Microsatellite DNA loci in the rock bream Oplegnathus fasciatus

Nine novel microsatellite loci were isolated from Oplegnathus fasciatus by screening an enriched genomic library using nonradioactive PCR (polymerase chain reaction) techniques. All loci were found to be polymorphic with an average of 8.1 alleles per locus (range 3–15). The mean observed and expected heterozygosities were 0.71 (range 0.40–1.00) and 0.74 (range 0.50–0.90), respectively. Two loci showed significant Hardy–Weinberg disequilibrium at the P < 0.05 level. The high variabilities revealed in this study suggest that these microsatellite loci should provide useful markers for genetic variation monitoring of O. fasciatus.     

Isolation and characterization of microsatellite DNA markers in the Pacific abalone,Haliotis discus hannai

We developed 17 new microsatellite markers in Haliotis discus hannai. All loci were found to be polymorphic with an average of 13.1 alleles per locus (range 3–28). The mean observed and expected heterozygosities were 0.77 (range 0.17–1.00) and 0.79 (range 0.42–0.96), respectively. Six loci deviated significantly from Hardy–Weinberg proportions, and thus should be used with caution. The high variabilities revealed in this study suggest that these microsatellite loci should provide useful markers for studies of trait mapping, kinship and population genetics.     

Development of thirty-five novel polymorphic microsatellite markers in Pseudosciaena polyactis (Perciformes:Sciaenidae) and cross-species amplification in closely related species,Pseudosciaena crocea

Small yellow croaker, Pseudosciaena polyactis, is an economically important marine fishery species. In this study, we isolated 35 novel polymorphic microsatellite primers in P. polyactis by using the combined biotin capture method. The polymorphism of each locus was assessed in 30 individuals from Donggang, Northern Yellow Sea, China. A total of 519 alleles were detected and the number of alleles per locus ranged from 3 to 23. The PIC values of these 35 microsatellite loci ranged from 0.367 to 0.940. The observed (H_o) and expected heterozygosity (H_e) per locus ranged from 0.233 to 1.000 and from 0.438 to 0.943, respectively. Seven loci significantly deviated from Hardy–Weinberg equilibrium (HWE) after Bonferroni correction and no significant linkage disequilibrium (LD) was found between pairs of loci. In addition, cross-species amplification was performed in Pseudosciaena crocea, a closely related species of P. polyactis, to assess the applicability of these markers. These polymorphic microsatellites will provide useful tools for the study of genetic diversity and population structure of P. polyactis and P. crocea.     

New microsatellite markers for the snow crab Chionoecetes opilio (Brachyura: Majidae)

Nine novel microsatellite loci were isolated from Chionoecetes opilio by screening an enriched genomic library using nonradioactive polymerase chain reaction techniques, and the polymorphisms were examined to estimate genetic variability. The genetic variabilities varied depending on the locus. All loci were found to be polymorphic with an average of 9.7 alleles per locus (range 3–25). The observed and expected heterozygosities ranged from 0.80 to 0.98 and from 0.56 to 0.95, respectively. Five loci showed significant Hardy–Weinberg disequilibrium at the P < 0.05 level. The high variabilities revealed in this study suggest that these microsatellite loci should provide useful markers for genetic variation monitoring of C. opilio.     

Isolation of 21 new polymorphic microsatellite loci in the phytopathogenic fungus Venturia inaequalis

Twenty‐one new polymorphic microsatellite markers were isolated in the phytopathogenic fungus Venturia inaequalis, the causal agent of apple scab. An enrichment protocol was used to isolate microsatellite loci and the level of polymorphism was assessed on 44 European isolates. All loci were polymorphic with an average of 9.1 alleles per locus (range 2–24). Tests of cross‐species amplifications suggest that at least some of these microsatellites could be used in different species, mainly Spilocaea pyracanthae and S. eriobotryae.     

Isolation and characterization of microsatellite loci in the two‐spotted spider mite,Tetranychus urticae (Acari: Tetranychidae)

Sixteen microsatellite loci are described for the two‐spotted spider mite Tetranychus urticae, which is an agricultural pest. The microsatellite loci were obtained through the construction of an enriched library; these loci exhibited polymorphisms (2–5 alleles per locus) and high levels of observed (0.033–0.667, average 0.415) and expected (0.033–0.602, average 0.336) heterozygosities. The isolated microsatellite markers are expected to be useful for the construction of a linkage map of this species.     

Microsatellite–Centromere Mapping in Large Yellow Croaker (<Emphasis Type="Italic">Pseudosciaena crocea</Emphasis>) Using Gynogenetic Diploid Families

The large yellow croaker (Pseudosciaena crocea) is an economically important marine fish in China. Inheritance of 22 heterozygous microsatellite loci was examined in normal crossed diploid families and meio-gynogenetic families in P. crocea. Two gynogenetic families were produced via inhibition of the second polar body in eggs fertilized with UV-irradiated sperm. The ratio of gynogenesis was proven to be 100% and 96.9% in the two families, respectively. Of the 22 examined loci, 4 showed a segregation distortion in both control and gynogenetic families. Microsatellite–centromere (M–C) map distances were examined using 18 loci with normal Mendelian segregation. Estimated recombination rates ranged between 0 and 1.0 under the assumption of complete interference. High recombinant frequencies between heterozygous markers and the centromere were found in large yellow croaker, as in other teleosts. The average recombination frequency was 0.586. Ten loci showed high M–C recombination with frequency greater than 0.67. M–C distances provide useful information for gene mapping in large yellow croaker.     

Development of 25 gene‐associated microsatellite markers of Atlantic cod (Gadus morhua L.)

Microsatellites were identified by screening 2294 GenBank entries available for Atlantic cod (Gadus morhua L.), mainly representing expressed sequence tags and cDNA sequences. Ninety‐two novel microsatellite loci (tetra‐, tri‐ and dinucleotides) were characterized on 96 individuals. This strategy yielded 25 gene‐associated polymorphic microsatellite markers (11 tri‐ and 14 dinucleotides) with two to 20 alleles and an average heterozygosity of 0.48 in the population studied (range 0.02–0.89). One marker exhibited significant homozygote excess, and one of the primer pairs amplified two linked markers. The gene identity was determined at nine of the loci, confirming the associated microsatellites as type I markers.     

Characterization of nine microsatellite loci on endemic kangaroo rats Dipodomys simulans peninsularis from southern Baja California Peninsula

Nine polymorphic microsatellite loci were isolated to investigate the effects of habitat fragmentation on gene flow and genetic variation of the peninsular kangaroo rat Dipodomys simulans peninsularis on agricultural landscape from the Baja California Peninsula. The markers had an average of 9.11 alleles per locus (range 2–14), with mean observed and expected heterozygosities 0.646 (range 0.333–0.900) and 0.788 (range 0.284–0.932), respectively. No evidence of linkage disequilibrium was found across pairs of loci, and only one locus exhibited evidence of null alleles.     

Polymerase chain reaction primers for polymorphic microsatellite loci from the Korean sandfish,Arctoscopus japonicus

We developed 12 polymorphic microsatellite markers from Arctoscopus japonicus by screening an enriched genomic library using polymerase chain reaction (PCR) techniques. The average of alleles size was 16.2, and the average observed and expected heterozygosities were 0.59 and 0.78, respectively. The observed genotypic frequencies in five loci were significantly deviated from Hardy–Weinberg expectations. The high variability revealed in this study suggested that these microsatellite loci should provide useful markers for population genetics of A. japonicus.     

Development of STMS markers from the medicinal plant Madagascar periwinkle [Catharanthus roseus (L.) G. Don.]

We report the isolation and characterization of the first set of sequence‐tagged microsatellites sites (STMS) markers in Catharanthus roseus, a plant with a vast range of medicinal uses. The microsatellite loci were cloned from an enriched library constructed using degenerate primers. Based on the microsatellite motifs, seven STMS primer pairs were designed. They were used to amplify 32 accessions of C. roseus and one accession of Catharanthus trichophyllus. The primers amplified an average of 3.86 alleles per locus. The observed heterozygosity ranged from 0.2903 to 0.9688 with an average of 0.7511. The STMS markers of C. roseus also amplified corresponding loci in a related species (C. trichophyllus) suggesting conservation of the loci across the genus. These markers will prove useful for genetic diversity analysis and linkage map construction in C. roseus.     

A panel of polymorphic microsatellite markers in Himalayan monal Lophophorus impejanus developed by cross-species amplification and their applicability in other Galliformes

Isolation and development of new microsatellite markers for any species is still labour-intensive and requires substantial inputs of time, money and expertise. Therefore, cross-species microsatellite amplification can be an effective way in obtaining microsatellite loci for closely related taxa in bird species. We have reported microsatellite loci for Himalayan monal for the first time. Fifteen microsatellite markers developed for chicken were cross-amplified in Himalayan monal. All the tested 15 microsatellite markers were polymorphic, with mean (± s.e.) allelic number of 4 ± 1.51, ranging 2–7 per locus. The observed heterozygosity in the population ranged between 0.285 and 0.714, with mean (± s.e.) of 0.499 ± 0.125, indicating considerable genetic variation in this population. While 12 loci conformed to Hardy–Weinberg equilibrium (P > 0.05), 3 loci, i.e. MCW0295, MCW0081, MCW0330 deviated from it (P < 0.05). No evidence for linkage disequilibrium was observed among pair of loci. Our study show that these 15 microsatellites loci could be employed in population genetic studies for Himalayan monal and their applicability in Jungle Bush Quail, Grey francolin and Kalij pheasant.

     

Eleven new microsatellite markers in jack mackerel (Trachurus japonicus) derived from an enriched genomic library

Jack mackerel (Trachurus japonicus, Carangidae) are a commercially important fisheries resource in Korea. To understand patterns of genetic variation for conservation and management efforts, we developed microsatellite DNA markers fromT. japonicus. We report the isolation and characterization of eleven microsatellite loci isolated using an enrichment method based on magnetic/biotin capture of microsatellite sequences from a size-selected genomic library. To characterize each locus, 50 individuals from a naturalT. japonicus population in southern Korea were genotyped. All loci except one, KTJ38, were polymorphic with an average of 14 alleles per locus (range 6–23). The mean observed and expected heterozygosities were 0.70 (range 0.46–0.92) and 0.81 (range 0.49–1.00), respectively. Significant deviation from Hardy-Weinberg equilibrium was observed at three loci, KTj3, KTJ20 and KTJ28. Such high variability indicates that these microsatellites are useful markers for high-resolution analysis for population gemetic studies.     

Isolation and characterization of microsatellite markers for Viola mirabilis (Violaceae) using a next‐generation sequencing platform

We isolated and characterized microsatellite loci in Viola mirabilis (Violaceae), an endangered species from South Korea. Twenty‐three polymorphic microsatellite loci were developed and tested in Korean, Chinese and Japanese populations. The number of alleles per locus varied from two to eight. The observed and expected heterozygosities within the three populations were 0.000–0.625 and 0.469–0.695, respectively. A total of six loci in the Korean population, one locus in the Chinese population and seven loci in the Japanese population deviated from Hardy–Weinberg equilibrium. We expect that these newly developed microsatellite markers will contribute to understanding the phylogeography and population genetics of V. mirabilis, which will aid in developing conservation strategies for this species.     

Eight microsatellite loci in Clark's anemonefish,Amphiprion clarkii

To determine the genetic relationship between different colour morphs (orange and black morphs) of Clark's anemonefish (Amphiprion clarkii) in Taiwan, we isolated eight polymorphic microsatellite loci. A large number of alleles (range, 6–30), and high levels of observed heterozygosity (range, 0.1231–0.8358) were resolved in 71 individuals from two populations, indicating that these markers should be useful in assessing the relationship between the two colour morphs of A. clarkii.     

Isolation and characterization of 12 microsatellite loci for cross-species amplification in the cyprinid gudgeons Squalidus chankaensis and S. japonicus

Twelve dinucleotide markers were successfully isolated and characterized from a microsatellite‐enriched genomic library obtained for the gudgeon Squalidus chankaensis biwae. These markers were also available for the congeners S. c. tsuchigae and S. japonicus from Japan, which had five to 46 alleles and an expected heterozygosity ranging from zero to 0.946. Linkage equilibrium was observed at all loci, and most loci did not show significant deviation from Hardy–Weinberg equilibrium. The isolated microsatellite markers will be useful for genetic diversity studies of Squalidus populations.     

Characterization of microsatellite markers in Fagus sylvatica L. and Fagus orientalis Lipsky

Using an enrichment procedure, we cloned microsatellite repeats from European beech (Fagus sylvatica L.) and developed primers for the amplification of microsatellite markers. Six polymorphic loci were characterized which produced 3–21 alleles in 70 individuals from one Italian population, with an observed heterozygosity between 0.58 and 0.85. All six loci amplified fragments which were polymorphic in the closely related species, Fagus orientalis, also. Owing to their very high degree of variation, these markers should be very useful in gene flow studies of these species.     

Isolation of microsatellite markers in Cannabis sativa L. (marijuana)

We have identified 15 variable microsatellite loci in Cannabis sativa. In 48 samples from five fibre crop seed accessions, we detected an average of 10 alleles per locus (range 2–28) with mean heterozygosity of 0.68 (range 0.28–0.94). Significant genetic differentiation was found between accessions (F_ST = 0.12, P < 0.001). These markers have utility for characterizing genetic diversity in cultivated and naturalized Cannabis populations.     

Isolation and characterization of microsatellite DNA loci from the golden cuttlefish,Sepia esculenta Hoyle (Cephalopoda)

The first microsatellite markers were isolated from the golden cuttlefish, Sepia esculenta Hoyle. Eleven primer sets were designed to amplify the marker sequences via polymerase chain reaction. The 45–50 individuals from one wild population in the coastal waters of Ehime Prefecture, Japan were used to screen polymorphism in the 11 microsatellite loci. All the microsatellite loci were polymorphic, with the range of alleles from seven to 27 per locus. The observed and expected heterozygosities ranged from 0.380 to 0.980 and from 0.654 to 0.940, respectively. These marker loci except for one locus showing significant deviation from Hardy–Weinberg equilibrium will be useful for the assessment of genetic variation and population structure of this species.