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Eucalyptus is an economically important genus comprising more than 890 species in different subgenera and sections. Approximately twenty species of subgenus Symphyomyrtus account for 95% of the world's planted eucalypts. Discrimination of closely related eucalypt taxa is challenging, consistent with their recent phylogenetic divergence and occasional hybridization in nature. Admixture, misclassification or mislabeling of Eucalyptus germplasm resources maintained as exotics have been suggested, although no reports are available. Moreover, hybrids with increased productivity and traits complementarity are planted worldwide, but little is known about their actual genomic ancestry. In this study we examined a set of 440 trees of 16 different Eucalyptus species and 44 interspecific hybrids of multi-species origin conserved in germplasm banks in Brazil. We used genome-wide SNP data to evaluate the agreement between the alleged phylogenetic classification of species and provenances as registered in their historical records, and their observed genetic clustering derived from SNP data. Genetic structure analyses correctly assigned each of the 16 species to a different cluster although the PCA positioning of E. longirostrata was inconsistent with its current taxonomy. Admixture was present for closely related species' materials derived from local germplasm banks, indicating unintended hybridization following germplasm introduction. Provenances could be discriminated for some species, indicating that SNP-based discrimination was directly proportional to geographical distance, consistent with an isolation-by-distance model. SNP-based genomic ancestry analysis showed that the majority of the hybrids displayed realized genomic composition deviating from the expected ones based on their pedigree records, consistent with admixture in their parents and pervasive genome-wide directional selection toward the fast-growing E. grandis genome. SNP data in support of tree breeding provide precise germplasm identity verification, and allow breeders to objectively recognize the actual ancestral origin of superior hybrids to more realistically guide the program toward the development of the desired genetic combinations. [ABSTRACT FROM AUTHOR]

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Confined field trials of genetically modified (GM) trees are the essential step toward the identification of the most productive cultivars and the assessment of the likely environmental impacts of the GM trees including the potential for gene flow by pollen and distance dispersal by seeds. Our study investigated the potential for wildling establishment and realized pollen flow from a clonal GM eucalypt field trial in Southeastern Brazil. The GM eucalypt stand was established in 2009, surrounded by a 3 m wide forest road and signal grass ( Bracharia sp.) fields. No seedling regeneration was found between 2010 and 2014 in and around the stand, confirming the expectations of the unlikelihood of eucalypt seedling establishment based on its limited invasive potential in competitive tropical environments. In 2014, open-pollinated seeds were collected from 28 non-GM eucalypts located between three and 650 m distance from the GM trial. A total of 420 seedlings were grown in a greenhouse and screened for the presence of the transgenic construct by a multiplexed PCR assay targeting two transgenes and an internal control. The highest average transgene pollen flow (16%) was seen at short distances (3–15 m), rapidly diminishing to 3% by a 240 m distance and continued at this low rate up to the furthest distance assessed (650 m) from the GM trial. The negative exponential distribution of GM pollination success was similar to that observed in non-GM eucalypt pollen flow studies, indicating that low levels of effective pollination are expected over long distances. To the best of our knowledge, this is the first experimental assessments of realized pollen flow measured by the effective production of seedlings from a genetically modified tree in field conditions. [ABSTRACT FROM AUTHOR]

We investigated the rate of pollen-mediated flow and realized reproductive success at increasing distances from the source, across fragmented clonal stands of hybrid eucalypts in Brazil by parentage analysis of grown out seedlings using genetic data at 15 microsatellite markers. Two study areas were employed: a pollen donor area composed of a clonal stand of a single pollen donor clone (PD) and a pollen sink (PS) area composed of a mixed clonal stand of two other clones (PS1 and PS2). In the pollen sink area four plots with 30 trees each, located at 25, 200, 400 and 550 m from the PD were established as sink islands. Before flowering, the entire clonal stands of clones PS1 and PS2, with exception of the sink islands were clear cut. Seeds were harvested from five randomly sampled trees in each sink island and the paternity of 15 seedlings per tree, 75 seedlings per island totaling a sample of 300 seedlings, was determined with PD as the alleged father. The self-pollination rate in the sink islands varied from zero to 24%. Paternity assignment to the PD was highest in the island at 25 m (17.3%) and rapidly decreased to 4.0% at 200 m and 2.7% at 550 m, suggesting a pattern of isolation by distance, while revealing a large pollen contribution from unaccounted sources across all islands. Our results in a fragmented clonal site agree with previous estimates of general pollen movement in eucalypt seed orchards, showing that pollination will take place by and large at relatively short distances of less than 200 m, consistent with the expected range of flight of pollinator bees. Nevertheless the exponential distribution observed also indicates that low levels of pollination success are to be expected over longer distances. Our data provide useful guidelines regarding the distance at which seed orchards should be established away from potentially large pollen pressure of clonal stands to minimize unwanted pollen introgression. Furthermore, our results on dispersal rate and distance of pollen have direct implications on gene containment strategies and modeling studies, as pollen-mediated gene flow is one of the key determinants of the potential ecological and biosafety impacts of prospective transgenic eucalypts. [ABSTRACT FROM AUTHOR]

The rs2476601-T allele at the protein tyrosine phosphatase non-receptor type 22 ( PTPN22) gene has been consistently associated with several autoimmune diseases in European-derived populations. However, little is known about the allele and haplotype frequency distributions in PTPN22 among populations derived from other ethnic groups. In the present study, the allele and haplotype frequency distributions of six single nucleotide polymorphisms (SNPs) in the PTPN22 gene were compared among Brazilian populations and HapMap phase 3 dataset. A total of 10 different population samples were evaluated. Additionally, in admixed populations, individual genetic ancestries were estimated for Native American, African, and European contributions. Estimated individual ancestries were used as quantitative traits in a conditional approach for single-marker and haplotype-specific regression analyses. It was shown that several SNPs and haplotypes have different frequencies among different ethnic populations. Individual genetic ancestries were not associated with the rs2476601-T allele, but were associated with PTPN22 haplotypes in Brazilian, Mexican, and African-American admixed populations. Our results suggest caution in the interpretation of results found in association studies involving PTPN22 polymorphisms in admixed populations. Correction for stratification generated by admixture should be mandatory to minimize or avoid chances of spurious association. [ABSTRACT FROM AUTHOR]

• Heritabilities for growth increase with age for most A. angustifolia provenances. • Greater genetic variation for growth is found within than between provenances. • Early selection at age 7–10 provides 85% prediction accuracy of growth at age 35. • Individual and family selection could reduce harvest age to 15–20 years. • More investments in breeding and plantation forestry of A. angustifolia are timely. Understanding the growth patterns of long-lived conifer tree species is important to devise breeding and early selection strategies, predict future biomass productivity and assess adaptive tree fitness for long term conservation efforts. We investigated the genetic variation for growth traits of Araucaria angustifolia, the grandiose renowned "Paraná pine" tree, in a trial involving 122 families across 15 provenances covering the entire natural range of the species in Brazil. Measurements at ages 7, 24, 32, 33 and 35 were used to adjust continuous growth curves based on nonlinear mixed-effect models for all 2158 trees, providing annual estimates for unmeasured ages in the 7-to-35-year interval. Estimated values closely matched observed ones and a reduction of the coefficient of residual variation was observed in the estimated data, possibly due to removal of random error in the observed measurements, making the estimated curves more reliable to predict growth patterns. Genetic variation for growth within provenances was greater than between, with a trend of increasing heritabilities over time for most provenances. Substantial genetic variation found both within and between families could drive efficient early selection at both levels. All provenances included individual trees and families with good potential to be selected for shorter rotations. Growth curves show that trees invest first in height and later in diameter growth. Considerable variation was observed across provenances for the optimal age and optimal tree volume at which annual growth increment peaks, a tipping point that could be used as a predictor of the optimal rotation age and expected tree volume. The data clearly indicate potential for early selection for growth at age 7–10 with an 85% prediction accuracy of growth at age 35. Additionally, growth data indicate potential of shortening harvest age from 30–35 to 15–20 years by selecting the best individuals and families. These results underscore the potential of expanding investments in breeding and plantation forestry of A. angustifolia, which in parallel could contribute to enhancing conservation efforts of this iconic subtropical conifer. [ABSTRACT FROM AUTHOR]

In this work, we report on the population genetic structure of the endangered tree species Manilkara huberi, an Amazonian tree species intensely exploited due to the high density and resistance of its wood. We investigated the patterns of spatial distribution, genetic structure, and mating system using 7 microsatellite loci and here discuss the consequences for conservation and management of the species. To examine the population genetic structure, 481 adult trees and 810 seedlings were sampled from an area of 200 ha from a natural population in FLONA Tapajós, PA, Brazil. We found relatively high and consistent inbreeding levels (intrapopulation fixation index [f] 0.175 and 0.240) and a significant spatial genetic structure up to a radius of approximately 300 m, most likely due to a limited seed and pollen flow. The multilocus (t[sub m]) population outcrossing rate was high (0.995), suggesting that the species is predominantly allogamous with a pollen flow restricted to 47 m. These results suggest that M. huberi spatially structured, consistent with a model of isolation by distance. Fragmentation may therefore cause the loss of subpopulations, suggesting that management programs for production and conservation should include large areas. The genetic data also revealed that for ex situ conservation, seeds should be collected from more than 175 maternal trees, in order to keep an effective population size of 500. Furthermore, as the species is widely distributed across the Amazon Forest, samples should include several populations in order to represent the highest genetic diversity possible. These results provide a blueprint to guide the production and conservation management policies of this valuable timber species. [ABSTRACT FROM AUTHOR]

Background: Brazil holds the largest commercial cattle populations worldwide. Local cattle breeds can be classified according to their origin, as exotic or Creole. Exotic breeds imported in the last 100 years, both zebuine and taurine, currently make up the bulk of the intensively managed populations. Locally adapted Creole breeds, originated from cattle introduced by the European conquerors derive from natural selection and events of breed admixture. While historical knowledge exists on the Brazilian Creole breeds very little is known on their genetic composition. The objective of this study was to assess the levels of genetic diversity, phylogenetic relationships and patterns of taurine/zebuine admixture among ten cattle breeds raised in Brazil. Results: Significant reduction of heterozygosity exists due both to within-population inbreeding and to breed differentiation in both subspecies (taurine and zebuine). For taurine breeds the number of markers that contribute to breed differentiation is larger than for zebuine. A consistently similar number of alleles was seen in both subspecies for all microsatellites. Four Creole breeds were the most genetically diverse followed by the zebuine breeds, the two specialized taurine breeds and the Creole Caracu. Pairwise genetic differentiation were all significant indicating that all breeds can be considered as genetically independent entities. A STRUCTURE based diagram indicated introgression of indicine genes in the local Creole breeds and suggested that occasional Creole introgression can be detected in some Zebuine animals. Conclusion: This study reports on a comprehensive study of the genetic structure and diversity of cattle breeds in Brazil. A significant amount of genetic variation is maintained in the local cattle populations. The genetic data show that Brazilian Creole breeds constitute an important and diverse reservoir of genetic diversity for bovine breeding and conservation. The genetic data was able to shed light on a number of issues related to the local breeds origin and structure. The Brazilian Creole breeds are all important and viable targets for conservation for they display peculiar traits both phenotypic and of cultural and historical nature that deserve conservation efforts. [ABSTRACT FROM AUTHOR]

A sample of 198 unrelated males distributed among the five geopolitical regions in Brazil were typed for the minimal Y-STR haplotype composed of microsatellite loci DYS19, DYS385I/II, DYS389I, DYS389II, DYS390, DYS391, DYS392 and DYS393. Gene frequency data, gene diversity, haplotype diversity and power of discrimination were estimated. An AMOVA indicated that 99.97% of the haplotypic variation is found within regions and only a small 0.03% and non significant variation is found among the five regions (Fst = 0.00031, P-value = 0.43). This result suggests that a single national database of Y-STR haplotypes can be used in the quantitative assessment of matches in forensic casework in the Brazilian population. A significant haplotype diversity of 99.8% was found and 172 different haplotypes were observed in 198 chromosomes. Haplotype (14–11, 14–13–29–24–11–13–13) with five occurrences in 198 chromosomes was the most frequent in Brazil. [Copyright &y& Elsevier]

Mahogany ( Swietenia macrophylla, Meliaceae) is the most valuable and intensively exploited Neotropical tree. No information is available regarding the genetic structure of mahogany in South America, yet the region harbours most of the unlogged populations of this prized hardwood. Here we report on the genetic diversity within and the differentiation among seven natural populations separated by up to 2100 km along the southern arc of the Brazilian Amazon basin. We analysed the variation at eight microsatellite loci for 194 adult individuals. All loci were highly variable, with the number of alleles per locus ranging from 13 to 27 (mean = 18.4). High levels of genetic diversity were found for all populations at the eight loci (mean HE = 0.781, range 0.754–0.812). We found moderate but statistically significant genetic differentiation among populations considering both estimators of FST and RST, θ = 0.097 and ρ = 0.147, respectively. Estimates of θ and ρ were significantly greater than zero for all pairwise population comparisons. Pairwise ρ-values were positively and significantly correlated with geographical distance under the isolation-by-distance model. Furthermore, four of the populations exhibited a significant inbreeding coefficient. The finding of local differentiation among Amazonian mahogany populations underscores the need for in situ conservation of multiple populations of S. macrophylla across its distribution in the Brazilian Amazon. In addition, the occurrence of microgeographical genetic differentiation at a local scale indicates the importance of maintaining populations in their diverse habitats, especially in areas with mosaics of topography and soil. [ABSTRACT FROM AUTHOR]

• Epigenetic changes play an important role in the adaptation response of forest trees. • Eucalyptus is a robust system to track epigenetic changes in response to environment. • Site-specific DNA methylation changes were identified for each of five eucalypt clones. • No consistently shared epigenetic marks were found for all clones across environments. • Results showed that the observed epigenetic variation is mainly genotype dependent. Phenotypic plasticity refers to the ability of a single genotype to express distinct phenotypes in response to the environment, a crucial feature for sessile organisms like forest trees, especially in a scenario of global climate change. Several studies show that epigenetic regulation plays an important role in this plastic adaptation response, driving the search for associations between natural epigenetic variation with environmental cues and phenotypic traits based on patterns of cytosine methylation. Clonally propagated trees across variable sites offer a robust system to control for the confounding effect of the background genetic variation among genotypes, allowing the analysis of epigenetic modifications in response to variable environments. In this study we investigated the overall patterns of epigenetic changes by the analysis of the genome-wide DNA methylation status based on high throughput MS-DArT-seq (Methyl Sensitive DArT-seq sequencing) of reduced genome complexity representations. We compared patterns of DNA methylation of biological replicates of leaf and xylem tissue samples of four commercially planted elite Eucalyptus grandis × Eucalyptus urophylla clones and one Eucalyptus urophylla in two contrasting sites in Brazil, and the association of these methylation patterns with the environments and growth traits. DNA sequence reads were mapped against the Eucalyptus grandis reference genome, counting and annotating differentially methylated sites. A total of 90,378 MS-DArT-seq sites were identified, the majority (~70%) located in genes and 10% in transposable elements. The distribution of methylation sites showed extensive variation between the five genotypes and the environments. Sets of methylation sites exclusive to each location were identified for each clone but no consistently shared epigenetic marks for all five clones were found across environments. Multiple correspondence analysis suggests a significant contribution of the genetic background on the distribution of methylation changes. We used a gene-environment association analysis to search for association of methylation patterns with growth traits. A total of 445 methylation sites across all 11 Eucalyptus chromosomes were found significantly associated with one or more of the three measured traits (total height, estimated volume and breast high diameter). The absence of clustered differentially methylated sites is consistent with the fact that complex growth traits are governed by a large number of loci of small effect across the entire genome suggesting that this same pattern will likely hold for what regards epigenetic marks. [ABSTRACT FROM AUTHOR]

The article offers information on the topics discussed at the International Union of Forestry Research Organizations (IUFRO) Tree Biotechnology Conference held in Bahia, Brazil from June 26-July 2, 2011. The conference focused on tree biotechnology and advances of genomics in regards to forest conservation, tree physiology, and molecular breeeding. It was attended by several scientists and foresters.

High-throughput SNP genotyping has become a precondition to move to higher precision and wider genome coverage genetic analysis of natural and breeding populations of non-model species. We developed a 44,318 annotated SNP catalog for Araucaria angustifolia, a grandiose subtropical conifer tree, one of the only two native Brazilian gymnosperms, critically endangered due to its valuable wood and seeds. Following transcriptome assembly and annotation, SNPs were discovered from RNA-seq and pooled RAD-seq data. From the SNP catalog, an Axiom® SNP array with 3,038 validated SNPs was developed and used to provide a comprehensive look at the genetic diversity and structure of 15 populations across the natural range of the species. RNA-seq was a far superior source of SNPs when compared to RAD-seq in terms of conversion rate to polymorphic markers on the array, likely due to the more efficient complexity reduction of the huge conifer genome. By matching microsatellite and SNP data on the same set of A. angustifolia individuals, we show that SNPs reflect more precisely the actual genome-wide patterns of genetic diversity and structure, challenging previous microsatellite-based assessments. Moreover, SNPs corroborated the known major north-south genetic cline, but allowed a more accurate attribution to regional versus among-population differentiation, indicating the potential to select ancestry-informative markers. The availability of a public, user-friendly 3K SNP array for A. angustifolia and a catalog of 44,318 SNPs predicted to provide ~29,000 informative SNPs across ~20,000 loci across the genome, will allow tackling still unsettled questions on its evolutionary history, toward a more comprehensive picture of the origin, past dynamics and future trend of the species' genetic resources. Additionally, but not less importantly, the SNP array described, unlocks the potential to adopt genomic prediction methods to accelerate the still very timid efforts of systematic tree breeding of A. angustifolia., Competing Interests: The authors have declared that no competing interests exist.

A thorough understanding of the heritability, genetic correlations and additive and non-additive variance components of tree growth and wood properties is a requisite for effective tree breeding. This knowledge is essential to maximize genetic gain, that is, the amount of increase in trait performance achieved annually through directional selection. Understanding the genetic attributes of traits targeted by breeding is also important to sustain decade-long genetic progress, that is, the progress made by increasing the average genetic value of the offspring as compared to that of the parental generation. In this study, we report quantitative genetic parameters for fifteen growth, wood chemical and physical traits for the world-famous Eucalyptus urograndis hybrid (E. grandis × E. urophylla). These traits directly impact the optimal use of wood for cellulose pulp, paper, and energy production. A population of 1,000 trees sampled in a progeny trial was phenotyped directly or following the development and use of near-infrared spectroscopy calibration models. Trees were genotyped with 33,398 SNPs and 24,001 DArT-seq genome-wide markers and genomic realized relationship matrices (GRM) were used for parameter estimation with an individual-tree additive-dominant mixed model. Wood chemical properties and wood density showed stronger genetic control than growth, cellulose and fiber traits. Additive effects are the main drivers of genetic variation for all traits, but dominance plays an equally or more important role for growth, singularly in this hybrid. GRM´s with >10,000 markers provided stable relationships estimates and more accurate parameters than pedigrees by capturing the full genetic relationships among individuals and disentangling the non-additive from the additive genetic component. Low correlations between growth and wood properties indicate that simultaneous selection for wood traits can be applied with minor effects on genetic gain for growth. Conversely, moderate to strong correlations between wood density and chemical traits exist, likely due to their interdependency on cell wall structure such that responses to selection will be connected for these traits. Our results illustrate the advantage of using genome-wide marker data to inform tree breeding in general and have important consequences for operational breeding of eucalypt urograndis hybrids., Competing Interests: The authors have declared that no competing interests exist. Author CG was employed by International Paper do Brasil. This commercial affiliation does not alter our adherence to all PLOS ONE policies on sharing data and materials.

Ancestry informative SNPs can be useful to estimate individual and population biogeographical ancestry. Brazilian population is characterized by a genetic background of three parental populations (European, African, and Brazilian Native Amerindians) with a wide degree and diverse patterns of admixture. In this work we analyzed the information content of 28 ancestry-informative SNPs into multiplexed panels using three parental population sources (African, Amerindian, and European) to infer the genetic admixture in an urban sample of the five Brazilian geopolitical regions. The SNPs assigned apart the parental populations from each other and thus can be applied for ancestry estimation in a three hybrid admixed population. Data was used to infer genetic ancestry in Brazilians with an admixture model. Pairwise estimates of F(st) among the five Brazilian geopolitical regions suggested little genetic differentiation only between the South and the remaining regions. Estimates of ancestry results are consistent with the heterogeneous genetic profile of Brazilian population, with a major contribution of European ancestry (0.771) followed by African (0.143) and Amerindian contributions (0.085). The described multiplexed SNP panels can be useful tool for bioanthropological studies but it can be mainly valuable to control for spurious results in genetic association studies in admixed populations., ((c) 2009 Wiley-Liss, Inc.)

The current study investigated the association between vitamin-D-receptor (VDR) genotypes with bone-mineral density (BMD) and its interaction with physical activity level (PAL). Individuals in a sample of 192 volunteers (67.84 +/- 5.23 years) underwent BMD evaluation and were genotyped for VDR ApaI, BsmI, FokI, and TaqI polymorphisms. Haplotypes were reconstructed through expectation-maximization algorithm, and regression-based haplotype-specific association tests were performed with studied phenotypes. None of the polymorphisms were associated with BMD at any site; however, haplotype was associated with femoral-neck and Ward's-triangle BMD. Interaction between PAL and VDR genotypes was significant for the FokI polymorphism at femoral-neck and Ward's-triangle BMD. The FokI T/T genotype was associated with higher BMD in active women. It was concluded that VDR haplotypes, but not genotypes, are associated with femoral-neck and Ward's-triangle BMD in postmenopausal women. Moreover, the results suggest that VDR FokI polymorphism might be a potential determinant of BMD response to physical activity.

Background: Brazil holds the largest commercial cattle populations worldwide. Local cattle breeds can be classified according to their origin, as exotic or Creole. Exotic breeds imported in the last 100 years, both zebuine and taurine, currently make up the bulk of the intensively managed populations. Locally adapted Creole breeds, originated from cattle introduced by the European conquerors derive from natural selection and events of breed admixture. While historical knowledge exists on the Brazilian Creole breeds very little is known on their genetic composition. The objective of this study was to assess the levels of genetic diversity, phylogenetic relationships and patterns of taurine/zebuine admixture among ten cattle breeds raised in Brazil., Results: Significant reduction of heterozygosity exists due both to within-population inbreeding and to breed differentiation in both subspecies (taurine and zebuine). For taurine breeds the number of markers that contribute to breed differentiation is larger than for zebuine. A consistently similar number of alleles was seen in both subspecies for all microsatellites. Four Creole breeds were the most genetically diverse followed by the zebuine breeds, the two specialized taurine breeds and the Creole Caracu. Pairwise genetic differentiation were all significant indicating that all breeds can be considered as genetically independent entities. A STRUCTURE based diagram indicated introgression of indicine genes in the local Creole breeds and suggested that occasional Creole introgression can be detected in some Zebuine animals., Conclusion: This study reports on a comprehensive study of the genetic structure and diversity of cattle breeds in Brazil. A significant amount of genetic variation is maintained in the local cattle populations. The genetic data show that Brazilian Creole breeds constitute an important and diverse reservoir of genetic diversity for bovine breeding and conservation. The genetic data was able to shed light on a number of issues related to the local breeds origin and structure. The Brazilian Creole breeds are all important and viable targets for conservation for they display peculiar traits both phenotypic and of cultural and historical nature that deserve conservation efforts.

A total of 1037 individuals living in five different sociogeographic regions of Brazil were studied in relation to 12 short tandem repeat polymorphisms. The objective was to assess the degree of European, African, and Amerindian contributions to their gene pools. Although most of the genetic variability was found within regions, significant differences were also observed between regions. The estimated relative proportions of the above-indicated continental contributions showed intermediate values between those obtained with uniparental (mtDNA, Y-chromosome) data, and a higher percentage of European heritage as compared to previous autosome results. A north-south trend of increasing European contribution was also found, in agreement with the history of the Brazilian population., (Copyright 2003 Wiley-Liss, Inc.)