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.     

Development and characterization of microsatellite markers for Berberis thunbergii (Berberidaceae)

? Premise of the study: Microsatellite markers were isolated and characterized in Berberis thunbergii, an invasive and ornamental shrub in the eastern United States, to assess genetic diversity among populations and potentially identify horticultural cultivars. ? Methods and Results: A total of 12 loci were identified for the species. Eight of the loci were polymorphic and were screened in 24 individuals from two native (Tochigi and Ibaraki prefectures, Japan) and one invasive (Connecticut, USA) population and 21 horticultural cultivars. The number of alleles per locus ranged from three to seven, and observed heterozygosity ranged from 0.048 to 0.636. ? Conclusions: These new markers will provide tools for examining genetic relatedness of B. thunbergii plants in the native and invasive range, including phylogeographic studies and assessment of rapid evolution in the invasive range. These markers may also provide tools for examining hybridization with other related species in the invasive range.     

PERMANENT GENETIC RESOURCES: Development of microsatellite markers for two nonviviparous mangrove species, Acanthus ilicifolius and Lumnitzera racemosa

Eight and nine of microsatellite loci were isolated from two nonviviparous mangrove species, Acanthus ilicifolius and Lumnitzera racemosa, respectively. The number of alleles per locus ranged from two to eight in A. ilicifolius and two to nine in L. racemosa. The observed heterozygosities ranged from 0.200 to 0.875 in A. ilicifolius and from 0.025 to 0.350 in L. racemosa. These loci would be effective for analysing genetic diversity and population genetic structure of these two mangrove species.     

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.     

Isolation and characterization of 15 polymorphic microsatellite DNA loci from Argyrosomus japonicus (mulloway), a new aquaculture species in Australia

Fifteen microsatellite loci were isolated for population genetic studies of mulloway (Argyrosomus japonicus), a commercial/recreational fish species in Southern Australia. A genomic library was screened randomly for di- tri- and tetranucleotide repeats. Fifteen microsatellite marker loci were developed that were highly polymorphic (allele number ranged from four to 18). Observed and expected heterozygosities ranged from 0.17 to 1 and from 0.27 to 0.91, respectively. These markers have proven useful for estimating genetic variation and for evaluating population structure across the species' natural distribution. They also provide powerful tools for optimizing hatchery practices to conserve genetic diversity.     

Microsatellite markers for Saussurea gnaphalodes (Asteraceae), a native Himalayan mountain species

? Premise of the study: Microsatellite markers were developed in Saussurea gnaphalodes to investigate its genetic variation and population structure. ? Methods and Results: Using the combined biotin capture method, 46 microsatellite primer sets were isolated and characterized across 48 S. gnaphalodes individuals from three Tibetan populations. Seventeen of these markers showed polymorphism, and the number of alleles ranged from two to 17. The observed and expected heterozygosities per population ranged from 0 to 0.938 and from 0 to 0.905, respectively. ? Conclusions: These markers provide a useful tool to investigate the genetic diversity and population structure of S. gnaphalodes, and to facilitate further studies on conservation and utilization.     

Development of microsatellite markers for Dimorphandra mollis (Leguminosae), a widespread tree from the Brazilian cerrado

? Premise of the study: Microsatellite markers were developed for Dimorphandra mollis (Leguminosae), a widespread tree in the Brazilian cerrado (a savanna-like vegetation). ? Methods and Results: Microsatellite markers were developed from an enriched library. The analyses of polymorphism were based on 56 individuals from three populations. Nine microsatellite loci were polymorphic, with the number of alleles per locus ranging from three to 10 across populations. The observed and expected heterozygosities per locus and population ranged from 0.062 to 0.850 and from 0.062 to 0.832, respectively. ? Conclusions: These microsatellites provide an efficient tool for population genetics studies and will be used to assess the genetic diversity and spatial genetic structure of D. mollis.     

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 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.     

Generation and characterization of 11 novel est derived microsatellites from Vicia faba (Fabaceae)

? Premise of the study: Simple sequence repeat (SSR) markers were developed for faba bean using expressed sequence tags (ESTs) from the NCBI database to study for genetic diversity. ? Methods and Results: A total of 11 novel EST-SSR loci were generated and characterized when tested on four populations of 29 faba bean individuals from China and Europe. The number of alleles (A) ranged from 1 to 3 in each population, and observed heterozygosity (H(O)) and expected heterozygosity (H(E)) ranged from 0 to 0.5000 and 0.6400, respectively. Furthermore, transferable analysis revealed that eight of these loci (72.73%) amplified in Pisum sativum L., six of which (75.00%) detected polymorphism. ? Conclusions: The developed markers in this study will provide valuable tools for genetic diversity, resource conservation, genetic mapping, and marker-assisted breeding of faba bean in the future.     

Development and characterization of microsatellite loci for two Caribbean Heliconia (Heliconiaceae: H. bihai and H. caribaea)

? Premise of the study: Microsatellite loci were developed to characterize genetic variation and population subdivision in Heliconia bihai and H. caribaea from the Caribbean Islands. ? Methods and Results: A total of 13 new microsatellite markers were developed and characterized in the two Caribbean heliconias. Di-, tri-, and tetranucleotide repeats were identified with one to 17 alleles per locus, and the observed heterozygosity ranged from 0.13 to 0.87. Additionally, cross-species amplification was successful in eight out of 13 loci. ? Conclusions: The microsatellite loci developed have discriminatory potential to be used in genetic characterizations of Caribbean Heliconia. Both H. bihai and H. caribaea are known to have adaptive interactions with their hummingbird pollinators, and the characterized microsatellite markers will be used to study mating system, genetic structure, and phylogeographic patterns in Caribbean Heliconia.     

Isolation and characterization of microsatellite markers for Plathymenia reticulata (Fabaceae)

? Premise of the study: Microsatellite loci were isolated and characterized for use in population genetic studies of Plathymenia reticulata (Fabaceae), a tropical tree widespread in the Atlantic Forest and cerrado biomes of South America. ? Methods and Results: Nine microsatellite markers were developed using a simple sequence repeat-enriched library. Polymorphism was analyzed in 51 individuals from two populations. All loci were polymorphic, with the number of alleles per loci ranging from five to 15 (mean number of alleles: 10.22). Observed and expected heterozygosities per loci and population ranged from 0.313 to 1.000 and 0.280 to 0.869, respectively. ? Conclusions: These highly informative loci are potentially useful to estimate population genetic structure and to understand evolutionary processes and taxonomy of the species.     

Isolation and characterization of 50 nuclear microsatellite markers for Cathaya argyrophylla, a Chinese endemic conifer

? Premise of the study: Microsatellite primers were developed for the endangered Cathaya argyrophylla (Pinaceae) to investigate its genetic diversity and population genetic structure, as well as its evolutionary history. ? Methods and Results: Fifty dinucleotide microsatellite loci were identified in two populations. The number of alleles per locus ranged from 1 to 6, with a mean of 2.84. The observed and expected heterozygosities ranged from 0 to 0.889 and from 0 to 0.779, respectively. ? Conclusions: These markers will facilitate further studies on the population genetics and evolutionary history of Cathaya argyrophylla.     

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.     

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.     

New microsatellite loci for Narcissus papyraceus (Amarillydaceae) and cross-amplification in other congeneric species

? Premise of the study: Microsatellite loci from a genomic library of the species Narcissus papyraceus were optimized and characterized for studies of population genetics. ? Methods and Results: Eleven markers that were successfully amplified showed polymorphism when tested on 50 individuals from two populations in southern Spain and northern Morocco. Overall, the number of alleles per locus ranged between 4 and 15. Between 8 and 11 loci successfully amplified in other eight Narcissus species. ? Conclusions: These markers will enable genetic diversity studies of N. papyraceus across its distribution range and conduct paternity analyses among individuals differing in flower morphology.     

Isolation and characterization of 10 SSR markers of Momordica charantia (Cucurbitaceae)

? Premise of the study: Microsatellite markers were isolated and characterized from the genome of Momordica charantia (bitter melon) to be applied in studies of genetic diversity and population structure. ? Methods and Results: Twenty-five microsatellite loci were isolated from the genome of bitter melon using the Fast Isolation by AFLP of Sequences COntaining Repeats (FIASCO) method. Ten loci were polymorphic, and the number of alleles per locus ranged from three to seven, with the observed heterozygosity ranging from 0.46 to 0.65. The markers also amplified successfully in the related species M. cochinchinensis and Cucurbita pepo. ? Conclusions: These markers will have potential utility for applications in genetic diversity evaluation, molecular fingerprinting, identification, comparative genomics analysis, and genetic mapping in Momordica species, as well as in C. pepo.     

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.     

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 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.