Genotype-Phenotype Study of the Middle Gangetic Plain in India Shows Association of rs2470102 with Skin Pigmentation

Abstract

Our understanding of the genetics of skin pigmentation has been largely skewed towards populations of European ancestry, imparting less attention to South Asian populations, who behold huge pigmentation diversity. Here, we investigate skin pigmentation variation in a cohort of 1,167 individuals in the Middle Gangetic Plain of the Indian subcontinent. Our data confirm the association of rs1426654 with skin pigmentation among South Asians, consistent with previous studies, and also show association for rs2470102 single nucleotide polymorphism. Our haplotype analyses further help us delineate the haplotype distribution across social categories and skin color. Taken together, our findings suggest that the social structure defined by the caste system in India has a profound influence on the skin pigmentation patterns of the subcontinent. In particular, social category and associated single nucleotide polymorphisms explain about 32% and 6.4%, respectively, of the total phenotypic variance. Phylogeography of the associated single nucleotide polymorphisms studied across 52 diverse populations of the Indian subcontinent shows wide presence of the derived alleles, although their frequencies vary across populations. Our results show that both polymorphisms (rs1426654 and rs2470102) play an important role in the skin pigmentation diversity of South Asians.

Skin Pigmentation Diversity in Central East Indian Populations and its Correlation with Mitochondrial Haplogroups

“…Both sampling area are only 0.2089% (E-UP) and 0.0832% (N-B) of total geographical area of India (3,287,263 km 2 ). Intriguingly, within this small area, we observed huge diversity of skin pigmentation by cohort 1 (phenotype database) analysis [14]. Middle gangetic belt of central-east region represents phenotype variation among populations with 46.45185 (SD +/-5.104557) MeI in Bhumihar cast to 70.83403 (SD +/-8.13) Majhi cast [14].…”

“…Intriguingly, within this small area, we observed huge diversity of skin pigmentation by cohort 1 (phenotype database) analysis [14]. Middle gangetic belt of central-east region represents phenotype variation among populations with 46.45185 (SD +/-5.104557) MeI in Bhumihar cast to 70.83403 (SD +/-8.13) Majhi cast [14]. In cohort-2 (phenotype-genotype database), E-UP, we observed Melanin Index (MeI) 47.67 ± 4.32 while in N-B, we observed MeI 60.77 ± 9.94.…”

“…The melanin index is marginally different between OBC and SC (p = 0.0142) while significantly different from GN vs OBC (p = 3.33 × 10 -12 ) and GN vs SC (p < 2 × 10 -16 ). We did not observe any significant diversity and the populations [13,14]. The central east region of India is one of the most fertile and densely populated regions (http://www.…”

“…The phenotype variation observed among central east populations of our earlier study is referred as cohort 1 or phenotype database and presented in Table 1B and Figure 1 [13,14]. The cohort 2 populations were selected from the cohort 1 database for genetic research and referred here as phenotype genotype database and presented in Table 1C.…”

“…We utilized the mean of foreheads and under arm Melanin Index (MeI) of our previous phenotype study which was measured with Derma spectrometer (Cortex Technology, Hadsund, Denmark) in duplicates [13,14]. We have used the data of underarm MeI for this study.…”