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A GWAS in Latin Americans highlights the convergent evolution of lighter skin pigmentation in Eurasia.

ABSTRACT: We report a genome-wide association scan in >6,000 Latin Americans for pigmentation of skin and eyes. We found eighteen signals of association at twelve genomic regions. These include one novel locus for skin pigmentation (in 10q26) and three novel loci for eye pigmentation (in 1q32, 20q13 and 22q12). We demonstrate the presence of multiple independent signals of association in the 11q14 and 15q13 regions (comprising the GRM5/TYR and HERC2/OCA2 genes, respectively) and several epistatic interactions among independently associated alleles. Strongest association with skin pigmentation at 19p13 was observed for an Y182H missense variant (common only in East Asians and Native Americans) in MFSD12, a gene recently associated with skin pigmentation in Africans. We show that the frequency of the derived allele at Y182H is significantly correlated with lower solar radiation intensity in East Asia and infer that MFSD12 was under selection in East Asians, probably after their split from Europeans.

SUBMITTER: Adhikari K

PROVIDER: S-EPMC6341102 | biostudies-literature | 2019 Jan

REPOSITORIES: biostudies-literature

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A GWAS in Latin Americans highlights the convergent evolution of lighter skin pigmentation in Eurasia.

Adhikari Kaustubh K Mendoza-Revilla Javier J Sohail Anood A Fuentes-Guajardo Macarena M Lampert Jodie J Chacón-Duque Juan Camilo JC Hurtado Malena M Villegas Valeria V Granja Vanessa V Acuña-Alonzo Victor V Jaramillo Claudia C Arias William W Lozano Rodrigo Barquera RB Everardo Paola P Gómez-Valdés Jorge J Villamil-Ramírez Hugo H Silva de Cerqueira Caio C CC Hunemeier Tábita T Ramallo Virginia V Schuler-Faccini Lavinia L Salzano Francisco M FM Gonzalez-José Rolando R Bortolini Maria-Cátira MC Canizales-Quinteros Samuel S Gallo Carla C Poletti Giovanni G Bedoya Gabriel G Rothhammer Francisco F Tobin Desmond J DJ Fumagalli Matteo M Balding David D Ruiz-Linares Andrés A

Nature communications 20190121 1

We report a genome-wide association scan in >6,000 Latin Americans for pigmentation of skin and eyes. We found eighteen signals of association at twelve genomic regions. These include one novel locus for skin pigmentation (in 10q26) and three novel loci for eye pigmentation (in 1q32, 20q13 and 22q12). We demonstrate the presence of multiple independent signals of association in the 11q14 and 15q13 regions (comprising the GRM5/TYR and HERC2/OCA2 genes, respectively) and several epistatic interact ...[more]

PMID: 30664655

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Project description:A recent genome-wide association study (GWAS) in African descent populations identified novel loci associated with skin pigmentation. However, how genomic variations affect skin pigmentation and how these skin pigmentation gene variants affect serum 25(OH) vitamin D variation has not been explored in African Americans (AAs). In order to further understand genetic factors that affect human skin pigmentation and serum 25(OH)D variation, we performed a GWAS for skin pigmentation with 395 AAs and a replication study with 681 AAs. Then, we tested if the identified variants are associated with serum 25(OH) D concentrations in a subset of AAs (n = 591). Skin pigmentation, Melanin Index (M-Index), was measured using a narrow-band reflectometer. Multiple regression analysis was performed to identify variants associated with M-Index and to assess their role in serum 25(OH)D variation adjusting for population stratification and relevant confounding variables. A variant near the SLC24A5 gene (rs2675345) showed the strongest signal of association with M-Index (P = 4.0 x 10-30 in the pooled dataset). Variants in SLC24A5, SLC45A2 and OCA2 together account for a large proportion of skin pigmentation variance (11%). The effects of these variants on M-Index was modified by sex (P for interaction = 0.009). However, West African Ancestry (WAA) also accounts for a large proportion of M-Index variance (23%). M-Index also varies among AAs with high WAA and high Genetic Score calculated from top variants associated with M-Index, suggesting that other unknown genomic factors related to WAA are likely contributing to skin pigmentation variation. M-Index was not associated with serum 25(OH)D concentrations, but the Genetic Score was significantly associated with vitamin D deficiency (serum 25(OH)D levels less than 12 ng/mL) (OR, 1.30; 95% CI, 1.04-1.64). The findings support the hypothesis suggesting that skin pigmentation evolved responding to increased demand for subcutaneous vitamin D synthesis in high latitude environments.

Dataset Information

A GWAS in Latin Americans highlights the convergent evolution of lighter skin pigmentation in Eurasia.

Publications

A GWAS in Latin Americans highlights the convergent evolution of lighter skin pigmentation in Eurasia.

Similar Datasets

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