Isolation and characterization of microsatellite markers for Bertholletia excelsa (Lecythidaceae) population genetic analysis.

Seven polymorphic microsatellite markers were developed and validated for Bertholletia excelsa (Brazil nut tree) population genetic studies. This species is a widespread monotypic Amazonian tree with high non-timber economic value. Unfortunately, Brazil nut production is currently less than 25% of historical production levels, because of extensive deforestation. All pairs of primers produced clearly interpretable and polymorphic bands. No linkage disequilibrium was observed in an analysis of 46 individuals from one population, three to seven alleles per locus were observed; the expected heterozygosity ranged from 0.378 to 0.978, with significant heterozygote excess for four loci. An analysis of individuals from two populations showed private alleles at all loci. These primer pairs will be useful for population studies, especially for comparing samples from different parts of the Amazon forest.

Diversity and genetic structure among subpopulations of Gossypium mustelinum (Malvaceae).

Gossypium mustelinum is the only cotton species native to Brazil; it is endemic to the semi-arid region of the northeast. The populations are found near perennial and semi-perennial sources of water, such as ponds or pools in intermittent streams. Problems with in situ conservation derive from human interference in its habitat, mainly because of excessive cattle grazing and deforestation. Establishing efficient strategies for in situ conservation requires knowledge of the genetic structure of the populations. We evaluated the structure and genetic variability of populations of G. mustelinum in the Tocó and Capivara Rivers (State of Bahia). Two hundred and eighteen mature G. mustelinum plants were genotyped with SSR markers. The molecular data were used to estimate the allelic frequencies, the heterozygosity, the F statistics, and the genetic distance among the populations and among individuals. We found high genetic diversity among the populations. The FST indexes for each population were also high and strongly correlated with physical distance. The high estimated level of endogamy and the low observed heterozygosity are indicative that the populations reproduce mainly by self-fertilization and crosses between related individuals. Consequently, strategies for in situ preservation should include at least three occurrence sites of G. mustelinum from each population. For ex situ conservation, the collections should include as many sites as possible.

Morphological and molecular characteristics do not confirm popular classification of the Brazil nut tree in Acre, Brazil.

In the State of Acre, the Brazil nut tree, Bertholletia excelsa (Lecythidaceae), is classified by the local population into two types according to morphological characteristics, including color and quality of wood, shape of the trunk and crown, and fruit production. We examined the reliability of this classification by comparing morphological and molecular data of four populations of Brazil nut trees from Vale do Rio Acre in the Brazilian Amazon. For the morphological analysis, we evaluated qualitative and quantitative information of the trees, fruits, and seeds. The molecular analysis was performed using RAPD and ISSR markers, with cluster analysis. Significant differences were found between the two types of Brazil nut trees for the characters diameter at breast height, fruit yield, fruit size, and number of seeds per fruit. Despite the significant correlation between the morphological characteristics and the popular classification, we observed all possible combinations of morphological characteristics in both types of Brazil nut trees. In some individuals, the classification did not correspond to any of the characteristics. The results obtained with molecular markers showed that the two locally classified types of Brazil nut trees did not differ genetically, indicating that there is no consistent separation between them.

Development and characterization of DNA microsatellite primers for buriti (Mauritia flexuosa L.f.).

Mauritia flexuosa L. (Arecaceae) is a palm tree species known as buriti that occurs in the Cerrado biome. It is characteristic of the vereda, a typical ecosystem of central Brazil. In this phytophysiognomy, M. flexuosa and other groups of arboreal-herbaceous species develop in open fields with very humid soils. M. flexuosa can be found in forest borders and is a palm tree with a wide distribution in South America (Brazil, Colombia, Venezuela, French Guyana Ecuador, Peru, and Bolivia). The main objectives of this study were to develop simple sequence repeat marker-enriched libraries and to characterize these loci in buriti palm to facilitate future population studies. A total of 40 sequences derived from the microsatellite-enriched libraries were selected for primer design. The optimization results showed that 9 primer pairs could successfully amplify polymorphic target fragments of the expected sizes. The data also show that the described primers can be used in population genetic studies in M. flexuosa to obtain information that will inform conservation and management strategies.

Permanent genetic resources added to molecular ecology resources database 1 October 2012-30 November 2012.

This article documents the addition of 153 microsatellite marker loci to the Molecular Ecology Resources Database. Loci were developed for the following species: Brassica oleracea, Brycon amazonicus, Dimorphandra wilsonii, Eupallasella percnurus, Helleborus foetidus, Ipomoea purpurea, Phrynops geoffroanus, Prochilodus argenteus, Pyura sp., Sylvia atricapilla, Teratosphaeria suttonii, Trialeurodes vaporariorum and Trypanosoma brucei. These loci were cross-tested on the following species: Dimorphandra coccicinea, Dimorphandra cuprea, Dimorphandra gardneriana, Dimorphandra jorgei, Dimorphandra macrostachya, Dimorphandra mollis, Dimorphandra parviflora and Dimorphandra pennigera.

Permanent Genetic Resources added to Molecular Ecology Resources Database 1 June 2010 - 31 July 2010.

This article documents the addition of 205 microsatellite marker loci to the Molecular Ecology Resources Database. Loci were developed for the following species: Bagassa guianensis, Bulweria bulwerii, Camelus bactrianus, Chaenogobius annularis, Creontiades dilutus, Diachasmimorpha tryoni, Dioscorea alata, Euhrychiopsis lecontei, Gmelina arborea, Haliotis discus hannai, Hirtella physophora, Melanaphis sacchari, Munida isos, Thaumastocoris peregrinus and Tuberolachnus salignus. These loci were cross-tested on the following species: Halobaena caerulea, Procellaria aequinoctialis, Oceanodroma monteiroi, Camelus ferus, Creontiades pacificus, Dioscorea rotundata, Dioscorea praehensilis, Dioscorea abyssinica, Dioscorea nummularia, Dioscorea transversa, Dioscorea esculenta, Dioscorea pentaphylla, Dioscorea trifida, Hirtella bicornis, Hirtella glandulosa, Licania alba, Licania canescens, Licania membranaceae, Couepia guianensis and 7 undescribed Thaumastocoris species.

Isolation of polymorphic microsatellite markers for the tetraploid Dipteryx odorata, an intensely exploited Amazonian tree species.

Dipteryx odorata is an intensely exploited Amazonian tree legume. Microsatellite markers were developed to study the genetic structure, gene flow and reproductive biology of D. odorata. Eight highly polymorphic microsatellite markers were isolated from enriched repeat libraries screened for microsatellite repeats. An average of 16 alleles and 0.964 phenotype diversity per locus were found in 76 individuals from the Tapajos National Forest, in the state of Pará in the Brazilian Amazon.

Eight variable microsatellite loci for a Neotropical tree, Jacaranda copaia (Aubl.) D.Don (Bignoniaceae).

The Dendrogene Project (Genetic Conservation within Managed Forests in Amazonia) aims to understand the genetic and ecological processes that underpin tree species survival and in particular their response to forest management regimes. As part of the project, we developed eight microsatellite markers for Jacaranda copaia to be used for genetic structure, gene flow and reproductive biology studies. Polymorphism was evaluated using 96 adult trees from the Tapajos National Forest in the Eastern Brazilian Amazon. An average of 22 alleles per locus were detected, with expected heterozygosity ranging from 0.731 to 0.94.

Isolation and characterization of microsatellite loci for Hymenaea courbaril and transferability to Hymenaea stigonocarpa, two tropical timber species.

Hymenaea courbaril is a tropical timber species, intensely exploited and found in the Amazon, Atlantic Forest and Brazilian Cerrado biome. Nine highly polymorphic microsatellite loci were developed from a genomic library enriched for AG/TC repeats. In a total of 41 individuals, from two natural populations, seven to 13 alleles per locus were detected and expected heterozygosity ranged from 0.75 to 0.90. Seven loci were effectively transferred to Hymenaea stigonocarpa. High levels of polymorphism make the present primers useful for population genetic studies and are a powerful tool to investigate mating system, gene flow and spatial genetic structure.

Development of microsatellite markers in Annona crassiflora Mart., a Brazilian Cerrado fruit tree species.

Annona crassiflora Mart. (Annonaceae) is a native fruit species of the region of Brazilian Cerrado with a high agronomic potential, although without any traces of domestication. A set of 10 microsatellite primer pairs was developed from an enriched genome library (TC13). An average of 19.3 alleles per locus was detected. Observed heterozygosity estimates were consistently lower than those obtained for gene diversity, evidencing a departure from Hardy-Weinberg expected proportions. The reported set of markers showed to be highly informative and constitutes a powerful tool for the development of genetic characterization studies in A. crassiflora.

Impact of selective logging on inbreeding and gene dispersal in an Amazonian tree population of Carapa guianensis Aubl.

Selective logging may impact patterns of genetic diversity within populations of harvested forest tree species by increasing distances separating conspecific trees, and modifying physical and biotic features of the forest habitat. We measured levels of gene diversity, inbreeding, pollen dispersal and spatial genetic structure (SGS) of an Amazonian insect-pollinated Carapa guianensis population before and after commercial selective logging. Similar levels of gene diversity and allelic richness were found before and after logging in both the adult and the seed generations. Pre- and post-harvest outcrossing rates were high, and not significantly different from one another. We found no significant levels of biparental inbreeding either before or after logging. Low levels of pollen pool differentiation were found, and the pre- vs. post-harvest difference was not significant. Pollen dispersal distance estimates averaged between 75 m and 265 m before logging, and between 76 m and 268 m after logging, depending on the value of tree density and the dispersal model used. There were weak and similar levels of differentiation of allele frequencies in the adults and in the pollen pool, before and after logging occurred, as well as weak and similar pre- and post-harvest levels of SGS among adult trees. The large neighbourhood sizes estimated suggest high historical levels of gene flow. Overall our results indicate that there is no clear short-term genetic impact of selective logging on this population of C. guianensis.