Single nucleotide polymorphisms from Theobroma cacao expressed sequence tags associated with witches' broom disease in cacao

In order to increase the efficiency of cacao tree resistance to witches¿ broom disease, which is caused by Moniliophthora perniciosa (Tricholomataceae), we looked for molecular markers that could help in the selection of resistant cacao genotypes. Among the different markers useful for developing marker-assisted selection, single nucleotide polymorphisms (SNPs) constitute the most common type of sequence difference between alleles and can be easily detected by in silico analysis from expressed sequence tag libraries. We report the first detection and analysis of SNPs from cacao-M. perniciosa interaction expressed sequence tags, using bioinformatics. Selection based on analysis of these SNPs should be useful for developing cacao varieties resistant to this devastating disease. (Résumé d'auteur

The hyperdominant tropical tree <i>Eschweilera coriacea</i> (Lecythidaceae) shows higher genetic heterogeneity than sympatric Eschweilera species in French Guiana

International audienceBackground and aims – The evolutionary history of Amazonia’s hyperabundant tropical tree species, also known as “hyperdominant” species, remains poorly investigated. We assessed whether the hyperdominant Eschweilera coriacea (DC.) S.A.Mori (Lecythidaceae) represents a single genetically cohesive species, and how its genetic constitution relates to other species from the same clade with which it occurs sympatrically in French Guiana.Methods – We sampled 152 individuals in nine forest sites in French Guiana, representing 11 species of the genus Eschweilera all belonging to the Parvifolia clade, with emphasis on E. coriacea. Samples were genotyped at four simple sequence repeat (SSR) markers. We delimited gene pools, i.e., genetically coherent putative taxa, using STRUCTURE software and principal component analysis. We compared the genetic assignment of individuals with their morphological species determination and estimated genetic diversity and differentiation for gene pools and species. We also estimated genome size using flow cytometry.Key results – SSR profiles commonly displayed up to four alleles per genotype, suggesting that the investigated Eschweilera species bear a paleopolyploid signature. Flow cytometry suggested that the studied species are diploid with haploid genome sizes of 871–1046 Mbp. We detected five gene pools and observed a good correspondence between morphological and genetic delimitation for Eschweilera sagotiana Miers and the undescribed morphospecies E. sp. 3 (which resembles E. grandiflora (Aubl.) Sandwith), and to a lesser extent for E. decolorans Sandwith and E. micrantha (O.Berg) Miers. Eschweilera coriacea was the most genetically diverse species and included individuals assigned to each gene pool.Conclusions – We found no conclusive evidence for cryptic species within E. coriacea in French Guiana. SSRs detected fewer gene pools than expected based on morphology in the Parvifolia clade but discriminated evolutionary relationships better than available plastid markers. A positive trend between demographic abundance of species and allelic richness illustrates that hyperdominants may have a high evolutionary potential. This hypothesis can be tested using more powerful genomic data in combination with tree phenotypic trait variation and characterization of niche breadth, to enhance our understanding of the causes of hyperdominance in Amazonian trees

Data from: Genetic differentiation in the stingless bee, Scaptotrigona xanthotricha Moure, 1950 (Apidae, Meliponini): a species with wide geographic distribution in the Atlantic rainforest

Stingless bees are important pollinators that are severely threatened by anthropic interference, resulting in a strong population decline. Scaptotrigona xanthotricha has a wide distribution in the Atlantic Rainforest, ranging from the northeastern state of Bahia to Santa Catarina in southern Brazil. To understand the genetic structure of S. xanthotricha, 12 species-specific microsatellite loci were analyzed in 42 colonies sampled throughout the species range. The results indicated 5 distinct clusters throughout the sampled area with high rates of genetic diversity, and the greatest diversity was found in southern Bahia. Greater differentiation was observed between samples from the extremes of the distribution, with an F ST value of 0.189 between cluster 1 and 5. The genetic differentiation analysis for all loci had an F ST value of 0.113, a result that is consistent with the analysis of molecular variance, which revealed 7.72% of the variation occurring between groups. The Mantel correlation between a genetic differentiation matrix and a geographic distance matrix (r = 0.184, P = 0.043) indicated a tendency toward increased differentiation with increased distance. This study revealed the profile of differentiation and distribution of genetic diversity in this species and indicates parameters that should be considered in future taxonomic revisions and activities for its management and conservation

Identificação molecular de plantas em regiões tropicais - dificuldades e desafios

O sequenciamento de DNA surge na atualidade como ferramenta potencial na identificação correta de espécies, estudos de evolução e filogenia, quantificação e monitoramento da biodiversidade, análise forense, entre outros. As regiões rbcL + matK foram definidas pelo Consórcio Internacional de Barcode (CBOL) como regiões padrões para barcode de plantas. Em 2011 foi criado o BR-BOL com o objetivo de promover de maneira sistematizada a identificação molecular da biodiversidade brasileira. Para identificação de plantas estão sendo analisadas as regiões propostas pelo CBOL e outros autores. Para algumas espécies da famí­lia Sapotaceae, entretanto, fica evidenciado que tais regiões não são eficientes na identificação molecular dessas espécies. Outras regiões conservadas, diferentes das propostas vêm sendo testadas e apresentam resultado satisfatório na discriminação molecular de espécies de regiões tropicais, como apresentado aqui para o gênero Manilkara

Identificação molecular de plantas em regiões tropicais - dificuldades e desafios

O sequenciamento de DNA surge na atualidade como ferramenta potencial na identificação correta de espécies, estudos de evolução e filogenia, quantificação e monitoramento da biodiversidade, análise forense, entre outros. As regiões rbcL + matK foram definidas pelo Consórcio Internacional de Barcode (CBOL) como regiões padrões para barcode de plantas. Em 2011 foi criado o BR-BOL com o objetivo de promover de maneira sistematizada a identificação molecular da biodiversidade brasileira. Para identificação de plantas estão sendo analisadas as regiões propostas pelo CBOL e outros autores. Para algumas espécies da famí­lia Sapotaceae, entretanto, fica evidenciado que tais regiões não são eficientes na identificação molecular dessas espécies. Outras regiões conservadas, diferentes das propostas vêm sendo testadas e apresentam resultado satisfatório na discriminação molecular de espécies de regiões tropicais, como apresentado aqui para o gênero Manilkara

Scaptotrigona Genotypes

Scaptotrigona Genotype

MICROSATELLITE MARKERS FOR PLATHYMENIA RETICULATA (LEGUMINOSAE)

Premise of the study: Microsatellite markers were developed and characterized to investigate genetic diversity and gene flow and to help in conservation efforts for the endangered timber species Plathymenia reticulata. Methods and Results: Eleven microsatellite loci were characterized using 60 adult trees of two populations of P. reticulata from the Atlantic Forest of southern Bahia, Brazil. Of these, nine loci were polymorphic, with an average of 4.39 alleles per locus. The average expected heterozygosity per population ranged from 0.47 to 0.55. The combined exclusion probability was 0.99996. Conclusions: Our results reveal that the microsatellite markers developed in this study are an effective tool for paternity and genetic structure analysis that may be useful for conservation strategies

Genetic Structure and Diversity of <i>Dalbergia nigra</i> from Brazilian Atlantic Forest Fragments

Dalbergia nigra is a long-living tree endemic to the Atlantic Rain Forest. Due to its high commercial value, this species has been widely exploited for timber production and is now endangered. It is widely known that understanding patterns of genetic structure is paramount for conserving threatened species. We analyzed the genetic diversity of 140 individuals from four different forest fragments in the southern region of Bahia, Brazil, to verify the possible effects of fragmentation on these populations and provide information for conservation initiatives. High polymorphism levels were detected from the genotyping of nine microsatellite loci (mean HE = 0.733). All populations showed high genetic diversity; however, a reduction of genetic diversity was detected in each population (HO HE). The average fixation index was high and significant (f = 0.167), which could be due to the occurrence of inbreeding, the Wahlund effect, reproductive system, or from null alleles. Genetic differentiation among populations was high (mean θP = 0.118), suggesting strong isolation, a pattern consistent with historically low gene flow. The Bayesian analysis revealed five different genetic groups, among which three groups correspond to three different forest fragments, and two groups showed the genetic subdivision of individuals from the other forest fragment. Based on our results, the suggested conservation strategy for D. nigra populations in the southern region of Bahia, Brazil, involves high environmental investments to protect all sampled forest fragments and individuals. Another strategy would be to collect seeds from all individuals from the sampled fragments and start a new population with human interference in its evolutive history inside a protection unit