RESUMO
We describe an ancestry-informative autosomal SNP multiplex designed to be a small-scale, flexible panel that can complement uniparental markers in assessing the American variability (i.e. pre-Colombian) found in contemporary indigenous American populations. This study centered on choosing SNPs with the specific characteristics of: 1) extreme allele frequency differences between indigenous Americans and the African, European and East Asian population groups that contribute to present-day population variation in the Americas; 2) high informativeness-for-assignment In values; and 3) well-spaced genomic distribution and chromosomal separation from existing small-scale forensic ancestry marker sets. The resulting capillary electrophoresis SNaPshot single base extension test was named: PIMA (Population Informative Multiplex for the Americas), comprising 26 autosomal SNPs, a single X-chromosome SNP plus the amelogenin sex marker adapted for SNaPshot. PIMA complements the established 34plex forensic ancestry panel to provide a powerful and simple tool for the analysis of American populations, including those with admixed histories, commonly encountered in America. Comparing the results obtained with the combined marker panels of PIMA and 34plex to SNP data from a much larger ancestry panel allowed us to gauge their relative efficiency. PIMA+34plex gives equivalent power to the 314-SNP 'LACE' genomic ancestry control panel, while requiring a much smaller genotyping effort. The ancestry profiles and genetic structure of 22 populations spread across the American continent were estimated using PIMA+34plex data, and those estimates were contrasted with information provided by uniparental markers (mtDNA and Y-chromosome loci) for a small set of admixed individuals from Venezuela. Our results indicate that an American genetic component is efficiently detected in contemporary American populations using a small set of ancestry informative SNPs, and these co-ancestry estimates are consistent with the known history and demography of the Americas. The small scale and high population differentiation power of PIMA, particularly when combined with 34plex, provides a practical and powerful tool for genetic studies of American populations as well as forensic DNA analyses.
Assuntos
Etnicidade/genética , Genética Populacional , Polimorfismo de Nucleotídeo Único , Grupos Raciais/genética , Amelogenina/genética , América , Cromossomos Humanos Y , DNA Mitocondrial , Eletroforese Capilar , Frequência do Gene , Marcadores Genéticos , Genótipo , Humanos , Reação em Cadeia da Polimerase MultiplexRESUMO
Chile is a disproportionately long and narrow country defined by the southern Andes and Pacific coastline where a level of genetic sub-structure resulting from distances of several thousand kilometers might be expected across the most distantly separated regions. Although STR databases created for the Chilean Legal Medical Service indicate an absence of sub-structure, such a characteristic requires further exploration when introducing additional forensic markers. Notably, Single Nucleotide Polymorphisms (SNPs) have a much lower mutation rate than STRs and can show more stable distributions of genetic variation if population movement is restricted. In this study we evaluated 451 Chilean urban samples from the North, North-Central, Central, South-Central and South regions of Chile for the 52 SNPs of the SNPforID forensic identification panel to explore the underlying genetic structure of Chilean populations. Results reveal similar genetic distances between groups suggesting a single SNP database for the whole of Chile is appropriate. To further understand the genetic composition of Chilean populations that comprise the bulk of individuals with both European and Native American ancestries, ancestral membership proportions were evaluated and pairwise comparisons to other American populations were made.
Assuntos
Marcadores Genéticos , Geografia , Polimorfismo de Nucleotídeo Único , Chile , DNA/genética , Genética Populacional , Humanos , Análise de Componente PrincipalRESUMO
Two sets of short amplicon binary markers (SABs): 50 single nucleotide polymorphisms (SNPs) and 38 insertion/deletion polymorphisms (Indels) were used to genotype bones of 35 years "post-mortem". Typing results of these binary markers were compared with those obtained for standard commercial STR and mini-STR DNA typing kits. We observed SAB marker performance to be better compared with conventional STR and mini-STR genotyping in degraded bone sample analysis. Furthermore, additional genetic information provided by these 88 binary markers, 50 SNPs and 38 Indels, combined with classical markers gave very high discrimination power even in severely degraded specimens, with all tested bone samples showing Random Match Probabilities (RMPs) higher than 1019. Missing person and disaster victim identification by kinship analysis is considerably strengthened by the addition of SAB markers since they can be successfully typed on degraded bone samples while adding considerable extra genetic data when poor or incomplete information is available from conventional forensic markers for the analysis of family pedigrees.
Assuntos
Degradação Necrótica do DNA , Impressões Digitais de DNA/métodos , Mutação INDEL , Polimorfismo de Nucleotídeo Único , Antropologia Forense , Marcadores Genéticos , Genótipo , Humanos , Reação em Cadeia da PolimeraseRESUMO
The fermentation of Pennisetum purpureum, alone (PP) or substituted with 0.30 of the tanniferous legumes Acacia cornigera (AC), Albizia lebbekoides (AL), Leucaena leucocephala (LL) and the saponin-rich Enterolobium cyclocarpum (EC) was studied in vitro, in presence or absence of polyethylene glycol (PEG) as tannin binder. Inactivation of tannins with PEG increased (p < 0.05) gas production with AL and LL from 8 and 12 h to the end of the incubation period respectively. When PEG was added, LL and AC promoted a higher (p < 0.05) gas volume than PP in the first 12 h incubation, and there were not differences between PP and AL. Substrate mixtures reduced (p < 0.05) methane volume produced compared with PP, but this was not related to PEG inclusion (p > 0.10). There was a trend (p = 0.06) for a higher 48 h bacterial attachment to the substrate when incubated without PEG. The decrease in fermentation of EC from 12 h incubation onwards could be associated with a negative mid-term effect of saponins over cellulolytic bacterial activity. It is concluded that the effects of tannins on microbial fermentation of mixed forage substrates are variable, depending on their nature, but do not have a marked impact on bacterial adhesion or methane production.
Assuntos
Fabaceae/metabolismo , Pennisetum/metabolismo , Rúmen/metabolismo , Taninos/química , Taninos/metabolismo , Animais , Fabaceae/química , Fermentação , Metano/metabolismo , Pennisetum/química , Polietilenoglicóis/químicaRESUMO
A set of autosomal single nucleotide polymorphism (SNP) loci was analyzed using the 52-plex assay previously described by Sanchez et al. [J.J. Sanchez, C. Phillips, C. Borsting, K. Balogh, M. Bogus, M. Fondevila, C.D. Harrison, E. Musgrave-Brown, A. Salas, D. Syndercombe-Court, P.M. Schneider, A. Carracedo, N. Morling, A multiplex assay with 52 single nucleotide polymorphisms for human identification, Electrophoresis 27 (2006) 1713-1724] in 140 samples of unrelated individuals born in the Colombian regions of, Risaralda, Caldas, Quindio, Antioquia, Tolima and Valle, and 164 samples of unrelated individuals with declared Native American ancestry from Colombia. Allele frequencies and statistical parameters of forensic interest are presented for the 52 SNPs. All loci were in agreement with Hardy-Weinberg equilibrium while comparisons with population samples of Argentina, Portugal, Spain, Mozambique, and Taiwan revealed significant differences in allele frequency distributions.
Assuntos
Genética Populacional , Polimorfismo de Nucleotídeo Único , Colômbia , Impressões Digitais de DNA , Genótipo , Humanos , Reação em Cadeia da PolimeraseRESUMO
The simple tetrameric STR D9S1120 exhibits a common population-specific allele of 9 repeats (9RA) reported to have an average frequency of 0.36 in Native Americans from both North and South of the continent. Apart from the presence of 9RA in two northeast Siberian populations, D9S1120 shows variability exclusive to, and universal in all American populations studied to date. This STR therefore provides an informative forensic marker applicable in countries with significant proportions of Native American populations or ancestry. We have re-designed PCR primers that reduce the amplified product sizes reported in NCBI UniSTS by more than a third and have characterized the repeat structure of D9S1120. The 9RA allele shares the same repeat structure as the majority of other D9S1120 alleles and so originates from a slippage-diminution mutation rather than an independent deletion. We confirm the previously reported allele frequencies from a range of populations indicating a global heterozygosity range for D9S1120 of 66-75% and estimate the proportion of Native American-diagnostic genotypes to average 53%, underlining the potential usefulness of this STR in both forensic identification and in population genetics studies of the Americas.