Analysis of genetic ancestry in the admixed Brazilian population from Rio de Janeiro using 46 autosomal ancestry-informative indel markers

Abstract

The Brazilian population is highly heterogeneous as a result of five centuries of inter-ethnic mating between native Amerindians, European colonizers and Africans arrived during slavery. This study aimed to assess the proportions of inter-ethnic admixture in the Brazilian population of Rio de Janeiro using autosomal Ancestry-Informative Markers (AIMs). The autosomal data were also compared to the results expected from uniparental genetic markers. A total of 413 individuals were genotyped for 46 AIM-Indels and ancestry estimates were then assessed using HGDP-CEPH samples as ancestral reference. Individuals from Rio de Janeiro presented highly diverse admixture patterns. The global admixture estimates showed a predominantly European ancestry, above 55%, followed by African and Amerindian contributions. A separate self-declared Afro-descendant group also included in this study revealed an increased African ancestry, from ∼30% to ∼50%. The inter-ethnic admixture landscape of Rio de Janeiro captured by autosomal AIM-Indels is in agreement with historical records and similar to that expected from uniparental mtDNA and Y-chromosome information. The AIM-Indel panel proved to be a rapid strategy to estimate autosomal genetic ancestry at individual and population levels in Rio de Janeiro, which is useful in population genetics and in case-control association studies.

Keywords::

• Admixture
• AIM
• insertion deletion polymorphism
• population structure

Declaration of interest: Financial support was granted by Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES), Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq), Fundação de Amparo à Pesquisa do Estado do Rio de Janeiro (FAPERJ) and DNA Program–State University and Justice Court of Rio de Janeiro (UERJ/TJRJ/MPRJ), Brazil. IPATIMUP is an Associate Laboratory of the Portuguese Ministry of Science, Technology and Higher Education and is partially supported by the Portuguese Foundation for Science and Technology (FCT). LG is supported by a grant from CAPES and RP by an FCT post-doctoral fellowship (SFRH/BPD/81986/2011). The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the paper.