Microsatellites for Tetracentron sinense (Trochodendraceae), a Tertiary relict endemic to East Asia

? Premise of the study: Tetracentron sinense (Trochodendraceae) is a Tertiary relict endemic to East Asia. Microsatellite markers were developed and characterized to investigate the population genetics of the species. ? Methods and Results: Microsatellite markers were isolated from the genome of T. sinense using the protocol of Fast Isolation by AFLP of Sequences COntaining repeats (FIASCO). Eight polymorphic microsatellite markers were assessed in 44 samples collected from three wild populations. The number of alleles observed for each locus ranged from two to five. The observed and expected heterozygosities ranged from 0.0000 to 0.9375 and 0.0000 to 0.7681, respectively. ? Conclusions: The microsatellite markers will be helpful in further studies of the population genetics and phylogeography of T. sinense.     

Development of microsatellite markers for the dove tree, Davidia involucrata (Nyssaceae), a rare endemic from China

? Premise of the study: Microsatellite primers were developed for the endangered Davidia involucrata to assess the population genetics and infer its evolutionary history. ? Methods and Results: Using both the modified magnetic bead hybridization method and the dual-suppression PCR method, we isolated and characterized 12 polymorphic microsatellite loci using 134 individuals from five populations in southwestern China. The number of alleles per locus ranged from six to 21 (mean = 10.8). The expected heterozygosity per locus ranged from 0.404 to 0.918 and observed heterozygosity ranged from 0.015 to 0.821. ? Conclusions: All of the 12 microsatellite markers developed for D. involucrata are polymorphic, and lay a solid foundation for further studies of the population genetics of this famous tree.     

Microsatellite markers for the endangered root holoparasite Dactylanthus taylorii (Balanophoraceae) from 454 pyrosequencing

? Premise of the study: Microsatellite loci were isolated and developed as polymorphic markers for the New Zealand endemic root holoparasite Dactylanthus taylorii for use in population and conservation genetics studies. ? Methods and Results: Shotgun 454 pyrosequencing was performed on genomic DNA pooled from three individuals of D. taylorii. From 61709 individual sequence reads, primers for 753 microsatellite loci were developed in silico and 72 of these were tested for consistent amplification and variability. Ten microsatellite loci were found to be polymorphic and consistently scorable when screened in 44 individuals from five geographically distant populations. The number of alleles per locus ranged from four to 16 with an average of 9.7, and average observed heterozygosity per locus was between 0.182 and 0.634. ? Conclusions: These polymorphic microsatellite markers establish an important resource for ongoing conservation initiatives and planned population genetic studies of D. taylorii.     

Microsatellite primers in the Chinese dove tree, Davidia involucrata (Cornaceae), a relic species of the Tertiary

? Premise of the study: The first microsatellite primers were developed for Davidia involucrata, an endangered relic species of the Tertiary in China, to further describe its genetic variability and population structure. ? Methods and Results: Using the Fast Isolation by AFLP of Sequences Containing Repeats (FIASCO) protocol, 15 polymorphic microsatellite loci were isolated and characterized in 20 individuals from the germplasm collections of D. involucrata at the Hunan Forest Botanical Garden. High levels of polymorphism were revealed, with the total number of alleles per locus and the number of alleles per locus per individual ranging from two to 13 and from one to six, respectively. ? Conclusions: The multibanded patterns of microsatellite loci obtained in the current study confirmed that D. involucrata might be a polyploid species. The primers will be useful for studies of genetic diversity and for guiding conservation strategies for D. involucrata.     

Microsatellite markers from Ceanothus roderickii (Rhamnaceae) using next-generation sequencing technology

? Premise of the study: Ceanothus roderickii is an endangered shrub endemic to California. To investigate the population genetics of this species, including the genetic consequences of population fragmentation and hybridization, 10 microsatellite markers were developed. ? Methods and Results: Using next-generation sequencing (454) data from a single C. roderickii individual, 10 microsatellite markers were developed. A group of 12 individuals representing all of the major C. roderickii populations were analyzed. All loci were found to be polymorphic, with a range from two to 12 alleles per locus. Observed heterozygosity ranged from 0.08 to 0.83 across loci. All 10 loci were also amplifiable in at least one other Ceanothus species. ? Conclusions: Results presented here indicate the utility of our new microsatellite primers in ongoing and future studies concerning population genetics and gene flow in C. roderickii, as well as the potential applicability of these primers in similar studies on other Ceanothus species.     

Polymorphic chloroplast microsatellite loci in Nelumbo (Nelumbonaceae)

? Premise of the study: To study population genetics, phylogeography, and hybridization of Nelumbo (Nelumbonaceae), chloroplast microsatellite markers were developed. ? Methods and Results: Seventeen microsatellite loci were identified from the chloroplast genomes of N. nucifera and N. lutea. Polymorphisms were assessed in three populations of N. nucifera and one population of N. lutea. Nine loci were found to be polymorphic in N. nucifera, and all 17 loci were found to be polymorphic in N. lutea. In N. nucifera, the number of alleles per locus ranged from two to six, and the unbiased haploid diversity per locus ranged from 0.198 to 0.790. In N. lutea, the number of alleles ranged from two to four, and the unbiased haploid diversity per locus ranged from 0.245 to 0.694. ? Conclusions: The identified chloroplast simple sequence repeat markers will be useful for the study of genetic diversity, phylogeography, and identification of Nelumbo cultivars.     

Isolation and characterization of 15 polymorphic microsatellite markers for the devastating dry rot fungus,Serpula lacrymans

Fifteen polymorphic microsatellite markers were developed from microsatellite‐enriched DNA libraries of the devastating dry rot fungus, Serpula lacrymans. The loci exhibited two to four alleles per locus and the expected heterozygosity ranged from 0.13 to 0.47. The codominant markers, described here for this fungus, will permit further studies in population genetics and phylogeography of this economically highly important species.     

Development of microsatellite loci for the endangered species Pityopsis ruthii (Asteraceae)

? Premise of the study: Microsatellite loci were developed for the endangered species Pityopsis ruthii and will permit genetic and conservation studies of the species. ? Methods and Results: A microsatellite-enriched library was used to develop 12 polymorphic microsatellite loci for P. ruthii. The loci amplified perfect and imperfect repeats with three to seven alleles per locus. Observed heterozygosity ranged from 0.05 to 0.80 and expected heterozygosity ranged from 0.23 to 0.75. ? Conclusions: These microsatellite loci provide a sufficient set of markers for further investigation of population genetics of P. ruthii.     

Isolation and characterization of eight polymorphic microsatellite loci for the endangered,endemic Chilean tree Gomortega keule (Gomortegaceae)

Queule (Gomortega keule) is an endangered, Chilean tree in the endemic, monotypic family Gomortegaceae. Eight polymorphic microsatellite loci were developed and characterized for this species. The number of alleles per locus ranged from four to 12 and the observed heterozygosity ranged from 0.2 to 1.0. These microsatellite markers will be valuable tools for population genetics studies and conservation planning.     

Isolation and characterization of 10 microsatellite loci in Cneorum tricoccon (Cneoraceae), a Mediterranean relict plant

? Premise of the study: The main aim of this study was to isolate and characterize microsatellite loci in Cneorum tricoccon (Cneoraceae), a Mediterranean shrub relict of the early Tertiary, which inhabits western Mediterranean islands and coasts. Microsatellites will be useful for investigating biogeography and landscape genetics across the species distribution range, including current or past gene flow. ? Methods and Results: Seventeen microsatellite loci were characterized, of which 10 were polymorphic and amplified for a total of 56 alleles in three populations of C. tricoccon. The markers revealed average coefficients of expected heterozygosity (H(e) = 0.425), observed heterozygosity (H(o) = 0.282), and inbreeding coefficient value per population (F(IS) = 0.408). ? Conclusions: These microsatellite primers will potentially be useful in the study of population and landscape genetics, conservation status of isolated populations, island-continental distribution, current or historical movements between populations, and in the investigation of the consequences of dispersal mechanisms of these plants.     

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.     

Development of 12 microsatellite markers for Platycrater arguta (Hydrangeaceae) endemic to East Asia

? Premise of the study: Microsatellite markers were characterized in Platycrater arguta, a rare endemic shrub from eastern China and southern Japan, to investigate its population genetic structure, phylogeographic patterns, and breeding system. ? Methods and Results: Using both the Fast Isolation by AFLP of Sequences COntaining repeats (FIASCO) protocol and the compound microsatellite marker technique, we developed 12 microsatellite markers. All primers showed polymorphism when assessed in 43 individuals from two populations in eastern China and southern Japan. Overall, the number of alleles ranged from five to 21, with an average of 14.91 alleles per locus. ? Conclusions: These markers can be used in further studies on population genetics, phylogeography, and breeding system of P. arguta.     

Isolation and characterization of microsatellite loci in the endangered tree Diplopanax stachyanthus (Araliaceae)

? Premise of the study: Microsatellite markers were developed in Diplopanax stachyanthus to investigate the population genetics of this endangered tree. ? Methods and Results: Using the Fast Isolation by AFLP of Sequences Containing repeats (FIASCO) protocol, 15 microsatellite markers were developed in D. stachyanthus and evaluated for their variability in 25 samples from a natural population. For the 11 polymorphic loci, the number of alleles ranged from two to eight, while the observed and expected heterozygosities ranged from 0.5200 to 0.7600 and 0.4200 to 0.7813, respectively. Their cross-taxa transferability was also examined in Acanthopanax gracilistylus, Tetrapanax papyrifer, Cornus controversa, and Dendrobenthamia japonica var. chinensis, and four to 15 loci proved amplifiable in these species. ? Conclusions: These microsatellite markers could be employed to investigate the population genetics of D. stachyanthus, and may potentially be applicable to other related species.     

Isolation and characterization of microsatellite loci in <Emphasis Type="Italic">Melicope quadrilocularis</Emphasis> (Rutaceae), an endemic plant species of the Bonin Islands,Japan, and cross-species amplification in closely related taxa

Twelve microsatellite loci were isolated and characterized for Melicope quadrilocularis, an insular endemic tree species of the Bonin Islands. The observed number of alleles at each locus ranged from 1 to 18. The range of expected heterozygosity was 0.0000–0.9445. The inter-specific applicability of these loci was evaluated by analyzing two other endemic species and one endemic variety of Melicope that are also distributed on the Bonin Islands. All primer pairs for the 12 loci tested successfully amplified the loci in all taxa, except for primers for four loci in M. nishimurae.     

Ten microsatellite markers in endangered species Sauvagesia rhodoleuca (Ochnaceae)

? Premise of the study: We developed microsatellite markers to investigate the level of genetic diversity within and among populations of the endemic shrub Sauvagesia rhodoleuca in China. ? Methods and Results: Ten polymorphic microsatellite loci were identified in five populations. The number of alleles per locus varied from 2 to 16. Observed and expected heterozygosities ranged from 0.000 to 1.000 and from 0.000 to 0.726, respectively. ? Conclusions: The results provide basic information on genetic diversity for future studies of population genetics in S. rhodoleuca.     

Identification and characterization of microsatellite loci in the rush Juncus effusus (Juncaceae)1

? Premise of the study: Microsatellite markers were developed for the common wetland plant Juncus effusus to assess levels of within- and among-population genetic diversity. ? Methods and Results: Using a next-generation sequencing approach we identified new microsatellite loci, from which 23 were further characterized in a large population of J. effusus. Expected heterozygosity ranged from 0 to 0.64 with a mean of 0.407. Inbreeding coefficients (mean = 0.984) were very high, confirming earlier suggestions of an inbred mating system. Cross-amplification was tested in J. conglomeratus, J. inflexus, J. drummondii, and J. filiformis, with best results in the former. ? Conclusions: The described microsatellite markers will be helpful in assisting studies on, e.g., reproduction, taxonomy, and phylogeography in J. effusus and related species.     

Development of seven novel EST-SSR markers from Cycas panzhihuaensis (Cycadaceae)

? Premise of the study: Cycas panzhihuaensis L. Zhou & S. Y. Yang is a vulnerable gymnosperm endemic to China, where its range represents the northernmost occupation of Cycas L. We developed EST-derived SSR markers to investigate its genetic diversity and population structure. ? Methods and Results: Based on the expressed sequence tag (EST) database for Cycas rumphii Miq., seven simple sequence repeat (SSR) markers were identified and screened in 55 individuals from seven wild populations of C. panzhihuaensis. Alleles numbered 2 to 5, and their observed heterozygosity and expected heterozygosity ranged from 0.0000 to 0.6545 and from 0.0535 to 0.6966, respectively. ? Conclusions: These new EST-SSR markers will enhance further studies of the population genetics of C. panzhihuaensis, allowing researchers to design reasonable conservation and management protocols.     

Development and characterization of microsatellite loci for lotus (Nelumbo nucifera)

This paper reports the development of microsatellite primers for Nelumbo nucifera Gaerten. By screening genomic libraries enriched with 10 kinds of probes, Seventeen polymorphic loci were isolated and primers were designed. Polymorphism of these 17 loci was assessed in 24 individuals. All the 17 loci are polymorphic and the number of alleles ranged from two to seven. Observed heterozygosity and expected heterozygosity ranged from 0.0000 to 0.9176 and from 0.2837 to 0.7917 respectively. These microsatellite loci should be useful for studying the genetic diversity of N. nucifera.     

Development and characterization of microsatellite markers for Emmenopterys henryi (Rubiaceae), a rare tree from China

? Premise of the study: Compound microsatellite primers were developed for Emmenopterys henryi, an endangered deciduous tree endemic to China, to assess its genetic diversity and population structure as well as its evolutionary history. ? Methods and Results: Using the compound microsatellite marker technique, 10 pairs of polymorphic microsatellite primers were isolated and characterized in E. henryi. Levels of polymorphism were tested across a total of 63 individuals from three natural populations. Allele numbers varied from 10 to 20 per locus, with an average of 14.50 alleles per locus. The observed heterozygosity per locus ranged from 0.125 to 0.962, and the expected heterozygosity ranged from 0.377 to 0.903. ? Conclusions: The highly polymorphic markers developed and characterized in this study will facilitate evolutionary and population genetic studies in E. henryi.     

Characterization of 31 EST-derived microsatellite markers for the pearl oyster Pinctada martensii (Dunker)

We developed and characterized 31 microsatellite markers from expressed sequence tags of Pinctada martensii (Dunker). The number of alleles per locus ranged from 4 to 18 as determined in 44 individuals from a wild population. The expected heterozygosity ranged from 0.4121 to 0.9436, while the observed heterozygosity ranged from 0.4054 to 0.7273. Most of the loci are in Hardy-Weinberg equilibrium. These markers should be useful for population genetics studies, parentage and genome mapping in this species.