A. Y. Ciampi

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.

Insights into the Musa genome: Syntenic relationships to rice and between Musa species

BackgroundMusa species (Zingiberaceae, Zingiberales) including bananas and plantains are collectively the fourth most important crop in developing countries. Knowledge concerning Musa genome structure and the origin of distinct cultivars has greatly increased over the last few years. Until now, however, no large-scale analyses of Musa genomic sequence have been conducted. This study compares genomic sequence in two Musa species with orthologous regions in the rice genome.ResultsWe produced 1.4 Mb of Musa sequence from 13 BAC clones, annotated and analyzed them along with 4 previously sequenced BACs. The 443 predicted genes revealed that Zingiberales genes share GC content and distribution characteristics with eudicot and Poaceae genomes. Comparison with rice revealed microsynteny regions that have persisted since the divergence of the Commelinid orders Poales and Zingiberales at least 117 Mya. The previously hypothesized large-scale duplication event in the common ancestor of major cereal lineages within the Poaceae was verified. The divergence time distributions for Musa-Zingiber (Zingiberaceae, Zingiberales) orthologs and paralogs provide strong evidence for a large-scale duplication event in the Musa lineage after its divergence from the Zingiberaceae approximately 61 Mya. Comparisons of genomic regions from M. acuminata and M. balbisiana revealed highly conserved genome structure, and indicated that these genomes diverged circa 4.6 Mya.ConclusionThese results point to the utility of comparative analyses between distantly-related monocot species such as rice and Musa for improving our understanding of monocot genome evolution. Sequencing the genome of M. acuminata would provide a strong foundation for comparative genomics in the monocots. In addition a genome sequence would aid genomic and genetic analyses of cultivated Musa polyploid genotypes in research aimed at localizing and cloning genes controlling important agronomic traits for breeding purposes.

Characterization of novel microsatellite markers in Musa acuminata subsp. burmannicoides , var. Calcutta 4

BackgroundBanana is a nutritionally important crop across tropical and sub-tropical countries in sub-Saharan Africa, Central and South America and Asia. Although cultivars have evolved from diploid, triploid and tetraploid wild Asian species of Musa acuminata (A genome) and Musa balbisiana (B genome), many of todays commercial cultivars are sterile triploids or diploids, with fruit developing via parthenocarpy. As a result of restricted genetic variation, improvement has been limited, resulting in a crop frequently lacking resistance to pests and disease. Considering the importance of molecular tools to facilitate development of disease resistant genotypes, the objectives of this study were to develop polymorphic microsatellite markers from BAC clone sequences for M. acuminata subsp. burmannicoides, var. Calcutta 4. This wild diploid species is used as a donor cultivar in breeding programs as a source of resistance to diverse biotic stresses.FindingsMicrosatellite sequences were identified from five Calcutta 4 BAC consensi datasets. Specific primers were designed for 41 loci. Isolated di-nucleotide repeat motifs were the most abundant, followed by tri-nucleotides. From 33 tested loci, 20 displayed polymorphism when screened across 21 diploid M. acuminata accessions, contrasting in resistance to Sigatoka diseases. The number of alleles per SSR locus ranged from two to four, with a total of 56. Six repeat classes were identified, with di-nucleotides the most abundant. Expected heterozygosity values for polymorphic markers ranged from 0.31 to 0.75.ConclusionsThis is the first report identifying polymorphic microsatellite markers from M. acuminata subsp. burmannicoides, var. Calcutta 4 across accessions contrasting in resistance to Sigatoka diseases. These BAC-derived polymorphic microsatellite markers are a useful resource for banana, applicable for genetic map development, germplasm characterization, evolutionary studies and marker assisted selection for traits.

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.

Diversidade genética de populações de andiroba no Baixo Acre

Abstract€–€The€objective of this work was to evaluate the genetic diversity of two Carapa guianensis Aubl.(crabwood) populations, in the S tate of Acre, Brazil, and to compare the diversity estimations with those obtainedin other populations of the species (in Brazil: Flona Tapajos, PA, Porto Acre, AC; and in Costa Rica). Seventy-seven individuals were assessed using seven polymorphic microsatellite loci. Fifty-one alleles were observed inthe two populations, in which the effective number of alleles per locus (A ^ e €=€3.2) was lower than the averagenumber of alleles per locus (A ^ €=€7.3), which indicates a high number of low frequency alleles. The estimatedf ^ values did not differ from zero, showing that inbreeding does not occur in these populations. The apparentoutcrossing rate was high for both populations ( t ^ a €=€1.1 1 in Porto Acre population, and t ^ a €=€0.88 in Rio Branco),indicating that this species reproduces by outcrossing. Comparing the estimates of A ^ e , H ^

Development of expressed sequence tag and expressed sequence tag-simple sequence repeat marker resources for Musa acuminata.

Many varieties of banana (Musa acuminata) lack resistance to biotic stresses. An EST collection was developed, including transcripts expressed in banana-Mycosphaerella fijiensis interactions. Developed polymorphic gene-derived SSR markers are applicable for genetic mapping, diversity characterization and marker assisted breeding.

Chloroplast DNA Variation of Carapa guianensis in the Amazon basin

Abstract Carapa guianensis is a widespread Neotropical tree species that produces a seed adapted for water dispersal. We conducted a pilot study of chloroplast DNA (cpDNA) variation in order to investigate the consequences of hydrochory on genetic diversity and geographic population structure in the lower Amazon basin. A survey of cpDNA haplotype variation reveals a strong regional structure, which suggests limited gene flow by seeds. Within site variation was detected only in one floodplain forest (varzea), suggesting that seed dispersal by water in these forests has the potential to mix maternal lineages. Several phylogeographic hypotheses are discussed with respect to these data.

High levels of genetic differentiation and selfing in the Brazilian cerrado fruit tree Dipteryx alata Vog. (Fabaceae)

Dipteryx alata is a native fruit tree species of the cerrado (Brazilian savanna) that has great economic potential because of its multiple uses. Knowledge of how the genetic variability of this species is organized within and among populations would be useful for genetic conservation and breeding programs. We used nine simple sequence repeat (SSR) primers developed for Dipteryx odorata to evaluate the genetic structure of three populations of D. alata located in central Brazil based on a leaf sample analysis from 101 adults. The outcrossing rate was evaluated using 300 open-pollinated offspring from 25 seed-trees. Pollen dispersal was measured by parentage analysis. We used spatial genetic structure (SGS) to test the minimal distance for harvesting seeds in conservation and breeding programs. Our data indicate that the populations studied had a high degree of genetic diversity and population structure, as suggested by the high level of divergence among populations . The estimated outcrossing rate suggested a mixed mating system, and the intrapopulation fixation index was influenced by SGS. We conclude that seed harvesting for genetic conservation and breeding programs requires a minimum distance between trees of 196 m to avoid collecting seeds from related seed-trees.

Diversidade genética e tamanho efetivo de duas populações de Myracrodruon urundeuva Fr. All., sob conservação ex situ

O objetivo deste trabalho foi investigar a diversidade, a estrutura genetica e o tamanho efetivo, retido em um banco de germoplasma, de duas populacoes de Myracrodruon urundeuva Fr. All. (aroeira), procedentes de Aramina-SP e Selviria-MS. As populacoes foram avaliadas a partir da amostragem de 25 progenies de polinizacao aberta de cada populacao. De cada progenie, 17 a 20 individuos foram amostrados e genotipados para oito locos microssatelites. Os maiores valores para o numero total de alelos (At), numero medio de alelos por loco (A), numero efetivo de alelos (Ae), heterozigosidade observada (H0) e esperada (He) foram detectados na populacao Selviria (At = 105, A = 13,13, Ae = 3,98, H0 = 0,669 e He = 0,749), enquanto Aramina teve At = 94, A = 13,75, Ae = 3,10, H 0 = 0,535 e He = 0,678. A diferenciacao nas frequencias alelicas das duas populacoes, com relacao ao polen cruzado (0,159) e do ovulo (0,235), indica que cerca de 84% e 77%, respectivamente, da diversidade genetica esta dentro das populacoes. O coeficiente medio de coancestria foi maior (Selviria Θ = 0,165, Aramina Θ = 0,169) e o tamanho efetivo medio das progenies (Selviria Ne(v) = 3,04, Aramina Ne(v) = 2,69) foi menor do que o esperado em progenies de populacoes panmiticas (Θ = 0,125, Ne(v) = 4). O tamanho efetivo total retido no banco ex situ foi estimado em 67,5 na populacao Selviria e 71,1 na populacao Aramina, valores menores do que o requerido (Ne = 150) para a conservacao de populacoes em curto prazo. Entretanto, as duas populacoes apresentaram alta diversidade genetica, o que as qualifica para serem utilizadas em programas de conservacao e melhoramento genetico da especie, desde que seja aumentado o tamanho efetivo populacional conservado ex situ.

Shotgun sequencing for microsatellite identification in Ilex paraguariensis (Aquifoliaceae).

Premise of the study: Ilex paraguariensis is a native tree species from Brazil, Argentina, and Paraguay that is used in the production of beverages, medicines, and cosmetics. Primers flanking microsatellites were developed to investigate genetic parameters in the species. Methods and Results: Using microsatellites cloned from an I. paraguariensis shotgun genomic library, 25 pairs of primers were designed and synthesized. Levels of polymorphism were evaluated in 24 individuals from two populations. Twenty loci were polymorphic, and an average of 4.8 and 4.5 alleles per locus were detected in the two populations, respectively. The mean observed heterozygosity was lower than the expected heterozygosity (0.54 vs. 0.60), indicating a departure from Hardy—Weinberg equilibrium and suggesting endogamy in both populations. Conclusions: The reported set of markers is highly informative and constitutes a powerful tool for the development of genetic characterization studies in I. paraguariensis.