New rare variants and interpretation of the genetic diversity at the group-specific component (GC) locus in populations of India

Abstract

As part of our ongoing genetic studies, 2635 samples from 30 populations of the Indian subcontinent have been analyzed for GC subtype variation. Several rare variants were found and have been characterized using isoelectric focusing in 3 M urea and with an immobilized pH gradient and by comparison with known standards. Six new variants, 1A33, 2A22, 2A23, 2A24, 1C56, and 1C59, have been discovered in geographically and ethnically distant populations of the Indian subcontinent. Variants 1C11 and 1C21 have been reported previously in the French population and variant 1C36 has been reported in Nepalis, but all three variants were observed for the first time in the populations of India. The distribution of the rare variants in the Indian subcontinent was examined for anthropological usefulness for differentiation of Indian populations. The data for GC allele frequencies from 144 populations of India were compared for geographic and ethnic variation. A high frequency of the GC*IF allele was observed in populations of eastern India, and various ethnic groups from the eastern zone were clearly differentiated from similar ethnic populations from the rest of India. GC*2 allele frequency data were further correlated with various geographic and climatic variables, such as longitude, latitude, sunshine, solar radiation, and mean annual temperature. A significant positive correlation between GC*2 frequency and latitude was observed. The GC*2 allele frequency showed a cline increasing from south to north. Significant negative correlation was also observed between GC*2 frequency and sunshine, solar radiation, and mean temperature. A possible interpretation for selection of the GC*2 allele in areas with low levels of insolation is provided.