Genetic Portrait of North-West Indian Population based on X Chromosome Alu Insertion Markers

Abstract

Alu insertion elements represent the largest family of Short Interspersed Nuclear Elements (SINEs) in the human genome. Polymorphic Alu elements are stable and conservative markers that can potentially be applied in studying human origin and relationships as they are identical by descent and known for lack of insertion in ancestral state. In this study, 10 Alu insertions of X chromosome were utilized to tabulate allele frequency distributions and compute parameters of forensic relevance in the 379 unrelated healthy individuals belonging to four different ethnic groups (Brahmin, Khatri, Jat Sikh and Scheduled Caste) of North-West India. Furthermore, the DA and FST values of pairwise interpopulation differentiations, multidimensional scaling and Bayesian structure clustering analysis were also computed to probe the genetic relationships between present studied populations and with other 21 reference populations. Six X-Alu insertions were observed to be polymorphic in all the populations, whereas the others appeared as monomorphic in at least one studied population. The insertion allele frequencies were in the range of 0.15 at Ya5DP3 to 0.9888 at Ya5DP77. Most polymorphic Alu elements showed moderate to low genetic diversity. The maximum value of power of exclusion (PE) was 0.1645 at Ya5NBC37 marker, whereas the minimum was 0.0001 at Ya5DP4 locus, implying the significance of X chromosome Alu elements in forensic genetic investigations. Genetic relationships agree with a geographical pattern of differentiation among populations. The results of present study establish that X chromosome Alu elements comprise a reliable set of genetic markers useful to describe human population relationships and structure.