CCMB researchers unravel the skin colour genetics of Indians

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(From left) Dr. Kumarasamy Thangaraj, Dr. S. Nizamuddin, Biswajit Roy and Dr. Niraj Rai have found a new SNP that is associated with skin colour in Indians.

A study of skin colour of 1,167 people belonging to 27 ethnic groups living in Uttar Pradesh and Bihar found that social structure defined by the caste system has a “profound influence on skin pigmentation”. The skin colour was found to vary significantly among ethnic groups and social categories studied.

Accordingly, Brahmins of Uttar Pradesh have the fairest skin while Manjhis (Majhwars) have the darkest skin (highest skin pigmentation). Bhagats exhibit maximum variation in skin pigmentation. Four social groups — general, scheduled caste, other backward caste and religious group — were studied. The results were published in The Journal of Investigative Dermatology.

The association of rs1426654, a key single nucleotide polymorphism (SNP) in SLC24A5 gene, with skin colour has been well established. In fact, this SNP explains 25-38 per cent of pigmentation differences between Europeans and west Africans. “In addition to rs1426654, our study found another SNP (rs2470102) to be significantly associated with skin colour in the Indian population,” says Dr. Kumarasamy Thangaraj from the Centre for Cellular and Molecular Biology (CCMB), Hyderabad and the corresponding author of the paper.

The new SNP was found to independently affect skin pigmentation variation among the Indian population. While the well known SNP (rs1426654) has been found to have a significantly larger effect on skin colour ranging from Europeans

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Brahmins of Uttar Pradesh have the fairest skin and Manjhis have the darkest skin.

to western Africans, the new SNP that the Indian researchers discovered is predominant in India/Asia. But both SNPs taken together are able to better explain the variation in skin colour among the Indian population than each of the SNP individually. The two SNPs together account for over 38 per cent of the variability in skin colour in the Indian population.

The researchers compared the skin colour with the genotype of the individuals. Homozygous (similar) mutant alleles tend to cause lighter skin colour while homozygous wild alleles tend to cause darker skin colour. “So those with homozygous mutant alleles of the new SNP had fairer skin compared with those who had homozygous wild type alleles,” he says. The difference in skin colour persisted even when the contribution by the well known SNP was adjusted. “This shows that the new SNP has an independent effect on skin colour,” says Dr. Thangaraj.

People who had a combination of similar (homozygous) mutant alleles of both the new and the known SNP had the fairest skin; they are said to belong to H1 haplotype. The frequency of the H1 haplotype was far higher (96 per cent) in people with lighter skin than in darker skin (37 per cent). “A particular haplotype is not exclusive to a social category. Though the frequency is less, we do find H1 haplotype in dark skinned social category. This is why we have fair skinned people even in the dark skin social category and dark skinned people in the otherwise fair skin social category,” he says.

India-wide study

In a subsequent study, Dr. Thangaraj and his team genotyped 1,825 individuals belonging to 52 diverse populations in India. They found the allele frequencies of the two SNPs were similar among the Indian population and spread across the population. “Like in Uttar Pradesh and Bihar, the proportion of both mutant and wild homozygous alleles is distributed in differently frequencies in different populations across the Indian population. Also, the H1 haplotype was not exclusive to any particular population or social category,” he says.

The study found that ultraviolet radiation-based selection model alone cannot account for the entire range of variation in skin colour seen in the Indian population. Rather, it is interplay between selection pressure for lighter skin in response to relatively less sunlight and admixture of the two founding populations of India.

Published in The Hindu on November 20, 2016

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