The highly polymorphic microsatellite markers for the greater long‐tailed hamster (Tscherskia triton)

We isolated 25 dinucleotide microsatellite loci from the greater long‐tailed hamster (Tscherskia triton) populations in North China. We developed the amplification conditions of polymerase chain reaction for producing high‐resolution genetic markers for each locus. We found 10 microsatellite loci were highly polymorphic in 90 individual hamsters from three areas of North China, and the number of alleles in each locus varied from three to 11. These markers are potential tools for studying the genetic variation of the natural populations of this species.     

Isolation and characterization of polymorphic microsatellite loci in the field vole,Microtus agrestis,and their cross‐utility in the common vole,Microtus arvalis

We developed nine polymorphic microsatellite loci for the field vole, Microtus agrestis. The number of alleles ranged from five to 15 and observed heterozygosities ranged from 0.40 to 1.00. We also tested the microsatellite loci for amplification and polymorphism in the congeneric species Microtus arvalis. Five of the nine loci were successfully analysed in this species. The microsatellite markers will be employed in studies of reproductive success and fine‐scale spatial genetic structure.     

Rapid,economical single‐nucleotide polymorphism and microsatellite discovery based on de novo assembly of a reduced representation genome in a non‐model organism: a case study of Atlantic cod Gadus morhua

By combining next‐generation sequencing technology (454) and reduced representation library (RRL) construction, the rapid and economical isolation of over 25 000 potential single‐nucleotide polymorphisms (SNP) and >6000 putative microsatellite loci from c. 2% of the genome of the non‐model teleost, Atlantic cod Gadus morhua from the Celtic Sea, south of Ireland, was demonstrated. A small‐scale validation of markers indicated that 80% (11 of 14) of SNP loci and 40% (6 of 15) of the microsatellite loci could be amplified and showed variability. The results clearly show that small‐scale next‐generation sequencing of RRL genomes is an economical and rapid approach for simultaneous SNP and microsatellite discovery that is applicable to any species. The low cost and relatively small investment in time allows for positive exploitation of ascertainment bias to design markers applicable to specific populations and study questions.     

Isolation and characterization of sequence‐tagged microsatellite sites markers in chickpea (Cicer arietinum L.)

In this study we report the isolation of microsatellite sequences and their conversion to sequence‐tagged microsatellite sites (STMS) markers in chickpea (Cicer arietinum L.). Thirteen putative recombinants isolated from a chickpea genomic library were sequenced, and used to design 10 STMS primer pairs. These were utilized to analyse the genetic polymorphism in 15 C. arietinum varieties and two wild varieties, C. echinospermum and C. reticulatum. All the primer pairs amplified polymorphic loci ranging from four to seven alleles per locus. The observed heterozygosity ranged from 0 to 0.6667. Most of the STMS markers also amplified corresponding loci in the wild relatives suggesting conservation of these markers in the genus. Hence, these polymorphic markers will be useful for the evaluation of genetic diversity and molecular mapping in chickpea.     

Development of microsatellite markers in Rhizophora stylosa using a dual‐suppression‐polymerase chain reaction technique

Rhizophora stylosa is an ecologically important mangrove tree species that is found in tropical and subtropical regions. We isolated five polymorphic microsatellite loci from R. stylosa using a dual‐suppression‐polymerase chain reaction technique. These loci provided microsatellite markers with polymorphism of four alleles in each locus for overall population. The mean expected heterozygosities ranged from 0.113 to 0.473.     

Polymorphic microsatellite loci in the black‐and‐gold chromis,Neoglyphidodon nigroris (Teleostei: Pomacentridae)

We describe 15 polymorphic dinucleotide microsatellite loci in the black‐and‐gold chromis, Neoglyphidodon nigroris (Cuvier: Teleostei: Pomacentridae). Microsatellites were isolated from a partial genomic library that was enriched for CA repeat motifs. The 15 loci yielded between two and 23 alleles per locus in a sample of 16 fish from two forereef sites off the island of Hoga, Wakatobi National Park, Indonesia. Observed and expected heterozygosities varied from 0.13 to 1.00 and 0.24 to 0.98, respectively. These markers should allow us to discriminate between closely related individuals and also to assess the connectedness of populations of N. nigroris that inhabit different reefs.     

Development of new polymorphic microsatellite markers for the New World screw‐worm Cochliomyia hominivorax (Diptera: Calliphoridae)

In this report, we describe the development of seven new polymorphic microsatellite markers for Cochliomyia hominivorax, a parasitic insect pest of primary agricultural and veterinary importance throughout the Neotropics. The number of alleles found ranged from 3 to 13 per locus, with the expected heterozygosity ranging from 0.4220 to 0.9045. The across‐taxa amplification of some of these new microsatellite loci was successful in four additional Calliphoridae species. In combination with the 10 polymorphic microsatellite markers previously described, the markers developed here should provide a high resolution for assessing the fine‐scale genetic structure of New World screw‐worms.     

Novel polymorphic microsatellites for the red‐legged partridge (Alectoris rufa) and cross‐species amplification in Alectoris graeca

The red‐legged partridge, Alectoris rufa, is an endemic species of the southwestern Mediterranean, and the most popular game bird in the Iberian Peninsula. A total of 27 microsatellite loci was isolated from an enriched genomic library of A. rufa. Six perfect GT microsatellites were characterized and optimized in 45 individuals of A. rufa. All loci revealed high levels of polymorphism with a number of alleles that ranged from three to 13. Observed heterozygosity ranged from 0.2 to 0.6. Cross‐species amplification showed that all loci were also polymorphic in rock partridge, Alectoris graeca. The new markers will be useful in determining hybridization between both species of Alectoris.     

Isolation and characterization of polymorphic microsatellite markers in the gray,short‐tailed opossum (Monodelphis domestica)

Twenty‐six polymorphic microsatellite markers were isolated from (AC)_n and (AG)_n microsatellite‐enhanced genomic libraries of the gray, short‐tailed opossum Monodelphis domestica. All 26 loci showed high allelic diversity, with allele numbers ranging from five to 11 in a subset of 35 animals. Normal Mendelian inheritance was confirmed for 24 loci by analysing allelic segregation in 10, two‐generation, families. Non‐amplifying (null) alleles were detected at two loci, which we recommend be used only if pedigree data are available. We conclude that all of these microsatellite markers would be useful for quantitative trait locus mapping and population genetic studies.     

Characterization of microsatellite loci in silver carp (Hypophthalmichthys molitrix), and cross‐amplification in other cyprinid species

Captive populations of silver carp (Hypophthalmichthys molitrix), a major aquaculture species in Asia, would undoubtedly benefit from genetic monitoring and improvement programs. We report the isolation and preliminary characterization of 16 microsatellite loci derived from both conventional and microsatellite‐enriched libraries. Inheritance studies confirmed the allelic nature of observed polymorphisms at all loci, while identifying null alleles at two loci. These loci, having varying degrees of polymorphism, should provide useful markers for applied genetic studies. A high degree of cross‐amplification among 10 other cyprinid species suggests that these loci may have more widespread utility.     

Isolation and cross‐species amplification of microsatellite loci from the fucoid seaweeds Fucus vesiculosus,F. serratus and Ascophyllum nodosum (Heterokontophyta,Fucaceae)

The Fucaceae is a family of brown seaweeds that dominate and frequently co‐occur on North Atlantic rocky shores. We developed nine polymorphic microsatellite markers for the fucoid seaweeds Fucus vesiculosus, F. serratus and Ascophyllum nodosum using a combined, enriched library. Six of these loci were polymorphic in at least two species, showing from two to eight alleles with heterozygosities ranging from 0.41 to 0.85. Loci were also tested on F. spiralis, revealing five polymorphic microsatellite loci in this species.     

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.     

Seventy‐five EST‐linked Atlantic salmon (Salmo salar L.) microsatellite markers and their cross‐amplification in five salmonid species

An Atlantic salmon (Salmo salar L.) expressed sequence tag (EST) database consisting of 58 146 ESTs was screened for microsatellite sequences. Subsequent development of 75 polymorphic EST‐associated microsatellite markers in this species is described together with cross‐species amplification results of 133 gene‐associated tandem repeat markers in five salmonid species (Salmo trutta, Oncorhynchus mykiss, Salvelinus aplinus, Thymallus thymallus, Coregonus lavaretus). The number of alleles among EST‐linked microsatellites in Atlantic salmon ranged from two to 41 with an average of 12 alleles per locus. Cross‐species amplification resulted in detection of a total of 111 polymorphic locus‐species combinations (12–32 loci per species).     

Development of EST‐SSRs in the Mediterranean blue mussel,Mytilus galloproviancialis

Eight polymorphic microsatellite repeat markers were identified from Mytilus galloproviancialis, expressed sequence tags (EST) deposited in public sequence database. Number of alleles per locus ranged from two to 10, and the observed and expected heterozygosities ranged from 0.029 to 0.872 and from 0.031 to 0.811, respectively. Three additional Mytiloida species assessed for cross‐species amplification revealed four loci could give positive amplifications. EST‐derived simple sequence repeats provide robust, informative and potentially transferable polymorphic markers suitable for population genetic, parentage, and mapping studies of M. galloproviancialis.     

Characterization of polymorphic microsatellite loci in a neotropical wood‐quail,Odontophorus leucolaemus

We developed a set of nine polymorphic microsatellite loci for black‐breasted wood‐quail, Odontophorus leucolaemus. We screened 50 individuals from Monteverde, Puntarenas Province, Costa Rica and found that locus‐specific allelic diversity ranges from two to 15 alleles (mean 10.2) and observed heterozygosity ranges from 0.24 to 0.96 (mean 0.78). These markers appear to be useful in other members of the Odontophorus genus.     

Characterization of 10 microsatellite loci in the spiny‐tailed iguana Ctenosaura hemilopha

Ten microsatellite loci were developed for the Baja California spiny‐tailed iguana Ctenosaura hemilopha, using an enriched genomic DNA library. In the Cerralvo Island population, seven loci were polymorphic and presented moderate levels of variation. Number of alleles ranged from two to eight (average 4.43), and observed heterozygosity from 0.150 to 0.857 (average 0.492). Polymorphism was detected at six loci on C. hemilopha individuals from the southern Baja California Peninsula. These markers will be useful to study familiar relationships and behaviour on the Cerralvo Island population.     

Development of microsatellite markers from an ectomycorrhizal fungus,Laccaria amethystina,by a dual‐suppression‐PCR technique

Laccaria amethystina is a major early successional ectomycorrhizal fungus. We isolated 10 polymorphic loci from L. amethystina using a dual‐suppression‐PCR (polymerase chain reaction) technique. These loci provided microsatellite markers with polymorphism of two to 10 alleles per locus. The observed and expected heterozygosities ranged from 0.136 to 0.545 and 0.206 to 0.877, respectively.     

Isolation and characterization of microsatellite loci in the Bang's leaf‐nosed bat Hipposideros turpis

The Bang's leaf‐nose bat, Hipposideros turpis, is an endangered cave‐dwelling species inhabiting the southwesternmost islands of Japan. We isolated six dinucleotide microsatellite markers from the partial genomic library of the bat, and examined their allelic variation using a sample (N = 33) from the largest colony in Japan. All the loci showed a moderate allelic variation ranging from two to eight alleles, with the observed heterozygosities from 0.33 to 0.73, and conformed to Hardy–Weinberg expectations. The present microsatellite markers will be useful in assessing population genetic structure and gene flow among populations of this species.     

EST‐SSR markers from the Pacific oyster,Crassostrea gigas

Ten polymorphic microsatellite repeat markers were identified from Crassostrea gigas, expressed sequence tags (EST) deposited in public sequence database. Number of alleles per locus ranged from three to 18, expected and observed heterozygosities ranged from 0.071 to 0.738 and from 0.306 to 0.913, respectively. Marker transferability was tested on other two Crassostrea species and polymorphic products were detected at nine loci. EST‐derived simple sequence repeats provide robust, informative and potentially transferable polymorphic markers suitable for population genetic, parentage, and mapping studies of C. gigas.     

Isolation,characterization and cross‐species amplification of microsatellite DNA loci in the tropical American yam Dioscorea trifida

We developed microsatellite markers in American yam (Dioscorea trifida). A microsatellite sequence‐enriched genomic library was screened, and after sequencing, primers were designed for 20 microsatellites. Among these, eight primer pairs yielded amplification products that were both interpretable and polymorphic in 24 yam cultivars. The number of alleles per locus ranged from two to 13 and the overall expected heterozygosity was around 0.5. Six of the eight Dioscorea trifida microsatellite loci gave amplification products in other Dioscorea species.