Association of genetic variants with self-assessed color categories in Brazilians.

Danielle Fernandes Durso,Mara Helena Hutz,Guilherme Suarez-Kurtz,Tiago R Magalhães,Sergio Paulo Bydlowski,Sérgio Danilo Junho Pena

doi:10.1371/journal.pone.0083926

Abstract

The Brazilian population was formed by extensive admixture of three different ancestral roots: Amerindians, Europeans and Africans. Our previous work has shown that at an individual level, ancestry, as estimated using molecular markers, was a poor predictor of color in Brazilians. We now investigate if SNPs known to be associated with human skin pigmentation can be used to predict color in Brazilians. For that, we studied the association of fifteen SNPs, previously known to be linked with skin color, in 243 unrelated Brazilian individuals self-identified as White, Browns or Blacks from Rio de Janeiro and 212 unrelated Brazilian individuals self-identified as White or Blacks from São Paulo. The significance of association of SNP genotypes with self-assessed color was evaluated using partial regression analysis. After controlling for ancestry estimates as covariates, only four SNPs remained significantly associated with skin pigmentation: rs1426654 and rs2555364 within SLC24A5, rs16891982 at SLC45A2 and rs1042602 at TYR. These loci are known to be involved in melanin synthesis or transport of melanosomes. We found that neither genotypes of these SNPs, nor their combination with biogeographical ancestry in principal component analysis, could predict self-assessed color in Brazilians at an individual level. However, significant correlations did emerge at group level, demonstrating that even though elements other than skin, eye and hair pigmentation do influence self-assessed color in Brazilians, the sociological act of self-classification is still substantially dependent of genotype at these four SNPs.

Highlights

Brazilians form one of the most heterogeneous populations in the world, the result of five centuries of interethnic crosses of peoples from three continents: the European colonizers, the African slaves, and the autochthonous Amerindians
Genetic natures of the associations On the basis of association studies present in the literature, we chose several genetic variants previously associated with differences in skin, eye and hair pigmentation among individuals from different parts of the world [12,13,14,15,16,17]
We have demonstrated that after correction for ancestry as a confounding covariate, haplotypes of rs2555364-rs1426654 within SLC24A5 and the SNPs rs16891982 in SLC45A2 and rs1042602 in TYR are significantly associated with skin color categories in a sample of the population of Rio de Janeiro, with confirmation with a second sample, from Sao Paulo, another large southeastern city in Brazil

Summary

Introduction

Brazilians form one of the most heterogeneous populations in the world, the result of five centuries of interethnic crosses of peoples from three continents: the European colonizers, the African slaves, and the autochthonous Amerindians. The relative proportion of these three ancestral roots in the makeup of the Brazilian population has changed considerably along time. After more than 100 years of heavy European immigration beginning in the second half of the 19th Century, all regions of Brazil show a preponderance of European ancestry, with proportions ranging from 60.6% in the Northeast to 77.7% in the South [1]. Since 1991, the Instituto Brasileiro de Geografia e Estatıstica (IBGE), responsible for the official census of Brazil, has employed only five pre-established discontinuous color categories, exclusively based on self-assessment: White, Browns, Blacks, Yellows, and Indigenous. In 2010, the IBGE census computed a population of 191 million Brazilians, into the following color percentages: 47.6%

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Results

Conclusion