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.

BackgroundPopulation stratification is the main source of spurious results and poor reproducibility in genetic association findings. Population heterogeneity can be controlled for by grouping individuals in ethnic clusters; however, in admixed populations, there is evidence that such proxies do not provide efficient stratification control. The aim of this study was to evaluate the relation of self-reported with genetic ancestry and the statistical risk of grouping an admixed sample based on self-reported ancestry.MethodsA questionnaire that included an item on self-reported ancestry was completed by 189 female volunteers from an admixed Brazilian population. Individual genetic ancestry was then determined by genotyping ancestry informative markers.ResultsSelf-reported ancestry was classified as white, intermediate, and black. The mean difference among self-reported groups was significant for European and African, but not Amerindian, genetic ancestry. Pairwise fixation index analysis revealed a significant difference among groups. However, the increase in the chance of type 1 error was estimated to be 14%.ConclusionsSelf-reporting of ancestry was not an appropriate methodology to cluster groups in a Brazilian population, due to high variance at the individual level. Ancestry informative markers are more useful for quantitative measurement of biological ancestry.

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Background: Despite the great advances in genomic technology observed in several crop species, the availability of molecular tools such as microsatellite markers has been limited in melon (Cucumis melo L.) and cucurbit species. The development of microsatellite markers will have a major impact on genetic analysis and breeding of melon, especially on the generation of marker saturated genetic maps and implementation of marker assisted breeding programs. Genomic microsatellite enriched libraries can be an efficient alternative for marker development in such species.

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 post-menopausal women. Moreover, the results suggest that VDR FokI polymorphism might be a potential determinant of BMD response to physical activity.