mtDNA), microsatellites and single nucleotide polymorphic sites (SNPs) to assay the level of hybridization and introgression between an introduced babbler, Chinese hwamei Leucodioptron canorus, and its close relative, the endemic Taiwan hwamei L. taewanus in Taiwan. Fifty‐five Chinese hwameis from the Asian mainland and 69 Taiwan hwameis, including nine morphological hybrids, were sampled and analyzed. Evidences of mitochondrial introgression were found in three hybrids and one Taiwan hwamei. Five unlinked interspecific SNPs were identified at nine anonymous nuclear loci with interspecific differentiation (total Fst=0.77) that was much higher than that at seven highly polymorphic microsatellite loci combined (total Fst=0.1). Bayesian cluster analysis based on five interspecific SNP loci and two highly differentiated microsatellite loci (Fst>0.08) suggested that twelve individuals sampled in Taiwan were likely F2 or backcross hybrids, among which eight were morphological intermediates. A total of 20.3% (14/69) individuals sampled in Taiwan were suggested to be hybrids, suggesting that fitness reduction in hybrids might be negligible. These results imply that without an effective management strategy, the entire Taiwan hwamei population could easily become an admixed with Chinese hwamei and loose its evolutionary integrity. To reduce introgressive hybridization, illegal trade of Chinese hwamei should be strictly regulated and only the expensive male Chinese hwameis should be legally imported to minimize the chance for Chinese hwameis being released into the field. In our study we also found interspecific SNP markers to outperform microsatellite loci in detecting hybridization and introgression between two closely related species, which may be ascribed to the lower level of homoplasy of SNP loci.     

Isolation and characterisation of microsatellite loci in Calystegia soldanella (Convolvulaceae), an endangered coastal plant isolated in Lake Biwa,Japan

Eight microsatellite loci of Calystegia soldanella useful for comparisons of the genetic structure of isolated populations in the ancient Lake Biwa and coastal populations in Japan were isolated and characterised. The number of alleles ranged from 2 to 5. The expected (H _E) and observed (H _O) heterozygosities were 0.097–0.583 and 0.000–0.380, respectively, from 100 individuals from Lake Biwa and coastal populations. Seven of the eight loci exhibited significantly fewer heterozygotes than expected based on the Hardy–Weinberg equilibrium (P < 0.05). These primers amplifying microsatellites in C. soldanella may provide a population genetics tool useful in the establishment of a conservation strategy.