Isolation and characterization of microsatellite markers from the camouflage grouper, Epinephelus polyphekadion (Epinephelidae)

We report the isolation and development of 12 novel microsatellite loci for the reef-associated camouflage grouper, Epinephelus polyphekadion, a near-threatened grouper which is widely distributed, little managed, and heavily fished throughout the Indo-Pacific region. The number of alleles ranged from two to 11. No evidence of linkage disequilibrium was found among loci, but two of the loci showed significant departure from Hardy–Weinberg equilibrium. These microsatellite loci will be useful for assessing population genetic structure and monitoring genetic diversity of the species.     

Isolation and characterization of polymorphic microsatellite markers for the endangered roughskin sculpin (Trachidermus fasciatus)

The roughskin sculpin (Trachidermus fasciatus) is an endangered species. It has been listed as an ??endangered aquatic wild animal under second class protection?? since late 1980s in China. In this study, 19 polymorphic microsatellite loci were isolated and characterized. The markers were tested on 60 individuals collected from Yalu River (YL) and the mouth of Yellow River (YR) in China. The number of alleles in these 19 markers ranged from 10 to 20. The observed (H _O) and expected (H _E) heterozygosity ranged from 0.8000 to 1.000 in YL and from 0.8638 to 0.9497 in YR, respectively. The polymorphism information content varied from 0.8230 to 0.9300 in the two populations. These microsatellite loci could help in genetic studies on this species and may provide essential information for its conservation.     

Isolation of microsatellite markers from tiger grouper (Mycteroperca tigris) and characterization in yellowfin grouper (Mycteroperca venenosa), coney (Cephalopholis fulva), and red hind (Epinephelus guttatus)

Thirty-six microsatellite markers were isolated from an enriched genomic library of tiger grouper (Mycteroperca tigris) and characterized in 20 individuals each for yellowfin grouper (Mycteroperca venenosa), coney (Cephalopholis fulva), and red hind (Epinephelus guttatus). The microsatellites include 23 dinucleotide repeats, twelve trinucleotide repeats, and one tetranucleotide repeat. The microsatellites characterized in this study will be useful for further evaluation of population-genetic indices in the economically important subfamily Epinephelinae.     

Characterization of thirteen new polymorphic microsatellite markers from the honeycomb grouper Epinephelus merra

Epinephelus merra (Serranidae) is the most common and widespread species of this genus, mostly found in reef habitats from South Africa to Central Pacific. Thirteen polymorphic microsatellite loci were isolated and characterized from this species. Polymorphism was studied in two localities from the Comoros archipelago—Mohéli and Moroni. Allelic diversity was 7.5, polymorphism ranging from 3 to 13 alleles. Overall heterozygosity was high with an average observed heterozygosity of 0.587. Three of these loci were characterised by heterozygote deficiencies for both populations. Finally, ten of the 13 developed primers could be used in future population genetics study of E.merra that might be useful in a context of marine biodiversity conservation.     

Isolation and characterization of 16 polymorphic microsatellite markers for the mudskipper (Boleophthalmus pectinirostris)

The mudskipper, Boleophthalmus pectinirostris (Perciformes, Gobiidae), is an amphibious gobioid fish and a good species for marine culture in China. In this paper, 16 polymorphic microsatellite loci were isolated and characterized. The markers were tested on 60 individuals collected from Beihai (BH) and Lianyungang (LYG) coast in China. The number of alleles (N _A ) in these markers ranged from 5 to 11. The polymorphism information content varied from 0.5946 to 0.8567 in the two populations. The observed (H _O ) and expected (H _E ) heterozygosity ranged from 0.5333 to 0.9000 in BH and from 0.5333 to 0.8729 in LYG, respectively. No significant linkage disequilibrium was detected at any pair of loci (P?>?0.01). These microsatellite loci will be useful for population genetic studies of B. pectinirostris.     

Isolation and characterization of polymorphic microsatellite markers for the invasive Senecio inaequidens DC. (Asteraceae)

Senecio inaequidens is an invasive plant native from South Africa where it is part of a polyploid complex. We developed nine polymorphic microsatellite markers for tetraploid and diploid plants of the complex. The loci described have between 3 and 28 alleles. They were amplified in both diploid and tetraploid populations with the exception of two loci that were not amplified in one of the diploid population. These markers can be used to clarify relationships within the complex, phylogeography of the invasive plants and diversity in the invaded area.     

Isolation and characterization of polymorphic microsatellite markers for the ariake icefish (Salanx ariakensis kishinouye)

Twenty microsatellite markers were isolated and characterized in the ariake icefish (Salanx ariakensis kishinouye). Analysis of 28 individuals from a single population revealed an average of 17.75 alleles per locus, which ranged from 8 to 26. The mean observed and expected heterozygosity (H _O and H _E) were 0.8410 and 0.9262, respectively. The average polymorphism information content was 0.8973, ranging from 0.7824 to 0.9521. These newly isolated markers will be useful in analyzing genetic diversity and genetic relations between the ariake icefish and its relatives.     

Characterization of 22 polymorphic microsatellite markers for seven-band grouper Epinephelus septemfasciatus developed using a 454 pyrosequencing approach

Seven-band grouper, Epinephelus septemfasciatus, is of considerable economic value and a candidate species of aquaculture in Eastern Asia. It is necessary to monitor the stocks for the sustainable use and aquaculture of the species. Monitoring genetic variation among marine resources necessitates the development of genetic markers. Here, we report 22 polymorphic microsatellite markers with 2–16 alleles per locus. The mean observed and expected heterozygosity per locus was 0.53 and 0.57, respectively. Cross-amplification revealed variability in Epinephelus bruneus and Epinephelus akaara. The 22 markers developed can be a valuable tool for genetic conservation of this species.     

Isolation and characterization of microsatellite markers for the endangered crab species Sesarmops intermedius

Sesarmops intermedius, which is designated as an endangered species in Korea, has been severely threatened by habitat destruction and pollution. From this species, we isolated 9 polymorphic microsatellites, which are independent of each other and represent allele frequencies under the Hardy?CWeinberg equilibrium, except for 1 locus. The number of alleles per locus ranged from 7 to 20. The expected and observed heterozygosities ranged from 0.77 to 0.96 and from 0.63 to 0.95, respectively. We also examined cross-species amplification of the 9 developed microsatellite loci in 2 other crabs designated as endangered species in Korea and 6 sesarmid crabs, which live in habitats similar to that of S. intermedius. These markers have the potential to contribute to establishing conservation plans for this endangered crab species.     

Isolation and characterization of twenty microsatellite markers for the endangered fish Alburnus chalcoides

Twenty polymorphic microsatellite loci were isolated from an enriched genomic library of Alburnus chalcoides. The polymorphism of these loci was tested on a population of 15 individuals from the Aral Sea, Uzbekistan. The number of alleles per locus ranged from 2 to 3. The observed and expected heterozygosity ranged from 0.2077–0.6720 to 0.1662–0.6837, respectively. One locus (CCA147) deviated from the Hardy–Weinberg expectations (P < 0.05) after Bonferroni correction. The polymorphic information content (PIC) for allelic diversity ranged from 0.12 to 0.8067 with 9 of these 20 loci revealing moderately high information content (PIC > 0.50). These loci will provide insights into species genetic diversity, population structure, and conservation strategy design.     

Isolation and characterization of polymorphic microsatellite markers in Schisandra chinensis (Turcz.) Baill. (Schisandraceae)

Fourteen polymorphic microsatellite markers were developed and characterized in Schisandra chinensis, a widely used traditional Chinese herbal medicine. The average number of alleles of these microsatellites was 6.071, ranging from 2 to 12 per locus. The effective number of alleles was from 1.645 to 7.119 per locus with an average of 3.916. The observed and expected heterozygosity were 0.107–0.871 and 0.399–0.874, respectively. Three loci significantly (P < 0.01) deviated from Hardy–Weinberg equilibrium. No significant (P < 0.01) linkage disequilibrium was detected for any pair of loci. Eleven out of 14 SSRs are also polymorphic in S. sphenanthera, a closely related medicinal species of S. chinensis. This set of microsatellite markers has provided a useful tool for the ongoing efforts in studying the population genetic variation of S. chinensis and S. sphenanthera, which will facilitate formulation of appropriate strategies for conservation and sustainable utilization of the two important officinal species.     

Isolation and characterization of polymorphic microsatellite markers from the spotted eagle ray (Aetobatus narinari)

Ten polymorphic microsatellites were isolated from the spotted eagle ray using an enrichment protocol. Primers were designed and tested on 30 individual samples collected in eastern Gulf of Mexico waters off Sarasota, FL. The number of alleles for these loci ranged from 2 to 19 and observed heterozygosities ranged from 0.345 to 0.966. All loci conformed to Hardy–Weinberg and linkage equilibrium. These markers are the first published microsatellites from A. narinari and will be valuable to studies investigating the population structure and conservation genetics of this near threatened species.     

Isolation and characterization of polymorphic microsatellite markers from Japanese grenadier anchovy (Coilia nasus)

We isolated and characterized 12 novel polymorphic microsatellite loci for the Japanese grenadier anchovy (Coilia nasus) using the method of PCR-based isolation of microsatellite arrays. Sixteen individuals of C. nasus from Ariake Bay in Japan were genotyped using 24 PCR primers to characterize the polymorphism at each locus. The average number of the observed alleles per locus was 11.08 (ranging from 8 to 20). The observed heterozygosity values ranged from 0.562 to 1.0, and the expected heterozygosity values ranged from 0.647 to 0.969. Only one of the twelve loci deviated significantly from Hardy?CWeinberg equilibrium, and linkage disequilibrium was not found in any pairs of the loci. These markers can be used to investigate the genetic structure of the C. nasus population.     

Isolation and characterization of microsatellite markers from yellowfin grouper, Mycteroperca venenosa

Twenty-seven nuclear-encoded microsatellites were isolated from an enriched genomic library of yellowfin grouper, Mycteroperca venenosa, and characterized in 24 individuals. The microsatellites include 17 dinucleotide repeats, eight trinucleotide repeats (one imperfect), one tetranucleotide repeat, and one pentanucleotide repeat. Yellowfin grouper are susceptible to fishing pressure targeted towards their spawning aggregations; data pertaining to stock structure and levels of genetic variability will aid in future management of this species.     

Isolation and characterization of polymorphic microsatellite loci in the endangered San Diego fairy shrimp (Branchinecta sandiegonensis)

A set of ten polymorphic microsatellite loci were isolated and characterized for the endangered San Diego fairy shrimp (Branchinecta sandiegonensis). These loci were amplified on a set of 24 fairy shrimp collected from vernal pools located throughout San Diego County. The loci selected are highly variable across a wide sampling range (3–29 alleles per locus, 3–20 heterozygotes observed). After directly testing for Mendelian inheritance through family screens, eight markers did not show evidence of null alleles. This novel set of microsatellite markers will be useful in future genetic studies to assess intraspecific diversity, population connectivity and mating patterns.     

Isolation and characterization of 16 polymorphic microsatellite loci in the leopard coral grouper Plectropomus leopardus

Plectropomus leopardus is an important commercial fish in South-East Asia. To date, there is little genetic information available about its population structure. In this study, 16 polymorphic microsatellite loci were developed for this species and characterized in 182 wild individuals. The observed and expected heterozygosity ranged from 0.236 to 0.912 and from 0.649 to 0.866, respectively. No linkage disequilibrium was detected between loci, and four loci were found to significantly depart from Hardy–Weinberg equilibrium. These polymorphic microsatellite markers are valuable for relative studies of population genetics.     

Isolation and characterization of 40 polymorphic microsatellite markers from Parambassis siamensis

We isolated and characterized a total of 40 polymorphic microsatellite loci from the genome of Parambassis siamensis. Flanking Polymerase Chain Reaction primers were developed and used to show that all loci were polymorphic with the number of observed alleles per locus in 32 individuals ranging from 2 to 29. The observed heterozygosity ranged from 0.063 to 0.969, while the expected heterozygosity varied from 0.062 to 0.960. All loci conformed to Hardy?CWeinberg equilibrium, none of the loci combinations showed significant linkage disequilibrium, and no loci showed evidence of null alleles. These 40 microsatellite loci should be useful for conducting future investigations into the genetic differentiation and structure of populations of P. siamensis.     

Isolation and characterization of 23 novel polymorphic microsatellite markers from the endangered Puerto Rican boa (Chilabothrus inornatus) using paired-end Illumina shotgun sequencing

We developed 23 microsatellite loci for the endangered Puerto Rican boa, Chilabothrus inornatus, from 100 bp reads obtained from a paired-end Illumina shotgun library. Importantly, these loci can be amplified using the same touchdown PCR program. All loci were highly polymorphic, with between 5 and 15 alleles found among 24 individuals genotyped from three populations. We anticipate that these loci will be extremely useful in conservation genetic studies of this species.     

Isolation and characterization of thirteen polymorphic tetranucleotide microsatellite markers in the Tokay gecko (Gekko Gecko)

Thirteen tetranucleotide microsatellite loci were isolated from tetranucleotide microsatellite enriched libraries for the Tokay gecko (gekko gecko). The species is endemic to Southeast Asia, known to be a habitat specialist, and exposed to severe hunting pressures in the mountainous areas of Southeast Asia. These highly polymorphic markers (6–25 alleles) will facilitate the population genetic analyses of this species. In particular, they will enable estimates of gene flow between the two types of the Tokay gecko: the black-spotted Tokay gecko and the red-spotted Tokay gecko-a critical element in assessing classification between the two.     

Isolation and characterization of 25 novel polymorphic microsatellite markers from grass carp (Ctenopharyngodon idella)

The grass carp (Ctenopharyngodon idella) is an important, widely distributed freshwater fish species in China. We reported the isolation and characterization of 25 novel polymorphic microsatellite markers from genomic DNA library of grass carp (C. idella) enriched by (CA)₁₀ probe. These loci showed high levels of genetic polymorphism testing on 60 individuals collected from the Heilongjiang River (China). The average allele number was 6.52 per locus, ranging from 3 to 15. The values of observed heterozygosity and expected heterozygosity ranged from 0.350 to 0.950 and from 0.439 to 0.843, respectively. The 22 of the 25 microsatellites conformed to Hardy–Weinberg equilibrium. These polymorphic microsatellite markers can be useful in population genetic studies, conservation strategies and further genetic improvement for this species.