A study of nearly 300 people living in different parts of India found that nine single-base variants (single-nucleotide polymorphisms or SNPs) account 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 have 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.
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. 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 was reflected in higher mean melanin index (a representation of the amount of melanin in the skin) of 48 compared with mean melanin index of 39 in the case of people in north India. The population in east and west India has intermediate values (mean MI of 41). The melanin index did not vary 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 are found close together as two blocks in the chromosome. While one block of the chromosome has two SNPs, the other block has three SNPs. SNPs found together tend to have combined effect on skin colour. Since children tend to inherit small blocks of chromosome from parents, the SNPs found close together are inherited as a whole from parents.
