Genomic diversity and affinities in population groups of North West India: An analysis of Alu insertion and a single nucleotide polymorphism

• Published in: Gene 2012-12, Vol.511 (2), p.293-299
• Main Authors: Saini, J.S., Kumar, A., Matharoo, K., Sokhi, J., Badaruddoza, Bhanwer, A.J.S.
• Format: Article
• Language: English
• Subjects: Alu Elements; Alu insertion polymorphism; Base Sequence; DNA Primers; genes; genetic distance; genetic variation; Genome, Human; heterozygosity; Heterozygote; Humans; inbreeding coefficient; India; introns; loci; nationalities and ethnic groups; North West India; Polymorphism, Single Nucleotide; Population; Population Groups; Punjab; single nucleotide polymorphism; SNP; statistical analysis
• ISSN: 0378-1119; 1879-0038
• DOI: 10.1016/j.gene.2012.08.034

The North West region of India is extremely important to understand the peopling of India, as it acted as a corridor to the foreign invaders from Eurasia and Central Asia. A series of these invasions along with multiple migrations led to intermixture of variable populations, strongly contributing to genetic variations. The present investigation was designed to explore the genetic diversities and affinities among the five major ethnic groups from North West India; Brahmin, Jat Sikh, Bania, Rajput and Gujjar. A total of 327 individuals of the abovementioned ethnic groups were analyzed for 4 Alu insertion marker loci (ACE, PV92, APO and D1) and a Single Nucleotide Polymorphism (SNP) rs2234693 in the intronic region of the ESR1 gene. Statistical analysis was performed to interpret the genetic structure and diversity of the population groups. Genotypes for ACE, APO, ESR1 and PV92 loci were found to be in Hardy–Weinberg equilibrium in all the ethnic groups, while significant departures were observed at the D1 locus in every investigated population after Bonferroni's correction. The average heterozygosity for all the loci in these ethnic groups was fairly substantial ranging from 0.3927±0.1877 to 0.4333±0.1416. Inbreeding coefficient indicated an overall 10% decrease in heterozygosity in these North West Indian populations. The gene differentiation among the populations was observed to be of the order of 0.013. Genetic distance estimates revealed that Gujjars were close to Banias and Jat Sikhs were close to Rajputs. Overall the study favored the recent division of the populations of North West India into largely endogamous groups. It was observed that the populations of North West India represent a more or less homogenous genetic entity, owing to their common ancestral history as well as geographical proximity. ► We examined genomic affinities in five population groups of Punjab. ► Alu insertion at ACE, PV92, APO, and D1 and an SNP in the ESR1 gene were analyzed. ► A very high inbreeding coefficient was observed for the D1 locus. ► The groups share closeness with each other and represent a nearly homogenous entity.