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Skin pigmentation and genetic variants in an admixed Brazilian population of primarily European ancestry

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Abstract

Although many genes have been shown to be associated with human pigmentary traits and forensic prediction assays exist (e.g. HIrisPlex-S), the genetic knowledge about skin colour remains incomplete. The highly admixed Brazilian population is an interesting study population for investigation of the complex genotype-phenotype architecture of human skin colour because of its large variation. Here, we compared variants in 22 pigmentary genes with quantitative skin pigmentation levels on the buttock, arm, and forehead areas of 266 genetically admixed Brazilian individuals. The genetic ancestry of each individual was estimated by typing 46 AIM-InDels. The mean proportion of genetic ancestry was 68.8% European, 20.8% Sub-Saharan African, and 10.4% Native American. A high correlation (adjusted R2 = 0.65, p < 0.05) was observed between nine SNPs and quantitative skin pigmentation using multiple linear regression analysis. The correlations were notably smaller between skin pigmentation and biogeographic ancestry (adjusted R2 = 0.45, p < 0.05), or markers in the leading forensic skin colour prediction system, the HIrisPlex-S (adjusted R2 = 0.54, p < 0.05). Four of the nine SNPs, OCA2 rs1448484 (rank 2), APBA2 rs4424881 (rank 4), MFSD12 rs10424065 (rank 8), and TYRP1 1408799 (rank 9) were not investigated as part of the HIrisPlex-S selection process, and therefore not included in the HIrisPlex-S model. Our results indicate that these SNPs account for a substantial part of the skin colour variation in individuals of admixed ancestry. Hence, we suggest that these SNPs are considered when developing future skin colour prediction models.

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Acknowledgements

We thank Major Tatiana L. S. Nogueira and Colonel Lucio Aparecido Luiz for organising the sample collection at IBEx, and Andrea Oliveira, Anna Carolina Chaves, Fernanda Mathias, and Romulo Vianna for helping with the sample collection at UERJ. We also thank João Marreiro, Silvia De Oliveira Loiola, Anja Ladegaard Jørgensen, and Nadia Jochumsen for the technical support.

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  1. Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2100, Copenhagen, Denmark

    Jeppe D. Andersen, Olivia S. Meyer, Vania Pereira, Claus Børsting & Niels Morling

  2. DNA Diagnostic Laboratory (LDD), Institute of Biology, State University of Rio de Janeiro (UERJ), Rio de Janeiro, Brazil

    Filipa Simão, Juliana Jannuzzi, Elizeu Carvalho & Leonor Gusmão

  3. Department of Mathematical Sciences, Aalborg University, DK-9000, Aalborg, Denmark

    Mikkel M. Andersen

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All procedures performed in the study were in accordance with the ethical standards of the Ethical Committee of Hospital Universitário Pedro Ernesto/UERJ (CAAE: 34301714.7.0000.5259).

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Andersen, J.D., Meyer, O.S., Simão, F. et al. Skin pigmentation and genetic variants in an admixed Brazilian population of primarily European ancestry. Int J Legal Med 134, 1569–1579 (2020). https://doi.org/10.1007/s00414-020-02307-y

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