Population genetic study of 17 Y-STR Loci of the Sorani Kurds in the Province of Sulaymaniyah, Iraq

BACKGROUND: The Kurds as an ethnic group are believed to be a combination of earlier Indo-European tribes who migrated and inhabited a mountainous area thousands of years ago. However, as it is difficult to describe the precise history of their origin, it is necessary to investigate their population relationship with other geographical and ethnic groups. RESULTS: Seventeen Short Tandem Repeat markers on the Y chromosome (Y-STR) included in the AmpFLSTR™ Yfiler™ PCR Amplification Kit (Thermo Fisher Scientific, USA) were used to type DNA samples from the Sorani (Central) Kurdish population in Sulaymaniyah province. One hundred fifty-seven haplotypes were obtained from 162 unrelated male individuals. The highest and lowest gene diversities were DYS385a/b (GD = 0.848) and DYS392 (GD = 0.392), respectively. The haplotypes were used to predict the most likely haplogroups in the Sulaymaniyah population. CONCLUSION: Haplogroup prediction indicated predominance (28%) of subclade J2 (44/157) in the Sorani Kurds, northeast of Iraq. The pairwise genetic distance results showed that the Kurdish group clustered along with Asian populations, whereas the furthest countries were Europeans and Africans. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12864-022-09005-6

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

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

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

Population structure analysis using investigator Argus X-12 STR markers.

The results show 6 clusters (K = 6) using 46 ethnic groups and populations from five different geographical regions (Europe, South America, the Middle East, Africa and South East Asia).</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

S2 File -

S1 Fig. Plot distribution of allele frequencies per locus using Investigator Argus X-12 QS kit. S2 Fig. Electropherogram shows variant alleles in three samples of the Sorani Kurd males. (A) An off-ladder allele was observed at locus DXS8378 (allele = 6). (B) Duplicated alleles (14, 15) were found at locus DXS7423. (C) A null allele was observed at locus DXS10079. S3 Fig. P-values for the pairwise exact test matrix for linkage disequilibrium among the 12 X-STR loci. S4 Fig. Ranking of Investigator Argus X-12 QS kit (Qiagen) markers by gene diversity (GD). Rank within continental residency groups, i.e. Middle East (n = 1224), Africa (n = 448), Far East Asia (n = 815), South America (n = 1167) and Europe (n = 2980). (DOCX)</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