Development of microsatellite markers for Anadenanthera colubrina (Leguminosae), a neotropical tree species

? Premise of the study: We developed and characterized nuclear microsatellite markers for Anadenanthera colubrina, a tropical tree species widely distributed in South America. ? Methods and Results: Leaf samples of mature A. colubrina trees, popularly called "angico," were collected from an area that is greatly impacted by agricultural practices in the region of Ribeir?o Preto in S?o Paulo State in southeastern Brazil. Twenty simple sequence repeat (SSR) markers were developed, 14 of which had polymorphic loci. A total of 96 alleles were detected with an average of 6.86 alleles per polymorphic locus. The expected heterozygosity, calculated at polymorphic loci, ranged from 0.18 to 0.83. Finally, we demonstrated that 18 loci were cross-amplified in A. peregrina. ? Conclusions: A total of 14 polymorphic markers suggest a high potential for genetic diversity, gene flow, and mating system analyses in A. colubrina.     

Development of microsatellite primers of the largest seagrass, Enhalus acoroides (Hydrocharitaceae)

? Premise of the study: Microsatellite primers were developed for the seagrass Enhalus acoroides to investigate genetic variation and identify clonal structure. ? Methods and Results: Four polymorphic loci and 32 monomorphic loci were developed in E. acoroides. Two to four alleles per locus were observed at the polymorphic loci across 60 individuals of two E. acoroides populations. The observed and expected heterozygosities within populations ranged from 0.100 to 0.5667 and from 0.0977 to 0.5079, respectively. ? Conclusions: Our study revealed very low polymorphism in E. acoroides, even at the polymorphic loci. Nevertheless, these primers are a useful tool to study genetic variation, clonal structure, and mating system.     

Isolation of novel microsatellites from Jatropha curcas L. and their cross-species amplification

Jatropha curcas L., a member of the Euphorbiaceae, is widely distributed in different parts of the globe. In the present study, 12 microsatellites were isolated from J. curcas and their cross-species amplification was checked in six species of genus Jatropha. Within J. curcas, observed and expected heterozygosities ranged from 0.94 to 0.54 and from 0.95 to 0.56, respectively. Of the 12 loci, five showed significant deviation from Hardy-Weinberg equilibrium. There was no significant linkage disequilibrium detected between any of the loci. The markers isolated in the present investigation will be useful for assessing the population diversity and genetic structure of J. curcas and also in other species of Jatropha.     

Nuclear and chloroplast SSR markers in Paeonia delavayi (Paeoniaceae) and cross-species amplification in P. ludlowii

? Premise of the study: Microsatellite primers were developed for Paeonia delavayi and P. ludlowii (Paeoniaceae) to study their population genetics and phytogeography. ? Methods and Results: Nine polymorphic nuclear microsatellite loci were isolated from an enriched library of P. delavayi and primers were designed. The number of alleles per locus ranged from two to 16; the observed and expected heterozygosities ranged from 0.014 to 0.687 and 0.042 to 0.875, respectively. Six polymorphic chloroplast microsatellite loci were identified in P. delavayi and primers were provided. The number of alleles per locus ranged from two to six and the polymorphic information content ranged from 0.08 to 0.716. Both nuclear and chloroplast primers were successfully applicable to P. ludlowii. ? Conclusions: The markers developed here will facilitate analyses of genetic diversity, population genetic structure, phytogeographical patterns, and conservation for P. delavayi and P. ludlowii.     

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.     

西南地区麻疯树天然种群遗传多样性的等位酶变异

为了揭示麻疯树(Jatropha curcas)天然种群的遗传多样性和遗传结构, 采用聚苯烯酰胺凝胶垂直平板电泳技术, 对采自四川、云南、贵州3个省的10个麻疯树天然种群的叶片样本进行了同工酶分析。7个酶系统10个位点的检测结果表明: 麻疯树种群水平上的遗传多样性较高, 每位点平均等位基因数为2.428 6, 多态位点百分率为97.14%, 平均期望杂合度为0.396 4。种群间遗传分化系数为0.041 3, 种群间总的基因流较高, 为5.808 9, 种群间遗传一致度较高(Shannon信息指数为0.921 7- 0.995 3)。非加权类平均法(UPGMA)聚类结果显示, 10个种群的遗传距离与地理距离相关性不显著。麻疯树天然种群具有较低程度的遗传分化、较高的基因流, 种内及种群内多样性丰富, 这为麻疯树优良品种的选育提供了良好的遗传基础。     

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.     

Development of microsatellite markers for Qualea grandiflora (Vochysiaceae), a typical species of the Brazilian cerrado

? Premise of the study: Microsatellite primers were developed to investigate genetic diversity and population structure of Qualea grandiflora, a typical species of the Brazilian cerrado. ? Methods and Results: Eight microsatellite loci were isolated using an enrichment cloning protocol. These loci were tested on a population of 110 individuals of Q. grandiflora collected from a cerrado fragment in S?o Paulo State, Brazil. The loci polymorphism ranges from seven to 19 alleles and the average heterozygosity value is 0.568, while the average polymorphic information content is 0.799. ? Conclusions: The developed markers were found to be highly polymorphic, indicating their applicability to studies of population genetic diversity in Q. grandiflora.     

Development of microsatellite markers in Byrsonima crassifolia (Malpighiaceae)

? Premise of the study: We developed and characterized microsatellite markers for Byrsonima crassifolia (Malpighiaceae), a widely distributed neotropical fruit tree. ? Methods and Results: Eight polymorphic and two monomorphic microsatellite loci were identified and screened in 60 samples from four geographically disparate populations (Bolivia, Brazil, Mexico, and Panama). Each locus exhibited between two and 11 alleles. Expected heterozygosity ranged from 0 to 0.839. All loci amplify in the congeners B. variabilis and B. basiloba, four amplify in B. bucidaefolia, and seven amplify in B. variabilis, although levels of polymorphism have not been assessed. ? Conclusions: These loci will provide novel tools for comparing genetic diversity present in cultivated and noncultivated populations of B. crassifolia throughout its range, and may prove valuable in related species.     

Cross-species amplification and optimization of microsatellite markers for use in six Neotropical parrots

Short amplicon primers were redesigned for 17 microsatellite loci developed in St. Vincent's Amazon and six loci developed in blue-and-yellow macaw and tested using six species of Neotropical parrot. Polymorphism was observed at 12 loci in blue-and-yellow macaw, 10 in red-and-green macaw, 11 in scarlet macaw, 10 in chestnut-fronted macaw, 11 in red-bellied macaw and 16 in mealy parrot. Number of alleles per locus ranged from two to 23 and expected heterozygosity ranged from 0.05 to 0.95. The resulting multiplexed loci will be useful in evaluating genetic diversity, genetic structure and mating system in Neotropical parrots.     

Isolation and characterization of microsatellite loci in Schizolobium parahyba (Leguminosae)

Primer sequences for 16 microsatellite loci were developed from Schizolobium parahyba, a tropical tree species. Twelve loci were found to be polymorphic after screening diversity in individuals from Belize. A total of 39 alleles were found at nine loci. The markers are invaluable tools for studying the population genetics and mating system of the species.     

Use of microsatellites to evaluate genetic diversity and species relationships in the genus Lycopersicon

In order to determine how informative a set of microsatellites from tomato is across the genus Lycopersicon, 17 microsatellite loci, derived from regions in and around genes, were tested on 31 accessions comprising the nine species of the genus. The microsatellite polymorphisms were used to estimate the distribution of diversity throughout the genus and to evaluate the efficacy of microsatellites for establishing species relationships in comparison with existing phylogeny reconstructions. Gene diversity and genetic distances were calculated. A high level of polymorphism was found, as well as a large number of alleles unique for species. The level of polymorphism detected with the microsatellite loci within and among species was highly correlated with the respective mating systems, cross-pollinating species having a significantly higher gene diversity compared to self-pollinating species. In general, microsatellite-based trees were consistent with a published RFLP-based dendrogram as well as with a published classification based on morphology and the mating system. A tree constructed with low-polymorphic loci (gene diversity <0.245) was shown to represent a more-reliable topology than a tree constructed with more-highly polymorphic loci. Received: 19 February 2001 / Accepted: 26 March 2001     

Development of novel chloroplast microsatellite markers for Miscanthus species (Poaceae)

? Premise of the study: A set of novel chloroplast microsatellite markers (cpSSRs) was developed for the bioenergy crop Miscanthus, and their utility in cross-species amplification was evaluated. ? Methods and Results: Twenty-eight novel primers flanking cpSSR loci were designed from a complete chloroplast genome sequence of Saccharum officinarum, a species closely related to Miscanthus. These primers were then tested on eight Miscanthus species, among which 16 cpSSR loci were found to be polymorphic. The number of alleles per polymorphic locus ranged from two to seven, with an average 3.94 alleles. ? Conclusions: These cpSSR markers can be applied to all Miscanthus species and will be useful for studying Miscanthus population structure, diversity, and phylogeography.     

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.     

Development of microsatellite markers in Lupinus luteus (Fabaceae) and cross-species amplification in other lupine species

? Premise of the study: Microsatellite primers were developed in Lupinus luteus L., an emerging temperate protein crop, to investigate genetic diversity, population structure, and to facilitate the generation of better yellow lupine varieties. ? Methods and Results: Thirteen polymorphic primer sets were evaluated in a European and Eastern European accession collection of L. luteus. The primers amplified di-, tri-, and tetranucleotide repeats with 2-4 alleles per locus. These revealed a moderate to low level of genetic variation, as indicated by an average observed heterozygosity of 0.0126. Select loci also amplified successfully in the closely related species L. hispanicus Boiss. & Reut. and in the New World species L. mutabilis Sweet. ? Conclusions: These results indicate the utility of primers for the study of genetic diversity across L. luteus populations and related lupine species. The use of these microsatellite markers will facilitate the implementation of several molecular breeding strategies in yellow lupine.     

Characterization of microsatellite loci in Festuca gautieri (Poaceae) and transferability to F. eskia and F. xpicoeuropeana

? Premise of the study: Enriched genomic libraries were used to isolate and characterize microsatellite loci in Festuca gautieri, an important plant component of subalpine calcareous grasslands of the eastern Iberian Peninsula, the Pyrenees, and the Cantabrian Mountains. Microsatellites were required to investigate landscape genetics across its distribution range and at a narrower geographical scale within the Ordesa y Monte Perdido, Aigüestortes, and Picos de Europa Spanish national parks. ? Methods and Results: Ten polymorphic microsatellite loci were characterized. They amplified a total of 116 alleles in a sample of 30 individuals of F. gautieri, showing high levels of genetic diversity (expected heterozygosity = 0.821). Cross-species transferability to two other close congeners, F. eskia and F ×picoeuropeana, increased the total number of alleles to 137. These taxa showed lower numbers of alleles but similar levels of genetic diversity to F. gautieri. ? Conclusions: These microsatellite primers will be useful in population and landscape genetics and in establishing conservation strategies for these characteristic elements of subalpine pastures.     

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.     

Isolation and characterization of microsatellite loci in Santalum austrocaledonicum,Santalaceae

The forest tree Santalum austrocaledonicum is endemic to the archipelagos of New Caledonia and Vanuatu, and is threatened by the reduction of the populations due to exploitation. In order to investigate the genetic diversity and structure of this species, we developed eight pairs of primers for nuclear microsatellites. These loci were polymorphic in all the populations, with a mean of three to 33 alleles per locus.     

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.     

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.