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

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.

Genetic portrait of North-West Indian population based on X chromosome Alu insertion markers

“…Significant deviations from HWE were found in few Alu insertion polymorphisms in female samples and on the other hand no significant linkage disequilibrium was present in any pair of the Alu markers in male samples. In general, the allele frequencies found range within the general patterns as described in previous studies (Athanasiadis et al 2007;Ferragut et al 2017;Di Santo et al 2018). In the present study, similar to many other studies, values of minor allele frequency (MAF) of some loci were generally low, further indicating that X chromosome Alu elements have high potential to detect population structure and to study relationship between populations (Da la and Raska 2014).…”

“…Likewise, the most diverse population seems to be the Khatri (H= 0.1087) followed by the Scheduled Caste (0.0891), Jat Sikh (0.0571) and Brahmin (0.0509). The average gene diversity value of X chromosome Alu insertions in the present study was 0.027 similar to that observed in other European and Asian populations (Ferragut et al 2017;Di Santo et al 2018). The value of polymorphic information content (PIC) was in the range of 0.0104 to 0.3608 with a mean value of 0.1521.…”

“…All PCR amplifications were carried out in 10 μl reactions for a set of 10 human-specific X chromosome Alu insertions (Ya5DP4, Ya5DP3, Ya5DP77, Yb8DP49, Ya5491, Ya5NBC37, Yb8NBC102, Yb8NBC634, Ya5DP62 and Ya5DP13). Primer sequences and amplification conditions were obtained from previous studies (Callinan et al 2003;Di Santo et al 2018). The efficiency and reliability of the PCR reactions were monitored using control reactions.…”

Comparative Study of 10 X-STR Markers in Populations of Northeast Argentina

“…Concerning Eldorado, samples were separated into two groups according to the grandparents reported origin. We labeled them as Eldorado A (n = 27; 13 females, 14 males) when donors knew that their four grandparents were German and/or Swiss, and we labeled donors who did not know the origin of all four grandparents as Eldorado B (n = 27; 11 females, 16 males) (Di Santo Meztler et al 2018). Adult donors were recruited in health facilities and or private health centers, and asked to participate in this project while waiting for a medical appointment.…”

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“…Genetic differences have also been found among different regions or provinces within Argentina, for several genetic polymorphisms, whether they were coding or non-coding markers (Corach et al, 2006;Di Santo Meztler et al, 2018;Muzzio et al, 2018;Sala et al, 2018;Caputo et al, 2021, among others). Interestingly, some differences emerged even when comparing Resistencia and MNP, which are located in the same province and only 425 km apart, as it was previously reported for non-coding markers (Di Santo Meztler et al, 2019).…”