Population data of 23 Y chromosome STR loci for Kyrgyz population from Kyrgyzstan

Abstract

Y-chromosomal short tandem repeats (Y-STRs) serve as essential markers in forensic genetics, population studies, and paternal lineage reconstruction due to their strict uniparental inheritance and high discriminatory power. Despite their global relevance, Central Asian populations, particularly the Kyrgyz, remain underrepresented in major Y-STR reference databases. These population data represent 23 Y-STR loci from 514 unrelated Kyrgyz males sampled from three geographically distinct regions: Northern East (N = 134), Northern West (N = 183), and Southern Kyrgyzstan (N = 197). Genotyping was conducted using the PowerPlex Y23 System, and the resulting dataset has been submitted to the Y Chromosome Haplotype Reference Database (YHRD) to strengthen forensic and anthropological research in the region. A total of 346 unique haplotypes were identified, demonstrating high haplotype diversity (HD = 0.981–0.990) and discrimination capacity (64–70 %). AMOVA analysis indicates that the division of Kyrgyz populations into northern and southern groups does not accurately represent their genetic structure, as over 99 % of genetic variation is distributed within subpopulations, indicating weak differentiation and substantial shared paternal ancestry among the regional Kyrgyz groups. The analysis also identifies four dominant haplogroup clusters (R1a, C2a, N1, and R1b), providing valuable insights into the historical and demographic dynamics of the Kyrgyz people. This dataset enhances our understanding of Kyrgyz genetic diversity, contributes to forensic applications, and fills a critical gap in population genetic research on Central Asian lineages.

Specifications Table

Subject	Genetics
Specific subject area	Forensic Genetics, DNA Profiling, Population Genetics
Data format	Raw and Analyzed
Type of data	Supplementary tables (6), table (2) and figures (3)
Data collection	Samples were collected from healthy male volunteers of the Kyrgyz population using the Oragene DNA Self-Collection Kit (OG-500, DNA Genotek, Canada) for saliva and EDTA-coated sterile vacutainers (BD Vacutainer®, Becton Dickinson, USA) for blood. Each participant was verified to be unrelated to others in the study up to the third generation. DNA was extracted from saliva using the prepIT-L2P kit (DNA Genotek, Canada) and from blood using phenol-chloroform extraction preceded by proteinase K digestion. The quality and concentration of the DNA were assessed using the NanoDrop One Spectrophotometer and Qubit 2.0 Fluorometer (both from Thermo Fisher Scientific, USA). The DNA was then amplified by PCR using the PowerPlex Y23 System (Promega, USA) in a SimpliAmp Thermal Cycler (Thermo Fisher Scientific, USA). The PCR products were separated by electrophoresis using the WEN Internal Lane Standard 500 (Promega, USA) in Hi-Di Formamide on an Applied Biosystems 3500 genetic analyzer with an 8 capillary array and POP-4 polymer, along with Cathode and Anode buffers (all of them from Thermo Fisher Scientific, USA). The analysis of STR alleles in the electropherograms was conducted using the GeneMapper IDx v.1.6 software. Subsequent data analyses were performed utilizing Microsoft Office Excel, the Arlequin software version 3.5.2.2, STRAF software version 2.1.5, NevGen software version 1.0 and AMOVA&MDS tool from YHRD (Y-chromosome haplotype research database).
Data source location	Laboratory of Human Genetics, National Center for Biotechnology, Astana, 010000, Kazakhstan
Data accessibility	Repository name: Mendeley Data Data identification number: 10.17632/5yrd8k7syp.2 Direct URL to data: https://data.mendeley.com/datasets/5yrd8k7syp/2

1. Background

Y-chromosomal short tandem repeats (Y-STRs) serve as indispensable markers in forensic genetics, kinship analysis, and population studies due to their strict paternal inheritance and high discriminatory power. These markers facilitate the reconstruction of paternal genealogies and provide insights into human migration patterns and demographic history. The forensic and anthropological utility of Y-STRs is further enhanced by databases such as the Y-Chromosome Haplotype Reference Database (YHRD), which enable comparative analyses and haplotype frequency estimation. Despite the global expansion of Y-STR reference datasets, Central Asian populations, particularly those from Kyrgyzstan, remain underrepresented. The absence of Y-STR profiles from the Kyrgyz population in YHRD limits the efficacy of forensic investigations and population genetic studies in the region. To address this gap, we compiled a dataset of 23 Y-STR loci from 514 unrelated male individuals representing three geographically distinct populations: Northern East Kyrgyzstan (N = 134), Northern West Kyrgyzstan (N = 183), and Southern Kyrgyzstan (N = 197). Samples were analyzed using standard forensic genotyping methods to generate a comprehensive dataset suitable for forensic and population genetic applications. This dataset expands the representation of Central Asian populations in forensic and anthropological Y-STR research and provides a valuable resource for future studies on genetic diversity and population structure in the region.

2. Value of the Data

• •The population data of 23 Y chromosome STR loci for the three subpopulation of Kyrgyz from Kyrgyzstan provide a detailed genetic signature within the broader Kyrgyz population, offering valuable insights into paternal lineage differentiation and the microstructure of sub-populations in Central Asia.
• •The submission of Y-STR profiles from the Kyrgyz population to the Y-Chromosomal Haplotype Reference Database (YHRD) supports global forensic research by enhancing the accuracy of kinship analysis, facilitating criminal investigations, and aiding in the identification of missing persons through the enrichment of comparative datasets.
• •This dataset represents a key resource for studies in population genetics and anthropological research, enabling a deeper understanding of the genetic diversity within Kyrgyz populations and their connections to neighboring and distant populations across Eurasia.
• •The comprehensive analysis of these Y-STR profiles holds great potential for future research, enabling more in-depth genetic genealogy studies to unravel the demographic history and cultural interactions of the Kyrgyz population.

3. Data Description

In this study, we analyze 514 Y-chromosomal haplotypes from three Kyrgyz subpopulations— Northern East Kyrgyzstan (N = 134), Northern West Kyrgyzstan (N = 183), and Southern Kyrgyzstan (N = 197) —genotyped using 23 Y-STR markers with the PowerPlex Y23 System (Promega, USA). Kyrgyzstan is a landlocked, mountainous country in Central Asia, characterized by a complex topography of intermontane basins and extensive mountain systems, primarily the Tien Shan and Pamir-Alay ranges. The northern part of the country encompasses major intermontane valleys, including the Chüy, Talas, and Issyk-Kul valleys, which have historically provided favorable conditions for sedentary agriculture and livestock breeding. In contrast, the central region, particularly the Naryn highlands, is dominated by a transhumant pastoral economy adapted to high-altitude environments, while the southern regions, including theOsh, Jalal-Abad, and Batken are known for the cultivation of cotton, melons, and fruit orchards [1].

As of 2024, Kyrgyzstan has an estimated population of over 6.7 million, of whom approximately 4.9 million belong to the titular ethnic group, the Kyrgyz (Joshua Project, https://joshuaproject.net/, accessed on 1 August 2024). Ethnohistorical evidence suggest that populations bearing the ethnonym “Kyrgyz” were historically distributed across a broad geographic expanse, including southern Siberia, Mongolia, and Central Asia. The formation of the modern Kyrgyz people was shaped by a complex admixture of steppe and sedentary populations, with history and cultural contributions from Saka-Wusun groups, early Turkic and Uyghur polities, Mongolic expansions, and Kipchak confederations. Linguistically, Kyrgyz belongs to the Kipchak branch of the Turkic language family, exhibiting close affiliations with Kazakh, Karakalpak, and Nogai, indicative of prolonged contact and shared linguistic evolution among Central Asian nomadic societies.

The Y-chromosomal diversity observed in contemporary Kyrgyz populations provides insight into the genetic legacies of these historical interactions, reflecting patterns of patrilineal inheritance shaped by demographic processes, social structure, and historical migration dynamics [[2], [3], [4], [5]]. Further analysis of Y-STR and Y-SNP variation in this population contributes to a deeper understanding of paternal lineage continuity, founder effects, and the broader genetic landscape of Central Asia.

The haplotype distribution within the Kyrgyz population is detailed in Supplementary Table 1, revealing a total of 346 distinct haplotypes identified across 514 individuals based on a 23-STR marker panel. The frequencies of these haplotypes within the three regional subpopulations—Northeastern Kyrgyzstan, Northwestern Kyrgyzstan, and Southern Kyrgyzstan—are provided in Supplementary Table 2. While some haplotypes were shared between pairs of individuals, a few were observed in larger clusters, with the most prevalent haplotypes occurring at a frequency of 0.082, each shared by 11 individuals. Summary metrics, including haplotype diversity (HD), discrimination capacity (DC), and haplotype match probability (HMP), are presented in Table 1.

Table 1.

Comparison of genetic polymorphism of 27 Y-STR haplotypes in the Kyrgyz populations.

Population	Number of samples	Number of distinct haplotypes	Frequency of unique haplotypes	Discrimination capacity	Haplotype match probability	Haplotype diversity
Northern East Kyrgyzstan	134	90	59 %	67 %	0.0267	0.981
Northern West Kyrgyzstan	183	118	51 %	64 %	0.0181	0.987
Southern Kyrgyzstan	197	138	57 %	70 %	0.0150	0.990

The allele frequencies of the 21 single-copy Y-STR loci within the Kyrgyz population are detailed in Supplementary Table 3, while those of the one multi-copy loci are provided in Supplementary Table 4. Fig. 1 illustrates the allele frequency distribution across 23 individual Y-STR loci. A total of 137 distinct alleles were identified at single-copy loci, with allele frequencies ranging from 0.004 to 0.866. The lowest allelic diversity (N = 3) was observed at the DYS393 locus, whereas the highest (N = 12) was recorded at DYS481. Gene diversity (GD) among single-copy loci varied from 0.243 at DYS437 to 0.753 at DYS481. At the multi-copy locus DYS385a/b, 36 distinct allelic combinations comprising 12 different alleles were identified, with an overall gene diversity of 0.721. Notably, abnormal alleles were detected at the DYS19 and DYS481 loci, including a copy number variation at DYS19 (alleles 16–17) and a microvariant allele at DYS481, as detailed in Supplementary Table 4.

Fig. 1.

Distribution of allelic frequencies per locus on 23 Y-STR loci in Kyrgyz population using STRAF software.

Table 2 presents the AMOVA results, which demonstrate that the vast majority of genetic variation in Kyrgyz populations is concentrated within populations (99.22 %), whereas differentiation among populations is minimal (0.78 %, FST = 0.00782, p = 0.000). When analyzed by geographic grouping (Northern and Southern), the proportion of variation among groups was negative (-0.25 %), indicating an absence of significant genetic structuring between these regions. The predominant source of genetic variation remains within populations (99.29 %), with only minor differentiation observed among populations within groups (0.96 %, FST = 0.00713, p = 0.000). These findings suggest that the dichotomous classification of Kyrgyz populations into northern and southern groups does not reflect the underlying genetic structure, as the genetic diversity is primarily distributed within populations rather than between them.

Table 2.

AMOVA results for Y-STR haplotypes in Kyrgyz populations.

No Groups
Source of variation	d.f.	Sum of squares	Variance component	% of variance	Fixation Indices	p-value
Among populations	2	2.303	0.00389 Va	0.78	FST: 0.00782	0.000 ± 0.000
Within populations	511	252.078	0.49330 Vb	99.22
Total	513	254.381	0.49719
Grouped by Geography (Two Groups: Northern and Southern)
Among groups	1	1.071	-0.00123 Va	-0.25	FSC (Va):0.00959	0.000 ± 0.000
Among populations within groups	1	1.232	0.00478 Vb	0.96	FST (Vb):0.00713	0.000 ± 0.000
Within populations	511	252.078	0.49330 Vc	99.29	FCT (Vc):-0.00248	1.000 ± 0.000
Total	513	254.381	0.49685

The distribution of predicted Y-chromosome haplogroups among the Kyrgyz population is presented in Supplementary Table 1. The majority of Y-chromosomal diversity (87 %) is concentrated within four predominant haplogroups, each exceeding a frequency threshold of 5 %: R1a (55 %), C2a (20 %), N1 (6 %), and R1b (5 %). Fig. 2 illustrates the founder effect within the R1a haplogroup, which comprises 276 haplotypes, and demonstrates that the derived haplotypes, originating from the putative ancestral haplotype, are present across all three geographic regions of Kyrgyzstan.

Fig. 2.

Median-joining network of 21 Y-STR (DYS385a/b loci were excluded) haplotypes for Kyrgyz population belonging to R1a haplogroup. The colors represent the geographical population of the Kyrgyz. Circles represent haplotypes (frequency > 1 criterion active), with the area proportional to the sample size, and lines between them proportional to the number of mutational steps. Haplotype clusters are delineated with a dotted circle and annotated according to haplogroups.

In the genetic landscape depicted in Fig. 3, the Kyrgyz population occupies a distinct position, which exhibits clear genetic differentiation from neighboring populations. Pairwise genetic distances (RST) between Kyrgyz subpopulations and other Central Asian groups, calculated based on 17 Y-STR loci, are detailed in Supplementary Table 5. The closest genetic affinity is observed between the Northern West and Northern East Kyrgyz subgroups (RST = 0.040). Notably, the Southern Kyrgyz population exhibits its closest genetic relationship with the Mongolian population from Ulaanbaatar (RST = 0.033). Further investigation into intra-population diversity at the clan level is warranted, as this may elucidate the genetic affinities observed between specific clans of the Southern Kyrgyz population and the Mongolian population from Ulaanbaatar.

Fig. 3.

Multidimensional scaling plot (stress – 0.156) based on pairwise genetic distance (RST) between Kyrgyz and neighboring populations on 17 Y-STRs.

4. Experimental Design, Materials and Methods

4.1. Sample collection

In this study, 112 saliva samples and 402 blood samples were collected from healthy Kyrgyz male participants representing three subpopulations from Northeast, Northwest, and Southern Kyrgyzstan, following the guidelines established by the population-genetic biobank [6]. Prior to sample collection, each individual signed a written informed consent form and provided information regarding their ancestral origins. All participants were verified to be unrelated to one another for at least three paternal generations. Saliva samples were collected using the Oragene DNA (OG-500) Self-Collection Kit (DNA Genotek, Canada), and blood samples were collected using EDTA-coated sterile vacutainers (BD Vacutainer®, Becton Dickinson, USA) according to the manufacturer’s instructions.

4.2. DNA isolation, amplification and STR genotyping

Genomic DNA was extracted from saliva using the prepIT-L2P kit (DNA Genotek, Canada) and from blood using phenol-chloroform extraction preceded by proteinase K digestion. The DNA concentration was measured with a Qubit 2.0 Fluorometer (Thermo Fisher Scientific, USA), and purity was assessed by NanoDrop One spectrophotometry (Thermo Fisher Scientific, USA). PCR amplification was carried out using the PowerPlex Y23 System (Promega, USA) on a SimpliAmp Thermal Cycler (Thermo Fisher Scientific, USA). The resulting amplicons were subsequently separated via capillary electrophoresis on an Applied Biosystems 3500 Genetic Analyzer (Thermo Fisher Scientific, USA), employing eight capillaries, POP-4 polymer, WEN Internal Lane Standard 500 (Promega, USA), and both Cathode and Anode buffers (Thermo Fisher Scientific, USA). For each genotyping run, Control DNA 007 (Thermo Fisher Scientific, USA) served as a positive control, whereas ddH2O was used as a negative control. The PowerPlex Y23 System (Promega, USA) includes 17 traditional Y-STR loci (DYS19, DYS385 a/b, DYS389I/II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, DYS635, and Y-GATA-H4) in addition to 6 fast-mutating sites (DYS481, DYS533, DYS549, DYS570, DYS576, DYS643). Negative and positive controls were run in parallel for every batch. Any samples displaying atypical profiles, off-ladder peaks, or microvariant alleles were reanalyzed. Furthermore, our laboratories successfully satisfied the Y-chromosome haplotype research database (YHRD) Quality Control Test (YC000343) to contribute haplotype data. In accordance with established population-genetic data guidelines [7], the haplotypes were deposited in the YHRD database (http://www.yhrd.org) under accession number YA006045, YA006046, YA006047. The corresponding population genetic data are provided in Supplementary Table 1.

4.3. Data analysis

STR allele calls were obtained from electropherograms using GeneMapper IDx v.1.6. Haplotype frequencies were subsequently estimated in Arlequin v3.5 [8]. The number of distinct haplotypes, frequency of unique haplotypes, discrimination capacity, haplotype match probability, and haplotype diversity were all quantified in Microsoft Office Excel. Haplotype diversity (HD) was calculated with the formula HD = n × (1 – ∑pᵢ²) / (n – 1), where n is the total number of samples and pᵢ is the frequency of the i-th haplotype [9]. The sum of squared haplotype frequencies was used to derive the haplotype match probability (HMP), while discrimination capacity (DC) was defined as the ratio of distinct haplotypes to total haplotypes. Additional forensic parameters—Random Match Probability (RM), Power of Discrimination (PD), Gene Diversity (GD), Polymorphism Information Content (PIC), Power of Exclusion (PE), Typical Paternity Index (TPI), and per-locus frequency—were calculated through STRAF 2.1.5 [10]. The YHRD platform’s “AMOVA and MDS” tool (http://www.yhrd.org) facilitated pairwise genetic distance (RST) calculations and multidimensional scaling (MDS). Haplogroup designations were determined using the Nevgen Y-DNA haplogroup predictor (https://www.nevgen.org/). Median-joining networks were generated in NETWORK v5.0.1.0 and visualized using NETWORK Publisher v2.1.2.5 [11]. Because the individual alleles at the DYS385a/b loci could not be definitively assigned to either copy, those loci were excluded from the network construction. Comparative population data included Kazakhs, Kalmyks, Mongolians, Turkmens, and Uyghurs [[12], [13], [14], [15], [16], [17], [18], [19], [20], [21], [22]].

Limitations

Not applicable

Ethics Statement

This research was approved by the Ethics Committee of the National Centre for Biotechnology (protocol No. 5 of 16 October 2020), Research Institute of Molecular Biology and Medicine (protocol No. 04-13/987 of 27 June 2019) and was performed following the standards of the Declaration of Helsinki 1964. All participants in this study provided their written informed consent prior to sample collection.

Credit Author Statement

Zhainagul Isakova: Investigation, Formal analysis, Writing - Original Draft. Alizhan Bukayev: Investigation, Validation, Visualization, Writing - Review & Editing. Moldobek Irsaliev: Investigation, Project administration, Writing - Review & Editing. Zhaxylyk Sabitov: Conceptualization, Data Curation, Funding acquisition, Writing - Review & Editing. Maxat Zhabagin: Formal analysis, Writing - Original Draft, Writing - Review & Editing, Supervision.

Data Availability

• Mendeley DataPopulation data of 23 Y chromosome STR loci for Kyrgyz population from Kyrgyzstan (Original data)