Detection of genetic variation in Indian population groups using a novel minisatellite probe and finding relationships through tree construction

Abstract

Genetic variation in HaeIII-digested genomic DNA samples from different individuals belonging to population groups from Bengal, Uttar Pradesh (UP), Punjab, and South India was assessed at hypervariable loci, using a minisatellite probe, pBA1.2 (accession number, AF 157691), the repeat unit of which was 24 mer long and rich in G-bases. Comparison of DNA profiles between individuals showed a very low probability of band sharing, which ranged from 0.18 to 0.24. A dendrogram, based on Nei's genetic distance, constructed by the neighbor-joining method, showed the formation of separate clusters by both South Indian and non-Indian samples, whereas the construction of a dendrogram based on the Unweighted pair group method arithmetic average (UPGMA) method with Jaccard's similarity coefficient at the individual level led to the formation of several small clusters which were interleaved; also, the subgroups for each of the populations were intermingled with the subgroups for the other populations. A separate analysis was carried out to check the consistency of the proximity between different individuals forming a cluster and between those individuals who were in the vicinity of two clusters. The dendrograms thus obtained did not change the relationship between the individuals from all the populations studied. Despite the distinct clustering observed in the population group comparison, a probable admixture was reflected in the finding that some individuals belonging to one population group were dispersed or embedded within a cluster generated by the individuals of another population group, when a minute dissection of the data for generating a tree at the individual level was carried out.