Isolation and characterization of fourteen microsatellite loci for striped field mouse (<Emphasis Type="Italic">Apodemus agrarius</Emphasis>)

We describe the isolation and characterization of 14 microsatellite loci in the striped field mouse from genomic DNA-enriched libraries in this paper. The 14 new loci were tested in 24 individuals from four populations in Southwest China. These loci were highly polymorphic with numbers of alleles per locus ranging from 6 to 14 and expected heterozygosities from 0.789 to 0.925. All loci followed Hardy–Weinberg expectations except SFM4, SFM11 and SFM13 loci. No significant linkage association was found among all loci. The 14 novel polymorphic microsatellite loci will be useful in studying phylogeography and population genetics of the striped field mouse.     

New microsatellite loci isolated from the field cricket Gryllus bimaculatus characterized in two cricket species, Gryllus bimaculatus and Gryllus campestris

We have developed a new set of 27 polymorphic markers for each of two cricket species, Gryllus bimaculatus and Gryllus campestris. Initially, 14 published G. bimaculatus loci were tested in G. campestris; however, only five loci were polymorphic. Therefore, we isolated an additional 50 new microsatellite loci from G. bimaculatus and tested these in both species. In a minimum of 20 individuals, 27 of the new loci were polymorphic in G. bimaculatus and 25 in G. campestris.     

Isolation and characterization of 14 microsatellite loci for the Chevrier's field mouse (Apodemus chevrieri)

We describe the isolation and characterization of 14 microsatellite loci in the Chevrier's field mouse from genomic DNA-enriched libraries. The 14 loci were highly polymorphic with numbers of alleles per locus in 24 individuals ranging from three to 13, observed heterozygosity from 0.381 to 0.867 and expected heterozygosity from 0.448 to 0.931. All loci followed Hardy-Weinberg expectations except for CFM3, CFM10 and CFM12 loci. No significant linkage association was found among all these loci. The 14 polymorphic microsatellite loci will be useful in studying phylogeography and population genetics of the Chevrier's field mouse.     

Isolation and characterization of new microsatellite markers in shea tree (Vitellaria paradoxa C. F. Gaertn)

Vitellaria paradoxa is one of the major components of African parkland agroforestry systems. In order to assess the genetic diversity and population structure of this species, we isolated and characterized 14 polymorphic nuclear microsatellite loci. Primers developed to amplify these loci were used to analyse 200 individuals of a shea tree population in Mali. Loci have shown a high number of alleles ranging from four to 26, and display an observed level of heterozygosity between 0.37 and 0.85. These new very polymorphic microsatellite markers will be useful for genetic and ecological studies of V. paradoxa.     

Isolation and characterization of 12 novel microsatellite loci for the red panda (Ailurus fulgens)

The information on dispersal patterns and mating systems of red pandas is quite important for the understanding of the genetic diversity and divergence of this species. And microsatellite marker is an ideal tool to analyze dispersal patterns and mating systems. Thus, we describe in this paper the isolation and characterization of 12 microsatellite loci in the red panda from genomic DNA-enriched libraries. These loci were highly polymorphic with numbers of alleles per locus in 24 individuals ranging from 2 to 14, observed heterozygosity from 0.143 to 0.864 and expected heterozygosity from 0.297 to 0.872. All loci except for RP6 locus followed Hardy–Weinberg expectations. No significant linkage association was found among all these loci. The 12 novel polymorphic microsatellite loci will be of use in studying dispersal patterns and mating systems of red pandas.     

Isolation and characterization of microsatellite markers for the heavily exploited rockfish Sebastes schlegeli, and cross-species amplification in four related Sebastes spp.

Here we report development and characterization of 14 polymorphic microsatellite loci from Sebastes schlegel. Polymorphism at these loci revealed from 3 to 23 alleles. The observed heterozygosity ranged from 0.34 to 1.00, and the expected heterozygosity ranged from 0.31 to 0.95. No linkage disequibrium was found. Two loci were significantly deviated from HWE (P < 0.01). The 14 loci were also surveyed in four other Sebastes species and 12 loci successfully amplified, where allelic diversity ranged from highly polymorphic to monomorphic. These results demonstrate these microsatellite markers can be used for the study of intra- and inter-specific genetic diversity.     

Microsatellite development for the endangered Yangtze sturgeon (Acipenser dabryanus Duméril, 1869) using 454 sequencing

The Yangtze sturgeon (Acipenser dabryanus) is an endemic species in China. Using 454 sequencing, eight polymorphic tri‐, tetra‐, penta‐, and hexanucleotide microsatellite loci were isolated in this study. The raw sequence data from a one‐eighth run of 454 sequencings were 38.0 Mbp containing 94 222 reads/sequences. Of 80 microsatellite loci, only eight loci were polymorphic in a population of 30 individuals. The number of alleles per locus ranged from 4 to 14 (mean 7.62), and the observed heterozygosities varied between 0.46 and 0.88 (mean 0.74). Cross amplification was tested in congeneric species Acipenser sturio and Acipenser sinensis. These new microsatellite markers will be useful for further studies on genetic variation, parentage analysis, and conservation management for this critically endangered species.     

Microsatellite markers isolated from saltgrass (Distichlis spicata)

Twelve polymorphic microsatellite DNA loci were isolated from saltgrass (Distichlis spicata) and optimized for future studies of its breeding system. The loci were screened for variability among 24 individuals from two populations. The primers amplified loci with numbers of alleles ranging from four to 14 per locus and polymorphic information content from 0.481 to 0.951. Observed heterozygosity varied from 0.227 to 0.958.     

Polymorphic microsatellite loci for population studies of <Emphasis Type="Italic">Bullacta exarata</Emphasis>

Nine polymorphic microsatellite loci were isolated and characterized from an AC-enriched genomic library of Bullacta exarata. They were polymorphic in 30 individuals from Qidong in Jiangsu Province, China. The number of alleles per polymorphic loci varied from 7 to 14 and the values of observed heterozygosity and expected heterozygosity ranged from 0.2593 to 0.9667 and from 0.7090 to 0.9164, respectively. Six of the nine microsatellites conformed to Hardy–Weinberg equilibrium, and inherited independently. These informative microsatellite markers will be useful in studies of population genetic structure for this species.     

Nine new tetranucleotide microsatellite markers for the fire‐bellied toad (Bombina bombina)

We describe nine new polymorphic tetranucleotide microsatellite loci isolated from the fire‐bellied toad (Bombina bombina). The relative yield of new loci was higher than described in previous studies in amphibians: out of 12 loci initially evaluated, nine were polymorphic and amplifying reliably. Number of alleles ranged from four to 10 and observed heterozygosities from 0.47 to 0.91. Seven loci were polymorphic also in Bombina variegata and five in Bombina orientalis. Enrichment protocols yielding long flanking regions potentially overcome difficulties (i.e, low yield of reliable loci relative to number of clones screened) which have been reported in microsatellite development in anurans.     

Isolation and characterization of microsatellite markers from the entomopathogenic fungus Metarhizium anisopliae

Fourteen polymorphic microsatellite markers were isolated from the entomopathogenic fungus, Metarhizium anisopliae, based on enriched genomic libraries. In order to assess allelic variability, the microsatellite loci were analysed in a collection of 34 isolates sampled from across Switzerland. The number of detected alleles in 14 loci ranged from two to eight and expected heterozygosity from 0.265 to 0.808. Because of the high expected heterozygosity, the 14 microsatellite loci are very useful for ecological studies and analysis of population diversity, and to identifying, monitoring, and tracking M. anisopliae strains applied as biological control agents.     

Polymorphic microsatellite loci for the Japanese anchovy Engraulis japonicus (Engraulidae)

We isolated and characterized 14 polymorphic microsatellite loci in the Japanese anchovy (Engraulis japonicus) using a (GT)(13)-enriched genomic library. The numbers of alleles per locus ranged from 6 to 31, with a mean of 17.8. The observed and expected heterozygosities ranged from 0.180 to 0.949 and from 0.172 to 0.966, with means of 0.731 and 0.825, respectively. All 14 loci were in Hardy-Weinberg equilibrium and no significant linkage disequilibrium between loci pairs was detected. These microsatellite markers will be useful for analyzing the population genetic structure and gene flow of E. japonicus.     

Isolation and Characterization of 14 Polymorphic Microsatellite Loci in the Big-Headed Turtle (Platysternon megacephalum)

The big-headed turtle (Platysternon megacephalum) is critically endangered because of overharvesting, illegal trade, and habitat destruction. Assessment of genetic variability in existing populations becomes very important to the taxonomy and conservation of this species. Here we describe 14 microsatellite loci isolated from an enriched genomic library of the big-headed turtle, and the polymorphisms of these loci were assessed in 28 individuals from Huizhou, Heyuan, Zhaoqing, and Shaoguan of Guangdong, China. The range of polymorphism information content is 0.305–0.738, and no evidence of significant linkage disequilibrium was found among any pairs of loci. These 14 new polymorphic microsatellite loci can be used in population genetics, taxonomy, phylogeography, behavior ecology, and conservation efforts of Platysternon megacephalum.     

Isolation and characterization of microsatellite loci from forest musk deer (Moschus berezovskii)

This study reported the isolation and characterization of eight polymorphic microsatellite loci in endangered forest musk deer Moschus berezovskii. An improved enrichment protocol was used to isolate microsatellites, and polymorphism was explored with samples from wild musk deer population collected in Miyalo of Sichuan Province in China. Approximately 70% of clones from the genomic library constructed in current study contained dinucleotide (AC) repeats. Eight microsatellite loci amplified were highly polymorphic within forest musk deer population. The number of alleles per locus ranged from 6 to 14, and the observed and expected heterozygosities ranged from 0.41 approximately 1.0 and from 0.8 approximately 0.9, respectively. The average polymorphic information content (PIC) value for these markers was 0.82. This demonstrated that the eight microsatellite loci developed here are highly polymorphic, and can be used as genetic markers for further investigation of musk deer. Also, the results showed that the musk deer distributed in Miyalo had a relatively higher level of genetic variation.     

Polymorphic tetranucleotide microsatellites for Cope's giant salamander (Dicamptodon copei) and Pacific giant salamander (Dicamptodon tenebrosus)

We present primers and amplification conditions for 15 microsatellite loci developed for the Cope's giant salamander (Dicamptodon copei), 14 of which are tetranucleotide repeats. Cross-species amplification revealed 10 of these loci to also be polymorphic in the Pacific giant salamander (Dicamptodon tenebrosus). Several loci produced nonoverlapping allelic ranges between the two species and may be useful in species identification. These polymorphic microsatellite loci are potentially useful for future studies of population genetics in dicamptodontid salamanders.     

Development and characterization of microsatellite markers for parentage analyses of the coral reef damselfish (<Emphasis Type="Italic">Pomacentrus amboinensis</Emphasis>: Pomacentridae)

Five new polymorphic microsatellite loci were developed for the coral reef damselfish Pomacentrus amboinensis. Twenty-four individuals from two Great Barrier Reef populations were genotyped at the five loci, with numbers of alleles per locus ranging from 6–23 and observed heterozygosity between 0.42–0.92. In addition, the cross-species testing of six primers developed for Stegastes partitus revealed one primer (SpGATA40) that was also polymorphic for P. amboinensis. Due to high levels of polymorphism (≥14 alleles) in at least four of the six loci and a high proportion of tetranucleotide repeats, these microsatellite markers should be useful for parentage assignment as well as other investigations of individual relatedness.     

Characterization of 35 novel microsatellite DNA markers from the duck (Anas platyrhynchos) genome and cross-amplification in other birds

In order to study duck microsatellites, we constructed a library enriched for (CA)n, (CAG)n, (GCC)n and (TTTC)n. A total of 35 pairs of primers from these microsatellites were developed and used to detect polymorphisms in 31 unrelated Peking ducks. Twenty-eight loci were polymorphic and seven loci were monomorphic. A total of 117 alleles were observed from these polymorphic microsatellite markers, which ranged from 2 to 14 with an average of 4.18 per locus. The frequencies of the 117 alleles ranged from 0.02 to 0.98. The highest heterozygosity (0.97) was observed at the CAUD019 microsatellite locus and the lowest heterozygosity (0.04) at the CAUD008 locus, and 11 loci had heterozygosities greater than 0.50 (46.43%). The polymorphism information content (PIC) of 28 loci ranged from 0.04 to 0.88 with an average of 0.42. All the above markers were used to screen the polymorphism in other bird species. Two markers produced specific monomorphic products with the chicken DNA. Fourteen markers generated specific fragments with the goose DNA: 5 were polymorphic and 9 were monomorphic. But no specific product was detected with the peacock DNA. Based on sequence comparisons of the flanking sequence and repeat, we conclude that 2 chicken loci and 14 goose loci were true homologous loci of the duck loci. The microsatellite markers identified and characterized in the present study will contribute to the genetic map, quantitative traits mapping, and phylogenetic analysis in the duck and goose.     

Development and Characterization of cDNA Resources for the Common Marmoset: One of the Experimental Primate Models

The common marmoset is a new world monkey, which has become a valuable experimental animal for biomedical research. This study developed cDNA libraries for the common marmoset from five different tissues. A total of 290 426 high-quality EST sequences were obtained, where 251 587 sequences (86.5%) had homology (1E⁻¹⁰⁰) with the Refseqs of six different primate species, including human and marmoset. In parallel, 270 673 sequences (93.2%) were aligned to the human genome. When 247 090 sequences were assembled into 17 232 contigs, most of the sequences (218 857 or 15 089 contigs) were located in exonic regions, indicating that these genes are expressed in human and marmoset. The other 5578 sequences (or 808 contigs) mapping to the human genome were not located in exonic regions, suggesting that they are not expressed in human. Furthermore, a different set of 118 potential coding sequences were not similar to any Refseqs in any species, and, thus, may represent unknown genes. The cDNA libraries developed in this study are available through RIKEN Bio Resource Center. A Web server for the marmoset cDNAs is available at http://marmoset.nig.ac.jp/index.html, where each marmoset EST sequence has been annotated by reference to the human genome. These new libraries will be a useful genetic resource to facilitate research in the common marmoset.     

Isolation and characterization of 16 novel microsatellite loci in two inbred strains of the Chinese hamster (Cricetulus griseus)

The Shanyi inbred A and E strains of the Chinese hamster are widely used in biomedical research, but detailed genetic characterization has been lacking. We developed microsatellite markers that could be used for genetic diversity analysis and linkage map construction. We isolated and characterized 16 novel microsatellite loci from a microsatellite-enriched genomic DNA library. These loci were genotyped in 48 animals from the two strains, and the polymorphic information content was determined. In the Shanyi A and E populations, 14 and 15 loci were found to be polymorphic, respectively, with polymorphic information content ranging from 0.1393 to 0.8082 and from 0.1109 to 0.7397, respectively. A total of 115 alleles were found for the 16 microsatellite loci in the two populations; the mean observed heterozygosity (H(O)) was 0.5191 and 0.4333 for the A and E populations, respectively, indicating marked genetic variation within the two populations. Correspondingly, the F(ST) values ranged from 0.002 to 0.9253, with an overall mean of 0.1935, indicating significant genetic difference between the two strains. The population differentiation levels were substantiated by Nei's genetic distance and full Bayesian analyses computed with STRUCTURE. Despite the genetic diversity and differentiation within and between the two inbred populations, the 48 individuals were correctly allocated into their original populations with high statistical confidence based on these 16 microsatellite loci. These novel microsatellite loci should be useful genetic markers for these two Chinese hamster inbred strains.