Isolation and characterization of novel microsatellite markers for Arctium minus (Compositae)

? Premise of the study: Microsatellite primers were developed for the invasive plant Arctium minus to investigate the effects of facultative self-pollination and the biannual habit on population genetic structure, as well as the colonization of the Americas by this Eurasian species. ? Methods and Results: Sixteen di- and trinucleotide microsatellite loci were identified in six populations. The number of alleles per locus ranged from one to 10, observed heterozygosities ranged from 0.000 to 0.897, and the mean value of F(IS) was 0.316. ? Conclusions: These results indicate the utility of these loci in future studies of population genetics in A. minus.     

Development and characterization of polymorphic microsatellite markers in Cyclobalanopsis glauca (Fagaceae)

? Premise of the study: We isolated and characterized polymorphic microsatellite loci in Cyclobalanopsis glauca (Fagaceae), an evergreen broadleaved monoecious tree, to provide tools for analyzing parentage and mating system. ? Methods and Results: Thirteen polymorphic microsatellite markers were developed and tested in three C. glauca populations. The number of alleles per locus varied from two to 22. The observed and expected heterozygosities within populations were 0.000-0.967 and 0.033-0.949, respectively. ? Conclusions: These polymorphic primers showed high levels of polymorphism within tested populations, and can be used in parentage analysis and mating system estimation of C. glauca.     

Isolation and characterization of 36 polymorphic microsatellite markers in Schima superba (Theaceae)

? Premise of the study: Our objective was to develop microsatellite markers to investigate the level of genetic diversity within and among populations in a dominant evergreen broad-leaved tree, Schima superba, in southern China. ? Methods and Results: Thirty-six microsatellite markers were developed and showed polymorphism in three populations. The number of alleles per locus ranged from six to 34, with an average of 19. The observed and expected heterozygosities ranged from 0.242 to 1.000 and from 0.504 to 0.945, respectively. ? Conclusions: The developed microsatellites will be useful for studying genetic diversity and population structure in S. superba.     

Characterization of microsatellite loci from Litsea hypophaea (Lauraceae), a tree endemic to Taiwan

? Premise of the study: Microsatellite primers were developed for the endemic tree Litsea hypophaea (Lauraceae) in Taiwan to investigate its genetic diversity and population genetic structure and to investigate species delimitation within Litsea. ? Methods and Results: Fifteen new simple sequence repeat markers were developed from L. hypophaea with a magnetic bead enrichment method. Most loci were also amplified from three closely related species, L. coreana, L. lii, and L. acutivena. The number of alleles and observed and expected heterozygosities across loci varied with a range of 1-25, 0.000-1.000, and 0.000-0.956, respectively. ? Conclusions: The application of these microsatellite markers of L. hypophaea provides a tool for understanding genetic diversity and population differentiation. In addition, interspecific amplification suggests that these markers will also be useful for species identification of related taxa within Litsea in Taiwan.     

Genetic diversity and differentiation of core vs. peripheral populations of eastern white cedar, Thuja occidentalis (Cupressaceae)

? Premise of the study: Geographically peripheral (marginal) populations are expected to have lower genetic diversity and higher genetic differentiation than geographically core (central) populations as a result of supposedly lower effective population size (N(e)) and higher genetic drift, founder effect, fragmentation, and isolation in peripheral than in core populations. Here we address this issue for a long-lived plant species, eastern white cedar (Thuja occidentalis). ? Methods: Genetic diversity and population structure of 13 natural populations of eastern white cedar from its Canadian eastern peripheral and core natural ranges in New Brunswick, Nova Scotia, and Prince Edward Island were studied using six nuclear microsatellite DNA markers. ? Key results: The core populations of eastern white cedar had significantly higher allelic diversity (mean A = 8.83, A(r) = 8.13, A(e) = 4.03) and N(e) (428) than the peripheral populations (A = 6.64, A(r) = 6.15, A(e) = 3.12, N(e) = 198). However, expected heterozygosity was similar in the core (H(e) = 0.64) and peripheral (H(e) = 0.60) populations. Genetic differentiation was significantly higher among the peripheral (F(ST) = 0.089) than among the core (F(ST) = 0.032) populations. No genetic differentiation (F(ST)/Φ(RT) = 0.000) was detected between core and peripheral regions. ? Conclusions: Peripheral populations have significantly lower N(e) and genetic diversity in terms of allelic diversity (richness) and significantly higher genetic differentiation than the core populations of eastern white cedar in its Canadian eastern range. However, core and peripheral populations have similar levels of expected heterozygosity. Implications for conservation of eastern white cedar genetic resources are discussed.     

Microsatellite primers in the endangered quillwort Isoetes hypsophila (Isoetaceae) and cross-amplification in I. sinensis

? Premise of the study: The first microsatellite primers were developed for Isoetes hypsophila, an endangered quillwort species endemic to the Qinghai-Tibetan Plateau in China, to further describe its genetic variability and population structure. We also examined their cross-amplification in a congeneric species, I. sinensis. ? Methods and Results: Using the Fast Isolation by AFLP of Sequences COntaining Repeats (FIASCO) protocol, nine microsatellite loci were isolated and characterized in 32 samples from four natural populations of I. hypsophila. The primers amplified di- and hexanucleotide repeats with three to 11 alleles per locus. Seven of nine primers were cross-amplified in I. sinensis with two to seven alleles per locus. ? Conclusion: The microsatellite loci primers will be useful for studies of genetic diversity and gene flow in natural populations of Isoetes species.     

Isolation of compound microsatellite markers for the endangered plant Neolitsea sericea (Lauraceae)

? Premise of the study: The development of compound microsatellite markers was conducted in Neolitsea sericea to investigate genetic diversity and population genetic structure of this endangered insular species. ? Methods and Results: Using the compound microsatellite marker technique, 10 compound microsatellite markers that were successfully amplified showed polymorphism when assessed in 55 individuals from two populations in East China and Japan. Overall, the number of alleles ranged from 3 to 17, with an average of 7.9 alleles per locus. In addition, these primers could be easily amplified in Neolitsea aurata var. paraciculata and N. aurata var. chekiangensis. ? Conclusions: The highly polymorphic markers developed and characterized in this study will be useful for population genetic studies of N. sericea.     

Development of microsatellite markers for the neotropical tree species Dipteryx alata (Fabaceae)

? Premise of the study: Microsatellite markers were developed for the population genetic analyses of the neotropical tree Dipteryx alata (Fabaceae). ? Methods and Results: Microsatellites were developed from a genomic shotgun library. Polymorphism at each microsatellite loci was analyzed based on 94 individuals from three populations. Eight loci amplified successfully and presented one to 10 alleles, and expected heterozygosities ranged from 0.097 to 0.862. Four loci also amplified in Pterodon emarginatus and presented similar polymorphism. ? Conclusion: The eight microsatellite primer pairs are potentially suitable for population genetic studies and successfully amplified in another Fabaceae species.     

Ten polymorphic microsatellite markers in Michelia maudiae (Magnoliaceae)

? Premise of the study: Michelia maudiae is a threatened species in the Magnoliaceae. Microsatellite markers were developed and characterized in M. maudiae for further investigation of its conservation genetics. ? Methods and Results: Microsatellite markers were developed in M. maudiae using the Fast Isolation by AFLP of Sequences Containing Repeats protocol. Ten polymorphic microsatellites were assessed in two populations of M. maudiae. The number of alleles detected per locus varied from 1 to 8. Observed and expected heterozygosities ranged from 0.000 to 0.792 and from 0.000 to 0.826, respectively. Six primer pairs showed transferability in the two related species Michelia foveolata and Michelia chapensis. ? Conclusions: This set of microsatellite markers provides a useful tool for future studies of the conservation genetics of M. maudiae and other congeneric species.     

Microsatellite primers for the endangered aquatic herb, Ottelia acuminata (Hydrocharitaceae)

? Premise of the study: Microsatellite primers were developed in the endangered aquatic herb, Ottelia acuminata, to characterize its genetic diversity and understand its population structure. ? Methods and Results: Eight polymorphic microsatellite markers were developed from two populations of O. acuminata in China. The number of alleles per locus ranged from one to 15; the observed and expected heterozygosities ranged from 0 to 0.885 and from 0 to 0.888, respectively, in the two populations. Selected loci also amplified successfully in O. sinensis. ? Conclusions: These microsatellite markers will facilitate further studies on the conservation genetics and evolutionary history of O. acuminata.     

Primers for 12 polymorphic microsatellite DNA loci from the guppy (Poecilia reticulata)

Twelve polymorphic microsatellite DNA loci were isolated from genomic guppy DNA. We assessed the level of genetic diversity for these loci using individuals from five native Trinidadian populations. All the loci were polymorphic although there were considerable differences among loci and populations in allele frequencies. Within populations, the number of alleles ranged from 1 to 22 and observed heterozygosities ranged from 0.000 to 0.990. Allele frequencies differed substantially between populations suggesting divergence.     

Development of polymorphic microsatellite markers in Camellia chekiangoleosa (Theaceae) using 454-ESTs

? Premise of the study: A set of microsatellite markers for Camellia chekiangoleosa was developed and characterized using 454 sequencing technology to study the population genetic structure and the diversity of germplasm collections. ? Methods and Results: Eighteen polymorphic microsatellite markers were identified and tested in 150 individuals from three natural populations of C. chekiangoleosa. Alleles numbered from two to seven, and the observed and expected heterozygosities ranged from 0.100 to 0.760 and 0.133 to 0.809, respectively. ? Conclusions: These markers will potentially be conducive to further genetic studies on C. chekiangoleosa.     

Development and characterisation of microsatellite markers for the medicinal plant Scutellaria baicalensis (Lamiaceae)

Scutellaria baicalensis is a popular medicinal plant that is on the verge of extinction due to uncontrolled harvesting, habitat destruction and deterioration of its ecosystem. We isolated and characterised 21 microsatellite loci in this species. Ninety-four individuals from six populations were used to test the polymorphism of the microsatellite loci. The number of alleles per locus ranged from 1 to 13, with a mean of 7.2. Observed and expected heterozygosities varied from 0.000 to 1.000 and 0.000 to 0.938, respectively. Among these new microsatellite markers, only two loci showed significant deviation from Hardy–Weinberg equilibrium. No locus pairs showed significant linkage disequilibrium. The 21 primer pairs were tested in other Scutellaria species. Most of these primer pairs worked successfully, except for Scut18. These new microsatellite markers could be applied to investigate the genetic diversity and population genetic structure of S. baicalensis and its closely related species.     

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.     

Genetic analysis of salt-marsh sedge Carex scabrifolia Steud. populations using newly developed microsatellite markers

Nine microsatellite loci were isolated and characterized from the clonal salt-marsh sedge Carex scabrifolia, and genetic diversities within four populations were analyzed. The number of alleles per locus ranged from 2 to 7, with an average of 4.7. The observed and expected heterozygosities ranged from 0.000 to 1.000 and 0.000 to 0.679, respectively. In two populations, almost all polymorphic loci showed a significant excess of heterozygotes due to their high clonal reproduction and low number of genotypes (genets) composing the populations. Thus, the number of identical genets varied greatly among populations and ranged from 1 to 28, irrespective of population size (i.e., population area and ramet number). When attempting to conserve and restore clonal plants such as C. scabrifolia, it is important to preserve sufficient genetic diversity within a population, which can be assessed using genetic markers such as the simple sequence repeat markers described here.     

Characterization of 14 microsatellite loci in a tropical palm, Attalea phalerata (Arecaceae)

? Premise of the study: We developed microsatellite primers for the widely distributed tropical palm Attalea phalerata for studies on the dispersal and spatial genetic structure of palm populations. ? Methods and Results: Fourteen di-, tri-, and tetra-nucleotide microsatellite primer pairs were identified. The number of alleles in the population tested ranged between 3 and 25, with a mean of 12.1. Ten microsatellite loci exhibited no significant deviations from Hardy-Weinberg Equilibrium or presence of null alleles, and their combined probability of exclusion was 0.998. ? Conclusions: These microsatellite loci will be useful in parentage analysis and population genetics studies of Attalea phalerata.     

Microsatellite primers for Halophila ovalis and cross-amplification in H. minor (Hydrocharitaceae)

?Premise of the study: Polymorphic microsatellite primers were developed in the seagrass Halophila ovalis to investigate genetic variation. ?Methods and Results: Ten polymorphic microsatellite loci were developed in Halophila ovalis. The number of alleles per locus ranged from 2 to 12 across 80 H. ovalis individuals. These loci were successfully amplified in H. minor, and four were monomorphic across 30 individuals. ?Conclusions: These results from four H. ovalis populations and one H. minor population show the broad utility of microsatellite loci in future studies of population genetics. Four distinct alleles were present in H. minor but absent in H. ovalis, indicating potential divergence between them.     

Chloroplast, mitochondrial, and nuclear microsatellites from the southern Appalachian hornwort, Nothoceros aenigmaticus (Dendrocerotaceae)

? Premise of the study: New microsatellite primers were developed for testing genetic differentiation within Nothoceros aenigmaticus and their potential use in other Nothoceros species. The microsatellites are designed to investigate partitioning of genetic variation in a taxon with a peculiar sex allopatry in the southern Appalachian Mountains and relationships with conspecific sexual populations from Mexico. ? Methods and Results: We used two methods for microsatellite development: an enriched library and second-generation shotgun sequence reads. From these two methods, a total of nine primer pairs were selected and tested on 89 southern Appalachian N. aenigmaticus accessions, nine Mexican accessions, and 16 N. vincentianus accessions. Three mitochondrial loci were recovered from the enriched library method and six loci from 454 shotgun sequencing: three were from the chloroplast and three from the nucleus. The primers amplified repeats with two to 20 alleles per locus. ? Conclusions: New microsatellite primers were developed for testing genetic differentiation within N. aenigmaticus and potentially for use in other Nothoceros species. We present one of the first reports of highly polymorphic mitochondrial microsatellites in plants.     

Development of microsatellite markers for Anadenanthera colubrina var. cebil (Fabaceae), a native tree from South America

? Premise of the study: Microsatellite primers were developed in the native legume tree Anadenanthera colubrina var. cebil to study the genetic diversity and genetic structure in natural populations in Argentina. ? Methods and Results: Nine microsatellite markers were identified using a genomic library enriched for tandemly repeated motifs, eight of which markers were polymorphic. The polymorphism of these markers was assessed by investigating 20 individuals for fragment polymorphism; three to 13 alleles were observed for each locus. Observed and expected heterozygosities ranged from 0.300 to 1.000 and from 0.463 to 0.900, respectively. ? Conclusions: These results confirm that these primers will be useful for investigating the genetic diversity and genetic structure of natural populations of A. colubrina var. cebil in future studies.     

Development of microsatellite markers in heterostylous Hedyotis chrysotricha (Rubiaceae)

? Premise of the study: Microsatellite primers were developed for a heterostylous herb, Hedyotis chrysotricha to investigate the effect of habitat fragmentation on its genetic diversity and population structure. ? Methods and Results: Twelve primer sets were developed and their polymorphisms were tested on 47 individuals from two island populations of H. chrysotricha in Thousand Island Lake of China. The number of alleles per locus ranged from five to 10, with an average of seven alleles. Expected heterozygosity per locus ranged from 0.284 to 0.821 and observed heterozygosity ranged from 0.191 to 0.851. ? Conclusions: We showed that all of the 12 microsatellite markers developed for H. chrysotricha are polymorphic within populations, which should provide a powerful tool for assessing population structure and genetic diversity across fragmented and continuous populations, and for studying the genetic effects of habitat fragmentation on this species.