A comprehensive portrait of Y-STR diversity of Indian populations and comparison with 129 worldwide populations

Mugdha Singh,Madhusudan R Nandineni,Anujit Sarkar

doi:10.1038/s41598-018-33714-2

Abstract

India, known for its rich cultural, linguistic and ethnic diversity, has attracted the attention of population geneticists to understand its genetic diversity employing autosomal, Y-chromosomal and mitochondrial DNA markers. Y-chromosomal short tandem repeats (Y-STRs) are useful in understanding population substructures and reveal the patrilineal affinities among populations. Previous studies on Indian populations based on Y-STR markers were either limited to restricted number of markers or focused on few selected populations. In this study we genotyped 407 unrelated male individuals from 12 states in India employing the suite of Y-STRs present in PowerPlex Y23 (Promega, Madison, WI, USA). These populations clustered genetically close to each other irrespective of their geographic co-ordinates and were characterized primarily by R1a, H and L haplogroups. Interestingly, comparison with 129 worldwide populations showed genetic affinity of the Indian populations with few populations from Europe and Levantine. This study presents the first pan-Indian landscape of 23 Y-STRs and serves as a useful resource for construction of an Indian Y-STR database.

Highlights

The male-specific human Y chromosome follows a strict mode of paternal inheritance and major portion comprises the non-recombining region (NRY)
We have genotyped 407 samples sourced from 12 different states representing North, South, East and West India using a multiplex of 23 Y-chromosomal short tandem repeats (Y-STRs) loci present in PowerPlex Y23 (PPY23) (Promega, Madison, WI, USA) system, to infer genetic relationship among the populations from different regions of the country
In order to obtain an estimate of molecular genetic diversity for the target STRs in Indian populations, we calculated genetic diversity (GD) values for each locus incorporated in the panel

Summary

Introduction

The male-specific human Y chromosome follows a strict mode of paternal inheritance and major portion comprises the non-recombining region (NRY). Y-chromosome is widely acknowledged for its utility in providing one of the highest resolution tools for studying human population genetics owing to the aforementioned features of uniparental inheritance and non-recombining nature[1]. Y-chromosomal markers provide interesting insights into the past demographic events of a population as illustrated by several studies examining the patrilineal affinities among different world populations, including India[2,3,4]. While investigating the genetic relationship with populations from other regions of the world[20], these populations interestingly showed greater genetic affinity with few populations from Europe and Levantine Since this chemistry was reported to be forensically potent in various worldwide populations[20,21]; this panel was evaluated to gauge its forensic efficacy in Indian populations as well. This study apart from providing a comprehensive picture of Y-STR-based diversity of Indian populations, would be of great utility for the development of a Y-STR database for forensic investigation purposes in India

Methods

Results

Conclusion