CDFD researchers find common genetic variants for skin colour in Indians

Sun tan-Optimized
A better knowledge of genotype-phenotype associations
could significantly improve our understanding of skin
cancer and the human tanning mechanism, the researchers say.

People in south India have darker skin as reflected in the higher mean melanin index of 48 compared with those in north India, who have a mean melanin index of 39. The population in east and west India has an intermediate skin colour with a mean melanin index value of 41.

A study of nearly 300 people living in different parts of India found nine single-base variants (single-nucleotide polymorphisms or SNPs) accounted for 31% variation in the colour of the skin.

Researchers at the Centre for DNA Fingerprinting and Diagnostics (CDFD), Hyderabad tested 30 SNPs that were earlier studied for skin colour in other parts of the world. Based on certain criteria, only 22 of the 30 SNPs were found suitable for statistical test in the Indian population. The two-member team of Dr. Madhusudan Reddy Nandineni and Anujit Sarkar found that only nine SNPs had significant association with skin colour in people living in India.

Samples were collected from people living in Karnataka and Telangana in the south, Maharashtra and Rajasthan in the west, Jammu and Kashmir and Uttarakhand in the north, and Jharkhand, West Bengal and Assam in the east.

The single-base variant rs1426654 accounts for 25-38% of skin colour variation between Africans and Europeans. Like earlier studies, this study too found this single-base variant was strongly associated with skin pigmentation in the Indian population. In fact, rs1426654 was one of the four SNPs that had maximum effect on skin pigmentation in people living here. The results were published in the American Journal of Human Biology.

Latitude of the sample location, and therefore being closer to the equator, was found to have significant contribution of about 19% of the skin colour variation in the Indian population studied.

People in south India are darker than their counterparts living in north India. The reason for this could be that the gene variants (allele) that give the skin a darker colour due to the presence of higher amount of melanin pigment are found in people living in south India while those living in north India have gene variants that make the skin lighter.

In short, though genes have a major role to play, the latitude defines which allele gets expressed and therefore whether a person has higher chances of having darker or lighter skin. Being closer to the equator, the darker skin in the south Indian population protects them from strong UV rays of the Sun.

The darker skin of people in south India is reflected in a higher mean melanin index (a representation of the amount of melanin in the skin) of 48 compared with a mean melanin index of 39 in the case of people in north India. The population in east and west India has an intermediate mean melanin index value of 41. The melanin index does not vary significantly within a given geographical region.

All the nine SNPs that are significantly associated with skin pigmentation are found in chromosome 15. The researchers found a few SNPs that are found close together as two haplotype blocks in the chromosome. While one haplotype block of the chromosome has two SNPs, the other has three SNPs. The SNPs found together tend to have a combined effect on skin colour. “Considering only the abundant haplotypes on chromosome 15, the haplotype GAC from three SNPs [from one haplotype block] could explain 18% of [skin] variance… [This] buttresses the importance of examining the haplotypes in addition to single markers while studying genotype-phenotype associations,” they write.

Since children tend to inherit small blocks of chromosome from parents, the SNPs found close together are inherited as a whole from parents.

Published in The Hindu on October 11, 2017

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