Abstract
The last decade has witnessed important advances in our understanding of the genetics of pigmentation in European populations, but very little is known about the genes involved in skin pigmentation variation in East Asian populations. Here, we present the results of a study evaluating the association of 10 Single Nucleotide Polymorphisms (SNPs) located within 5 pigmentation candidate genes (OCA2, DCT, ADAM17, ADAMTS20, and TYRP1) with skin pigmentation measured quantitatively in a sample of individuals of East Asian ancestry living in Canada. We show that the non-synonymous polymorphism rs1800414 (His615Arg) located within the OCA2 gene is significantly associated with skin pigmentation in this sample. We replicated this result in an independent sample of Chinese individuals of Han ancestry. This polymorphism is characterized by a derived allele that is present at a high frequency in East Asian populations, but is absent in other population groups. In both samples, individuals with the derived G allele, which codes for the amino acid arginine, show lower melanin levels than those with the ancestral A allele, which codes for the amino acid histidine. An analysis of this non-synonymous polymorphism using several programs to predict potential functional effects provides additional support for the role of this SNP in skin pigmentation variation in East Asian populations. Our results are consistent with previous research indicating that evolution to lightly-pigmented skin occurred, at least in part, independently in Europe and East Asia.
Highlights
The remarkable variation observed in skin, hair and iris pigmentation in human populations is the result of differences in the amount, type and distribution of the pigment melanin, which is synthesized by specialized cells known as melanocytes
The ADAM17 gene is significant for the locus-specific branch length (LSBL), lnRH and Tajima’s D tests, and is significant for the whole genome long range haplotype (WGLRH) test, indicating that ADAM17 has haplotypes characterized by derived alleles that have risen to very high frequencies and have longer than expected levels of Linkage Disequilibrium (LD)
We analyzed the association of 10 Single Nucleotide Polymorphisms (SNPs) within 5 pigmentation candidate genes (OCA2, DCT, ADAM17, ADAMTS20 and TYRP1) with skin melanin content measured quantitatively in an East Asian sample
Summary
The remarkable variation observed in skin, hair and iris pigmentation in human populations is the result of differences in the amount, type and distribution of the pigment melanin, which is synthesized by specialized cells known as melanocytes. The last decade has witnessed impressive advances in our understanding of the genetics of normal pigmentation variation, driven by functional studies, gene expression studies, studies in animal models, analyses of signatures of natural selection and candidate gene or genome-wide association studies. At least 11 genes are known to be associated with normal pigmentation variation: TYR, TYRP1, OCA2/HERC2, SLC45A2, SLC24A5, SLC24A4, MC1R, ASIP, KITLG, IRF4 and TPCN2 [Reviewed in 1,2]. The most important genes involved are SLC24A5, SLC45A2 and KITLG, which explain a large portion of the skin pigmentation differences observed between European and West
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