Characterization of 10 microsatellite markers for the understorey Amazonian herb Heliconia acuminata

We characterized 10 microsatellite loci for the plant Heliconia acuminata from the Biological Dynamics of Forest Fragments Project (Manaus, Brazil). Markers were screened in 61 individuals from one population and were found to be polymorphic with an average of eight alleles per locus. We found moderate to high levels of polymorphic information content, and observed and expected heterozygosities. All 10 markers are suitable for spatial genetic structure and parentage analyses and will be used for understanding H. acuminata dynamics across a fragmented landscape.     

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.     

Isolation and characteristics of eight novel polymorphic microsatellite loci in Lippia alba (Verbenaceae)

? Premise of the study: A set of eight microsatellite (simple sequence repeat [SSR]) markers for Lippia alba, an important medicinal and cosmetic plant, was developed to aid studies of genetic diversity and to define efficient strategies for breeding programs. ? Methods and Results: Using a (CT)(8)- and (GT)(8)-enriched library, a total of 11 SSR loci were developed and optimized in L. alba. Of the 11 loci, eight were found to be polymorphic after screening 61 accessions from two populations. The parameters used to characterize loci were expected heterozygosity (H(e)) and number of alleles. A total of 44 alleles were identified, with an average of 5.5 alleles per loci, which were moderately to highly informative according to H(e). ? Conclusions: These new SSR markers have potential for informing genetic diversity, allele mining, and mapping studies and will be used to generate information for breeding programs of L. alba.     

Isolation and characterization of polymorphic microsatellite loci in Camellia nitidissima Chi (Theaceae)

? Premise of the study: Microsatellite markers were developed in Camellia nitidissima for further population genetic studies. ? Methods and Results: Eight microsatellite markers were newly developed from C. nitidissima and 7 were transferred from other Camellia species. Two to 13 alleles per locus were identified for these microsatellites. Observed and expected heterozygosities ranged from 0.040 to 0.909, and 0.184 to 0.916, respectively. Four loci showed a significant deviation from Hardy-Weinberg equilibrium and five locus pairs displayed linkage disequilibrium. ? Conclusions: These microsatellite markers will be useful to assess the genetic variation and genetic structure of C. nitidissima.     

Development and characterization of microsatellites in Torreya jackii (Taxaceae), an endangered species in China

? Premise of the study: Polymorphic microsatellite loci were developed in Torreya jackii, an endangered species in China, to provide markers for further studies on the genetic diversity of this species. ? Methods and Results: Eight polymorphic loci and one monomorphic locus were developed and characterized in four T. jackii populations (Xianju, Songyang, Pujiang, and Tonglu) from Zhejiang Province, China. The number of alleles per locus ranged from one to eight across 80 T. jackii individuals. At the eight polymorphic loci, the observed heterozygosity ranged from 0.150 to 1.000 and the expected heterozygosity ranged from 0.185 to 0.796. ? Conclusions: The microsatellite loci developed and characterized in this study will facilitate future analyses of the genetic diversity of T. jackii. Such information will aid in designing strategies to conserve this currently endangered species.     

Isolation and characterization of microsatellite markers for Thujopsis dolabrata var. hondai (Cupressaceae)1

? Premise of the study: Microsatellite markers were developed for the endemic Japanese species Thujopsis dolabrata var. hondai for studies on forest ecology and tree breeding. ? Methods and Results: We characterized 10 dinucleotide microsatellite loci by screening primers developed using a simple sequence repeat-enriched library. The number of alleles per locus ranged from eight to 44 with an average of 20.3. The observed and expected heterozygosities ranged from 0.326 to 0.854 and from 0.670 to 0.976, respectively. ? Conclusions: The development of these markers can be used to assess useful genetic information for ecological studies and tree breeding in T. dolabrata var. hondai.     

Nuclear microsatellite loci for Arabidopsis halleri (Brassicaceae), a model species to study plant adaptation to heavy metals

? Premise of the study: Arabidopsis halleri is a model species to study the adaptation of plants to soils contaminated by zinc, cadmium, and lead. To provide a neutral genetic background with which adaptive genetic markers could be compared, we developed highly polymorphic neutral microsatellite markers. ? Methods and Results: Using a microsatellite-enriched library method, we identified 120 microsatellite loci for quantitative trait locus (QTL) mapping analysis, of which eight primer pairs were developed in a single multiplex for population genetic studies. Analyses were performed on 508 individuals from 26 populations. All loci were polymorphic with six to 23 alleles per locus. Genetic diversity varied between 0.56 and 0.76. ? Conclusions: Our results demonstrated the value of these eight microsatellite markers to investigate neutral population genetic structure in A. halleri. To increase the resolution of population genetic analyses, we suggest adding them to the 11 markers previously developed independently.     

Development of microsatellite markers for Ophiocordyceps sinensis (Ophiocordycipitaceae) Using an ISSR-TAIL-PCR method

? Premise of the study: Microsatellite primers were developed for Ophiocordyceps sinensis, an endangered medicinal fungus endemic to the Tibetan Plateau, to investigate its genetic diversity and population structure. ? Methods and Results: An inter-simple sequence repeat (ISSR)-thermal asymmetric interlaced (TAIL)-PCR method was established to develop microsatellite markers. A total of 30 perfect and imperfect microsatellites were identified in 48 individuals of O. sinensis from five provinces within China representing different populations. Seventeen loci were polymorphic with two to four alleles per locus, while 13 were monomorphic. ? Conclusions: The results indicate that the microsatellite markers developed here may be used in studies of population genetics and conservation biology of O. sinensis. Furthermore, the ISSR-TAIL-PCR method is a simple strategy for microsatellite marker development.     

Development and characterization of microsatellite markers for Arenaria grandiflora L. (Caryophyllaceae)

Genomic libraries of Arenaria grandiflora enriched for di- and trinucleotide repeats were used for the development of novel microsatellite markers. The subset of 13 polymorphic markers was characterized on 40 individuals of A. grandiflora originating from lowland locations in France. The loci amplified 3 to 10 alleles per locus and expected heterozygosities ranged from 0.46 to 0.83. The newly developed markers will be used for population genetic studies and for assessing genetic composition of a restoration experiment of lowland A. grandiflora populations that are protected in France.     

Isolation and characterization of novel microsatellite markers for Avena sativa (Poaceae) (oat)

? Premise of the study: A new set of microsatellite primers was developed for Avena sativa and characterized to assess the level of genetic diversity among cultivars and wild genotypes. ? Methods and Results: Using an enrichment genomic library, 14 simple sequence repeat markers were identified. The loci of these markers were characterized and found to be polymorphic in size among 48 genotypes of oat from diverse geographical locations. The number of alleles per locus ranged from two to eight, while the observed heterozygosity ranged from 0.031 to 0.75. ? Conclusions: These newly identified microsatellite markers will facilitate genetic diversity studies, fingerprinting, and genetic mapping of oat. Moreover, these new primers for A. sativa will aid future studies of polyploidy and hybridization in other species in this genus.     

Development of microsatellite markers from Cercis chinensis (Fabaceae)

? Premise of the study: Microsatellite markers were developed to characterize the level of genetic diversity and population genetic structure of Cercis chinensis, a widely cultivated garden plant in China with congeneric species disjunctly distributed in East Asia, North America, and the Mediterranean. ? Methods and Results: Using the Fast Isolation by AFLP of Sequences COntaining repeats (FIASCO) protocol, eight microsatellite markers were developed in C. chinensis. Seven of the markers displayed polymorphism, with the number of alleles ranging from one to four in four populations of C. chinensis. Four to six microsatellite loci exhibited interspecific transferability in C. glabra, C. chuniana, and C. chingii. ? Conclusions: These are the first microsatellite markers developed for C. chinensis, which will be further used in investigation of population genetic structure and phylogeographic pattern of C. chinensis and its congeneric species.     

Isolation and characterization of microsatellite markers in an endangered species Dracaena cambodiana (Liliaceae)

?Premise of the study: The development of microsatellite primers in the endangered species Dracaena cambodiana will be the foundation for genetic and conservation studies of D. cambodiana and several Dracaena species. ?Methods and Results: A total of 26 microsatellite markers were developed in Chinese populations of D. cambodiana, using the Fast Isolation by AFLP of Sequences Containing Repeats (FIASCO) protocol. Among them, sixteen primer pairs generated polymorphic loci (fourteen of them successfully amplified in other four Dracaena species) and ten primer pairs produced monomorphic loci. ?Conclusions: These microsatellite markers could be used in the further investigation of population genetics of D. cambodiana and other Dracaena species.     

Microsatellite markers for population studies of Phytophthora megakarya (Pythiaceae), a cacao pathogen in Africa

? Premise of the study: Phytophthora megakarya is the agent of black pod disease of cacao and is the main pathogen of this crop in Africa. Population genetic studies are required to investigate how this pathogen emerged. To this end, we developed 12 novel polymorphic microsatellite markers for P. megakarya. ? Methods and Results: Microsatellite sequences were obtained by pyrosequencing of multiplex-enriched libraries. Candidate loci with di- or trinucleotide motifs were selected, and primer pairs were tested with nine P. megakarya isolates. The 12 most polymorphic and unambiguous loci were selected to develop three multiplex PCR pools. The total number of alleles varied from two to nine, depending on loci, and higher than expected heterozygosity was observed. ? Conclusions: These markers were used for population genetic studies of P. megakarya in Cameroon and for comparison with reference strains from West Africa. This is the first time that microsatellite markers have been developed for P. megakarya.     

Development and characterization of 38 polymorphic microsatellite markers from an economically important fruit tree, the Indian jujube

? Premise of the study: A total of 38 polymorphic microsatellite loci of the Indian jujube (Ziziphus mauritiana), an economically important fruit tree, were developed to evaluate genetic diversity and aid in the identification of cultivars. ? Methods and Results: The 38 microsatellite markers were isolated from the Indian jujube using a magnetic bead enrichment method, and polymorphisms were identified in 24 Indian jujube cultivars. The number of alleles ranged from two to 13, with expected heterozygosity ranging from 0.261 to 0.898. The polymorphism information content ranged from 0.248 to 0.889, with a mean of 0.616. Of these 38 simple sequence repeat loci, 20 loci from Z. jujuba (Chinese jujube) were successfully amplified using the simple sequence repeat primer sets. ? Conclusions: These polymorphic loci should be useful in further studies of the genetic diversity and the identification of cultivars of both the Indian jujube and the Chinese jujube.     

Isolation and characterization of microsatellite markers in Acca sellowiana (Berg) Burret

Acca sellowiana has commercial potential because of the quality and the unique flavor of its fruit. Conservation of natural populations and management of breeding programmes would benefit from the availability of molecular markers that could be used to characterize levels and distribution of genetic variability. Thus, 13 microsatellite markers were developed from an enriched genomic library of A. sellowiana. They were characterized using 40 samples. The expected and observed heterozygosities ranged from 0.513 to 0.913 and from 0.200 to 0.889, respectively. These are the first microsatellite loci characterized from A. sellowiana that will contribute to improve researches on the genetic conservation, characterization and breeding.     

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 development for an endangered riparian inhabitant, Lilaeopsis schaffneriana subsp. recurva (Apiaceae)

? Premise of the study: Microsatellite markers were developed and characterized to evaluate genetic diversity and population structure in Lilaeopsis schaffneriana subsp. recurva, an endangered species endemic to wetlands dispersed throughout southeastern Arizona, USA, and northern Sonora, Mexico. ? Methods and Results: Eight loci (one of which was monomorphic) were developed and characterized in 48 individuals from two populations. The total number of alleles was 35, ranging from one to 10 per locus. Many of the primers amplified in L. carolinensis, L. chinensis, L. masonii, L. occidentalis, L. schaffneriana subsp. schaffneriana, Oxypolis fendleri, and Eryngium lemmonii. ? Conclusions: Development of these novel microsatellite loci will facilitate a deeper understanding of genetic diversity, mode of reproduction, and population structure not only in L. schaffneriana subsp. recurva, but also in apiaceous relatives.     

Isolation and Characterization of Microsatellite Loci for Striped Bass (Morone saxatilis)

Genetic variation has been difficult to detect in striped bass (Morone saxatilis). Therefore, we identified and characterized 13 microsatellite loci to provide additional genetic markers for striped bass. Microsatellites were identified by screening a striped bass genomic library or by using primers developed for European sea bass (Dicentrarchus labrax) microsatellite loci. We found that 6 of the 13 microsatellite loci were polymorphic in DNA samples obtained from wild populations of striped bass. The number of alleles per locus varied from 3 to 12, and the observed heterozygosities ranged from 0.55 to 0.78. These results indicate that microsatellite loci provide more alleles and higher heterozygosities than other genetic markers developed for striped bass. Received November 9, 1999; accepted February 11, 2000.     

Isolation and characterization of a first set of polymorphic microsatellite markers in saffron, Crocus sativus (Iridaceae)

? Premise of the study: Twelve novel polymorphic microsatellite loci were developed and characterized from a repeat-enriched genomic library of Crocus sativus to study population and conservation genetics of this economically and medically important species. ? Methods and Results: The microsatellite loci were isolated using a modified Fast Isolation by AFLP of Sequences COntaining repeats (FIASCO) method. The average number of alleles per locus was 2.6. The observed and expected heterozygosities varied from 0.07 to 0.92 and 0.1 to 0.58, respectively. Polymorphic information content value ranged from 0.09 to 0.55 with an average of 0.34. Four out of twelve loci showed significant departures from Hardy-Weinberg equilibrium. ? Conclusions: The microsatellite markers reported here will be useful for evaluating genetic diversity and will likely serve as an ideal resource for use in marker-assisted breeding programs, germplasm analysis, and varietal identification.