Genetic Differentiation of North-East Argentina Populations Based on 30 Binary X Chromosome Markers.

Gabriela P Di Santo Meztler,Isaías Armoa,Carina F Argüelles,María E Esteban,Santiago Del Palacio,Cecilia I Catanesi

doi:10.3389/fgene.2018.00208

Abstract

Alu insertions, INDELs, and SNPs in the X chromosome can be useful not only for revealing relationships among populations but also for identification purposes. We present data of 10 Alu insertions, 5 INDELs, and 15 SNPs of X-chromosome from three Argentinian north-east cities in order to gain insight into the genetic diversity of the X chromosome within this region of the country. Data from 198 unrelated individuals belonging to Posadas, Corrientes, and Eldorado cities were genotyped for Ya5DP62, Yb8DP49, Ya5DP3, Ya5NBC37, Ya5DP77, Ya5NBC491, Ya5DP4, Ya5DP13, Yb8NBC634, and Yb8NBC102 Alu insertions, for MID193, MID1705, MID3754, MID3756 and MID1540 Indels and for rs6639398, rs5986751, rs5964206, rs9781645, rs2209420, rs1299087, rs318173, rs933315, rs1991961, rs4825889, rs1781116, rs1937193, rs1781104, rs149910, and rs652 SNPs. No deviations from Hardy-Weinberg equilibrium were observed for Posadas and Corrientes. However, Eldorado showed significant values, and it was found to have an internal substructuring with two groups of different origin, one showing higher similarity with European countries, and the other with more similarities to Posadas and Corrientes. Fst pairwise genetic distances emerged for some markers among the studied populations and also between our data and those from other countries and continents. Of particular interest, Alu insertions demonstrated the most differences, and could be of use in ancestry studies for these populations, while INDELs and SNPs variation were informative for differentiation within the country.

Highlights

The human X chromosome contains multiple types of non coding markers distributed along its sequence, including Alu insertions, insertion-deletions (INDEL), and single nucleotide polymorphisms (SNP) markers
INDELs and SNPs have many genetic advantages for population studies: (i) they are widely spread throughout the genome, including the X chromosome; (ii) the majority of these polymorphisms derive from a single mutation event; (iii) mutation rates are much lower than those of repetitive markers; (iv) they can show significant allele frequency differences among geographically distant populations; and (v) they can be genotyped, even from degraded DNA samples, given the short length of amplicons (Tomas et al, 2008; Pereira et al, 2009; Ribeiro-Rodrigues et al, 2009; Casto et al, 2010; Li et al, 2010)
All four populations adjusted to Hardy-Weinberg equilibrium (HW) equilibrium for most of the polymorphisms analyzed (Tables S8–S11); the exceptions were MID3754 for Posadas and EldoradoB (p−values = 0.01), rs1781104 for Posadas (p−values = 0.04), Yb8NBC634 for EldoradoA (p−values = 0.04), and Yb8NBC102, rs9781645, 1781104 for Corrientes (p−value = 0.01, p−value = 0.04, p−value = 0.03), respectively

Summary

Introduction

The human X chromosome contains multiple types of non coding markers distributed along its sequence, including Alu insertions, insertion-deletions (INDEL), and single nucleotide polymorphisms (SNP) markers. Genetic Differentiation of Argentinian Populations gene, inserted into the genome through an intermediate RNA single strand generated through transcription by RNA polymerase III (Batzer and Deininger, 1991) These polymorphisms consist of the presence or absence of Alu elements at a particular locus. They are selectively neutral and, as their location hardly changes or rearranges, they are considered to be derived from one unique event in which the absence of the insertion is the ancestral state for Alu markers (Batzer et al, 1994). INDELs and SNPs have many genetic advantages for population studies: (i) they are widely spread throughout the genome, including the X chromosome; (ii) the majority of these polymorphisms derive from a single mutation event; (iii) mutation rates are much lower than those of repetitive markers; (iv) they can show significant allele frequency differences among geographically distant populations; and (v) they can be genotyped, even from degraded DNA samples, given the short length of amplicons (Tomas et al, 2008; Pereira et al, 2009; Ribeiro-Rodrigues et al, 2009; Casto et al, 2010; Li et al, 2010)

Methods

Results

Conclusion