An X-STRs analysis of the Iraqi Sorani Kurds

A database for the Iraqi Sorani Kurds, specifically focused on the 12 X-short tandem repeat (STR) loci, has been developed to fascilitate forensic and population genetics investigations. The present study involved genotyping 117 unrelated individuals from the Sorani Kurds ethnic group using the Investigator Argus X-12 QS kit. The analysis revealed that the DXS10135 locus exhibited the highest degree of polymorphism, as indicated by a polymorphism information content (PIC) value of 0.94565 and a gene diversity (GD) value of 0.95623. Conversely, the DXS8378 locus displayed the lowest level of polymorphism, with a PIC value of 0.61026 and a GD value of 0.68170. Notably, two individuals were found to possess a rare allele (allele = 6) at the DXS8378 locus, which was not included in the allelic ladder of the kit. Furthermore, a significant linkage disequilibrium (LD) (p < 0.05/117) was observed between the DXS10103 and DXS10101 loci on linkage group 3 (LG3). The ancestral composition of the five primary geographic regions, namely Africa, Middle East, East Asia, Europe, and South America, was determined through the utilization of the FST/FSTmax ratio. The findings of this analysis revealed that the Middle Eastern populations exhibited the lowest FST/FSTmax ratio, measuring at 0.23243, indicating a relatively lower ancestral diversity. Conversely, the European populations showcased the highest FST/FSTmax ratio, measuring at 0.27122, indicative of a greater ancestral diversity within this region. Additionally, the allelic richness indicators, namely distinctive and private alleles, indicated that Africa and the Middle East displayed the highest levels, while Far East Asia exhibited the lowest. This analysis supports the hypothesis of repeated founder effects during outward migrations, as evidenced by both the ancestry variability and the allelic richness. Consequently, the findings of this study have important implications for forensic genetics and population genetics research, particularly in relation to the consideration of genetic predispositions within specific ethnic groups

An X-STRs analysis of the Iraqi Sorani Kurds

A database for the Iraqi Sorani Kurds, specifically focused on the 12 X-short tandem repeat (STR) loci, has been developed to fascilitate forensic and population genetics investigations. The present study involved genotyping 117 unrelated individuals from the Sorani Kurds ethnic group using the Investigator Argus X-12 QS kit. The analysis revealed that the DXS10135 locus exhibited the highest degree of polymorphism, as indicated by a polymorphism information content (PIC) value of 0.94565 and a gene diversity (GD) value of 0.95623. Conversely, the DXS8378 locus displayed the lowest level of polymorphism, with a PIC value of 0.61026 and a GD value of 0.68170. Notably, two individuals were found to possess a rare allele (allele = 6) at the DXS8378 locus, which was not included in the allelic ladder of the kit. Furthermore, a significant linkage disequilibrium (LD) (p < 0.05/117) was observed between the DXS10103 and DXS10101 loci on linkage group 3 (LG3). The ancestral composition of the five primary geographic regions, namely Africa, Middle East, East Asia, Europe, and South America, was determined through the utilization of the FST/FSTmax ratio. The findings of this analysis revealed that the Middle Eastern populations exhibited the lowest FST/FSTmax ratio, measuring at 0.23243, indicating a relatively lower ancestral diversity. Conversely, the European populations showcased the highest FST/FSTmax ratio, measuring at 0.27122, indicative of a greater ancestral diversity within this region. Additionally, the allelic richness indicators, namely distinctive and private alleles, indicated that Africa and the Middle East displayed the highest levels, while Far East Asia exhibited the lowest. This analysis supports the hypothesis of repeated founder effects during outward migrations, as evidenced by both the ancestry variability and the allelic richness. Consequently, the findings of this study have important implications for forensic genetics and population genetics research, particularly in relation to the consideration of genetic predispositions within specific ethnic groups

Fig 8 -

The mean number of (A) distinct alleles per locus and (B) private alleles per locus of the five regions: Middle East, Africa, Far East Asia, South America and Europe.</p

Matrix plot showing population average pairwise differences based on 12 loci and between 36 populations.

The area above the diagonal (green) shows the average number of pairwise differences between populations (PiXY); the diagonal (orange) shows the average number of pairwise differences within the population (PiX); and below the diagonal (blue) shows the corrected average pairwise difference (PiXY-(PiX+PiY)/2). The scale of differences is shown on the right side of the matrix. This matrix was generated using Arlequin 3.5.2.2 software.</p

Phylogenic tree of genetic relationships among the 36 global populations.

This phylogenic tree was generated using POPTREE2 software. Five clusters (K = 5) were created. Iraqi Sorani Kurds fell into the biggest cluster. The cyan-coloured cluster is the largest (17 populations), followed by the purple-coloured cluster (8 populations), and the remaining clusters each have two populations.</p

Box plot, violin plot and empirical cumulative distribution function (ECDF) plot of the bootstrap distribution of for each Q matrix in the STRUCTURE analysis.

Box plot, violin plot and empirical cumulative distribution function (ECDF) plot of the bootstrap distribution of for each Q matrix in the STRUCTURE analysis.</p

S1 Table. Haplotype frequencies for 12 X‐STRs markers in four linkage groups (LGs), N = 117.

LG1 = (DXS8378, DXS10135, DXS10148), LG2 = (DXS7132, DXS10074, DXS10079), LG3 = (DXS10101, DXS10103, HPRTB), LG4 = (DXS7423, DXS10134, DXS10146). S2 Table: Allele frequencies and sample size by locus of the Sorani Kurd. S3 Table: Forensic parameters, Number of alleles (Aall), Gene diversity (GD), polymorphism information content (PIC), match probability (PM), power of discrimination (PD) and Mean Exclusion Chance (MEC) of the Sorani Kurd males. S4 Table: Pairwise p values of linkage disequilibrium test for all pairs of loci using 117 male samples from Sorani Kurdish population. S5 Table: Forensic parameters, Gene diversity (GD), polymorphism information content (PIC), match probability (PM) and power of discrimination (PD), of the five geographical regions Middle East, Africa, Far East Asia, Europe and South America. S6 Table: Pairwise genetic distances (Fst) based on haplotypes of 36 global populations. S7 Table: Average number of pairwise differences using data from 36 populations. Above diagonal: Average number of pairwise differences between populations (PiXY), Diagonal elements: (yellow highlighted): Average number of pairwise differences within population (PiX), Below diagonal: Corrected average pairwise difference (PiXY-(PiX+PiY)/2). S8 Table: Pairwise genetic distances based on FST between the five continents. S9 Table: average number of pairwise differences (FST) within and between continents. Above diagonal: Average number of pairwise differences between populations (PiXY), Diagonal elements (yellow highlighted): Average number of pairwise differences within population (PiX), Below diagonal: Corrected average pairwise difference (PiXY-(PiX+PiY)/2). S10 Table: (A) Q statistics for the five poulations Middle East, Africa, Far East Asia and South America. (B) Pairwise comparisons using Wilcoxon rank sum test with continuity correction. S11 Table: distinctive alleles and private alleles on a continental scale: Middle East, Africa, Far East Asia, South America and Europe. (A) Distinctive alleles, (B) Private alleles. (XLSX)</p

The matrix of pairwise genetic distance F_ST of X-STRs 36 populations based on 12 X-STRs markers.

This matrix was generated using Arlequin 3.5.2.2 software.</p

Plots displaying the average number of pairwise differences within and between the five continents.

These matrices were generated using Arlequin 3.5.2.2 software.</p

Multidimensional scaling plot of the 36 populations.

Population codes are as follows: ALB: Albania; ARG: Argentina; BLR: Belarus; BGD: Bangladesh; BHR: Bahrain; CHE: Switzerland; CHN [H]: China [Han]; CHN [HH]: China [Hebie Han]; DEU: Germany; EGY: Egypt; ETH: Ethiopia; GNB: Guinea Bissau; HRV: Croatia; HUN: Hungary; IRN: Iran; IQ: Iraq; IQ [Ku]: Iraq [Sorani Kurd]; ITA: Italy; Jew [Ash]: Jews [Ashkenazim]; Jew [Chu]: Jews [Chuetas]; Jew [Maj]: Jews [Majorca]; Jew [ME]: Jews [Middle East]; Jew [NA]: Jews [North Africa]; Jew [Seph]: Jews [Sephardim]; KOR: Korea; LTU: Lithuania; MEX: Mexico; MGN: Mongolia; MYS: Malaysia; PHL: Philippines; PRT: Portugal; SUA: Saudi Arabia; SVN: Slovenia; SWE: Sweden; TUR: Turkey; UAE: United Arab Emirates. The MDS fig was generated using R statistical software version 4.0.3.</p