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The Muslim population of India is known for its historical and socioreligious significance. Literature on the genetic structure of this segment of India’s population is scanty. Therefore we have investigated the allele frequency distribution of haptoglobin (HP) and transferrin (TF) phenotypes among the Muslims to explore the genetic diversity of the Muslim immigrant populations of Aligarh. Aligarh is a city in Uttar Pradesh, India (latitude 27°54′ N, longitude 78°5′ E), situated 130 km southeast of Delhi. The population is mainly represented by Muslim immigrants from the eastern, northern, southern, and western regions of India and from abroad. Differences in allele frequencies of both HP and TF were statistically significant for the population of immigrants from western India and insignificant for others. The alleles HP*2 and TF*C2 show maximum frequencies in the southern population (0.882 and 0.822, respectively) followed by the eastern population (0.862 and 0.807) and the northern population (0.806 and 0.650). In the northern population a third allele, TF*C3, is also detected, with a mean frequency of 0.044. The average heterozygosity (HL) values for HP and TF are 0.273 and 0.361, respectively, and the pooled values for gene diversity parameters for both loci are HT = 0.4294 ± 0.0351, HS = 0.4225 ± 0.0271, and DST = 0.0069±0.0051. The pooled GST value is 0.0153±0.0108. The magnitude of these values indicates genetic similarity among the investigated populations. Our AMOVA results also demonstrate similarity among populations of the same geographic region. However, we note substantial differentiation among different regions (ΦCT = 0.221). The UPGMA dendrogram shows a cluster between the eastern and southern populations, to which the northern population joins. Our results reveal genetic similarity among different immigrant populations, with the western population being the most distant. Therefore the present study on culturally, geographically, and linguistically different endogamous groups of Muslims may have significance in understanding their genetic relationship.