Isolation and characterization of microsatellite loci in the endangered tree Berchemiella wilsonii var. pubipetiolata and cross-species amplification in closely related taxa

Twenty-eight polymorphic microsatellite loci were developed and characterized for the endangered tree Berchemiella wilsonii var. pubipetiolata. The observed number of allele ranged from two to seven. The ranges of observed and expected heterozygosity were 0.039–1.000 and 0.038–0.816, respectively. In addition, this set of microsatellites produced robust cross-species amplification in other two endangered taxa: Berchemiella berchemiaefolia and Berchemiella wilsonii, suggesting these microsatellite markers should provide a useful tool for genetic and conservation studies of the globally endangered genus Berchemiella.     

Development of 12 novel microsatellite loci in a traditional Chinese medicinal plant, Epimedium brevicornum and cross-amplification in other related taxa

A total of 12 polymorphic microsatellite loci were developed and characterized for a Chinese medicinal plant, Epimedium brevicornum (Berberidaceae). A genomic DNA enrichment protocol was used to isolate microsatellite loci and polymorphism was explored using 38 individuals from one natural population. The observed number of alleles ranged from 2–14. The ranges of observed and expected heterozygosity were 0.00–0.83 and 0.15–0.88, respectively. In addition, successful cross-species amplification of this set of microsatellite markers in other four medicinal Epimedium species suggested that they would provide a useful tool for the genetic and conservation studies of Epimedium species.     

Development and characterization of polymorphic microsatellite loci in endangered fern Adiantum reniforme var. sinense

Fourteen polymorphic microsatellite loci in the endangered fern Adiantum reniforme var. sinense were developed and characterized using the Fast Isolation by AFLP of Sequences Containing repeats (FIASCO) protocol. Polymorphism of each locus was assessed in a bulked sample of 30 individuals from 8 natural populations. The number of alleles per locus varied from 2 to 11, with an average value of 6.2. The ranges of observed and expected heterozygosity were 0.000–0.895 and 0.226–0.868, respectively. These microsatellite markers provide useful tools for the ongoing conservation genetic studies of Adiantum reniforme var. sinense.     

Characterization of 14 novel microsatellite loci in the endangered <Emphasis Type="Italic">Liriodendron chinense</Emphasis> (Magnoliaceae) and cross-species amplification in closely related taxa

Fourteen polymorphic microsatellite loci were isolated and characterized from an AC-enriched genomic library of Liriodendron chinense (Magnoliaceae). The average allele number of these microsatellites was 5.2 per locus, ranging from three to eight. The observed and expected heterozygosity at population level were 0.07–1.00 and 0.10–0.83, respectively. These sets of microsatellites will be useful for studies of population genetic structure of L. chinense and L. tulipifera as well as to estimate fine-scale gene flow rates.     

Isolation and characterization of polymorphic microsatellite loci in <Emphasis Type="Italic">Ardisia crenata</Emphasis> (Myrsinaceae)

Ardisia crenata, an evergreen shrub native to East Asia, has been a serious invasive plant to the southeastern USA. Here 13 polymorphic microsatellite loci were isolated and characterized from an enrichment genomic library of A. crenata. The average allele number of these microsatellites was four per locus, ranging from two to seven. The ranges of observed and expected heterozygosity were 0.000–1.000 and 0.239–0.789, respectively. These microsatellite markers will be useful for investigating population genetics and reproductive ecology of A. crenata.     

Isolation and characterization of 11 microsatellite loci for the Sichuan snub-nosed monkey,Rhinopithecus roxellana

We report on the isolation and characterization of 11 microsatellite loci in the Sichuan snub-nosed monkey (Rhinopithecus roxellana) from AC-enriched genomic libraries. 20 microsatellite loci were screened from the libraries, of which 11 were polymorphic. The number of observed alleles among 32 samples of snub-nosed monkey ranged from three to nine. The observed and expected heterozygosity were 0.071–0.815 and 0.201–0.819, respectively. The high variability revealed in this study should be useful tools for further study on social structure and population genetics of snub-nosed monkey in the future.     

Characterization of six microsatellite loci in the Baltic blue mussel <Emphasis Type="Italic">Mytilus trossulus</Emphasis> and cross-species amplification in North Sea <Emphasis Type="Italic">Mytilus edulis</Emphasis>

The blue mussel Mytilus trossulus occurs in the Pacific and in the North Atlantic. We developed and characterized six microsatellite loci for Baltic M. trossulus. Seventeen microsatellite loci were screened, of which six were polymorphic. The number of alleles among 50 individuals ranged from 3 to 13 and the observed and expected heterozygosity were 0.09–0.46 and 0.34–0.86, respectively. The loci were also tested for cross amplification in M. edulis, in which four of the six microsatellite loci were successfully amplified.     

Isolation and characterization of polymorphic microsatellite loci in Castanopsis chinensis Hance (Fagaceae)

Twelve novel microsatellite loci were isolated and characterized from enriched genomic libraries of Castanopsis chinensis. Four previously reported microsatellites from Castanopsis cuspidata were cross-amplified in C. chinensis. Forty-two sample trees from a wild population were tested for polymorphism using a set of the 16 polymorphic microsatellites. The average allele number of these microsatellites was 4.6 per locus, ranging from 2 to 7. The ranges of observed and expected heterozygosity were 0.262–1.000 and 0.238–0.818, respectively. Significant deviations from Hardy–Weinberg equilibrium were detected at five loci and no linkage disequilibrium was observed.     

Isolation of microsatellite markers in the Emys orbicularis complex and development of multiplex PCR amplification

We report the development of 15 new microsatellite markers for Emys orbicularis and Emys trinacris. A survey of 20 individuals showed that all loci are highly polymorphic with 3–14 alleles per locus. Additionally, 22 Glyptemys muhlenbergii primers were checked for cross-species amplification, with 14 being amplified successfully and polymorphic (2–14 alleles). A set of eight markers was selected and combined into two multiplex PCRs. Levels of genetic diversity were assessed in 648 individuals covering the complete distribution area. The number of alleles ranged from 13 to 24 and observed heterozygosity varied between 0.515 and 0.852.     

Isolation and characterization of microsatellite loci in <Emphasis Type="Italic">Pedicularis verticillata</Emphasis> L. using PCR-based isolation of microsatellite arrays (PIMA)

Pedicularis verticillata L. is a highly valuable herb for traditional Chinese medical treatment. In this report, 11 microsatellite loci from P. verticillata were isolated. The simple sequence repeat (SSR) markers were screened in 23 samples of wild populations of P. verticillata, and eight samples from its sister P. ikomai. The number of alleles ranged from 4 to 13, and value of expected (H _E) and observed (H ₀) heterozygosity was 0.62609–0.89662 and 0–0.95652, respectively. All loci were significantly deviated from Hardy–Weinberg expectations due to the heterozygote deficiency, indicating a dramatic loss of genetic polymorphisms in the restrictedly distributed species. The markers amplified well in the two species are useful for examining genetic diversity and population genetic structure, which, in turn, can provide information for establishing conservation strategy for these endangered species.     

Isolation and characterization of microsatellite loci in Pratt’s Leaf-nosed Bat (<Emphasis Type="Italic">Hipposideros pratti</Emphasis>) and cross-species amplification in closely related taxa

We developed nine microsatellite loci using an enriched library method from the genomic DNA of Pratt’s leaf-nosed bat (Hipposideros pratti). These loci were tested on 96 individuals sampled from Sichuan Province, China. The number of alleles per locus varied from 4 to 14. The expected and observed heterozygosity values ranged from 0.513 to 0.886 and from 0.375 to 0.966, respectively. Three microsatellite loci departed significantly from Hardy–Weinberg equilibrium (HWE). No linkage disequilibrium was found. These microsatellite loci will be used in studies of conservation genetics in this species.     

Isolation and characterization of 11 microsatellite loci from Camellia sinensis in Taiwan using PCR-based isolation of microsatellite arrays (PIMA)

We report 11 novel microsatellite primer pairs for the wild tea, Camellia sinensis (L.) O. Kuntze forma formosensis Kitamura. These simple sequence repeat markers were tested in 24 samples collected from wild tea populations, and in cultivars and C. japonica. The number of alleles ranged from 4 to18. The expected (H _E) and observed (H _O) heterozygosity were 0.687–0.946 and 0.042–0.792, respectively. All loci were significantly deviated from Hardy-Weinberg expectations due to the heterozygote deficiency, indicating a dramatic loss of genetic polymorphisms in the rare species. Significant LD was discovered in most loci. These primers may provide a tool for understanding demography and population structure in wild tea.     

Development of tetranucleotide microsatellite loci for the finless porpoise (<Emphasis Type="Italic">Neophocaena phocaenoides</Emphasis>)

The finless porpoise, Neophocaena phocaenoides, is endemic to the coastal waters of the Indo-Pacific, ranging from the Persian Gulf to Japan. Nine tetranucleotide microsatellite loci were isolated from the finless porpoise (Neophocaena phocaenoides). Polymorphism of each locus was assessed in 39 unrelated individuals from the Yellow Sea and the South China Sea of the Chinese waters. The number of alleles per locus varied from 2 to 11. The ranges of observed and expected heterozygosity were 0.154–0.795 and 0.146–0.839, respectively. Cross-species amplification of these loci was tested in other cetacean species. These microsatellite markers described here will be suitable for population genetic studies of finless porpoises and other cetacean species.     

Tetranucleotide markers from the loggerhead sea turtle (Caretta caretta) and their cross-amplification in other marine turtle species

The loggerhead sea turtle (Caretta caretta) is a federally threatened species and listed as endangered by the World Conservation Union (IUCN). We describe primers and polymerase chain reaction (PCR) conditions to amplify 11 novel tetranucleotide microsatellite loci from the loggerhead sea turtle. We tested primers using samples from 22 females that nested at Melbourne Beach, Florida (USA). Primer pairs yielded an average of 11.2 alleles per locus (range of 4–24), an average observed heterozygosity of 0.83 (range 0.59–0.96), and an average polymorphic information content of 0.80 (range 0.62–0.94). We also demonstrate the utility of these primers, in addition to primers for 15 loci previously described, for amplifying microsatellite loci in four additional species representing the two extant marine turtle families: olive ridley (Lepidochelys olivacea), hawksbill (Eretmochelys imbricata), green turtle (Chelonia mydas), and leatherback (Dermochelys coriacea).     

Isolation and characterization of polymorphic microsatellite loci from a dinucleotide-enriched genomic library of spotted maigre (Nibea albiflora)

In the present study, we reported 13 polymorphic microsatellite loci isolated from a dinucleotide-enriched genomic library of Nibea albiflora. The number of alleles, observed and expected heterozygosity per locus in 44 individuals ranged from 2 to 13, from 0.0909 to 0.9773 and from 0.0886 to 0.9073, respectively. Three loci significantly deviated from Hardy–Weinberg equilibrium after Bonferroni correction. Analysis of linkage disequilibrium showed non-significant among the two pairs of loci. As a result, 13 microsatellite loci probably located on different chromosome pairs and these polymorphic microsatellite loci should provide sufficient level of genetic diversity to investigate the fine-scale population structure and evaluate the breeding strategy in Nibea albiflora. Shichao Xing, Changwei Shao contributed equally to this work.     

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.     

A set of polymorphic dinucleotide and tetranucleotide microsatellite markers for the Indo-Pacific humpback dolphin (Sousa chinensis) and cross-amplification in other cetacean species

Eleven dinucleotide and five tetranucleotide polymorphic microsatellite loci were presented for the Indo-Pacific humpback dolphin Sousa chinensis, a species categorized as ‘data deficiency’ in the IUCN Red List. These markers were developed to allow future population studies, such as characterization of population structure and genetic diversity that are important for the species’ conservation. The number of alleles ranged from 2 to 9 with observed heterozygosity ranging from 0.167 to 0.917, and expected heterozygosity ranging from 0.159 to 0.913. Test of these loci in five additional cetacean species found that 10–13 loci have successful cross-amplifications.     

Isolation and characterization of nine microsatellite loci for the takin (<Emphasis Type="Italic">Budorcas taxicolor</Emphasis>)

We report on the isolation and characterization of nine microsatellite markers in the takin (Budorcas taxicolor) from genomic DNA-enriched libraries. Twenty-eight microsatellites were screened from the libraries, and nine of the screened microsatellites were polymorphic. The number of observed alleles for each locus in 28 individuals ranged from two to seven, and the expected and observed heterozygosity was 0.105–0.758 and 0.071–0.821, respectively. Four loci (TK01, TK02, TK04 and TK08) of nine 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 takin.     

Isolation and characterization of polymorphic microsatellite loci from a repeat-enriched genomic library of stone flounder (Kareius bicoloratus) and cross-species amplification

Stone flounder (Kareius bicoloratus) is a rare fish species in China. Here, we reported 11 polymorphic microsatellite loci isolated from a repeat-enriched genomic library of stone flounder. The number of alleles, observed and expected heterozygosity per locus in 32 individuals ranged from 3 to 6, from 0.1613 to 0.8667 and from 0.1549 to 0.7932, respectively. Two loci significantly deviated from Hardy–Weinberg equilibrium after Bonferroni correction and no significant linkage disequilibrium between pairs of loci was found. Cross-species amplification of these microsatellite loci in additional three fish species was performed. These polymorphic microsatellite loci would be useful for investigating genetic population structure and construction of genetic linkage map in Kareius bicoloratus. Yong-Sheng Tian and Gui-Dong Miao are contributed equally.     

Characterization of novel microsatellite loci in the great leaf-nosed bat, Hipposideros armiger and cross-amplification in other related species

Eight microsatellite loci were isolated from an enriched genomic library of the great leaf-nosed bat, Hipposideros armiger. The polymorphism of these loci was tested on a population of 48 individuals from Anhui Province, China. All loci revealed the polymorphism ranging from three to 12 alleles. The observed heterozygosity values were from 0.213 to 0.875 and expected heterozygosity from 0.232 to 0.820. No significant linkage disequilibrium was detected. Two loci significantly deviated from Hardy–Weinberg equilibrium after Bonferroni correction. In addition, successful cross-amplification also suggested that these microsatellite markers will facilitate research on the population genetics and gene flow of H. armiger and other related species.