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Exploring Y-chromosomal STRs and SNPs for forensic and genetic insights in the Jiangsu Han population

BMC Genomics volume 26, Article number: 440 (2025) Cite this article

Abstract

Y-chromosome short tandem repeats (Y-STRs) and single nucleotide polymorphisms (Y-SNPs) are valuable genetic markers used for individual identification, forensic applications, and the study of paternal lineage history. This study analyzed the genetic polymorphism and paternal genetic structure of the Han population in Jiangsu Province by examining 374 unrelated male individuals using 29 Y-STRs and 183 Y-SNPs. Forensic parameters were calculated, and the discriminatory power of five Y-STR systems (MHT, EXT, PPY12, Yfiler, and Y29) was compared. Genetic structure was assessed in the context of the Jiangsu Han and other Chinese populations. Results showed that the Y29 system had the highest discriminatory capacity, identifying 374 unique haplotypes with HD and DC values of 1. Seven major haplogroups (C, D, J, K, O, Q, R) and 83 terminal haplogroups were identified, with haplogroup O being the most predominant (approximately 85%). Subdivision of haplogroup O revealed that the Jiangsu Han population exhibits genetic characteristics of both Southern and Northern Han groups. Population genetic analyses further confirmed that the Jiangsu Han clustered closely with Southern Han populations. Genetic admixture results revealed that the Jiangsu Han population derives 89% of their ancestry from Southern Han populations, while retaining 11% Northern Han contributions. The study provides valuable insights into the genetic structure of the Jiangsu Han population, with significant implications for forensic genetics, anthropological research, and broader population genetics studies.

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Introduction

The human Y chromosome spans approximately 60 megabases (Mb), with its terminal regions comprising pseudoautosomal regions (PARs) that account for ~ 5% of its total bases [1]. These PARs facilitate homologous recombination with the X chromosome during meiosis. The remaining 95% constitutes the non-recombining region (NRY), which lacks pairing capability with the X chromosome [2]. Due to the absence of recombination, the NRY is inherited as a haplotype from father to son, theoretically preserving identical genetic information within the same paternal lineage in the absence of mutations [3]. These characteristics make the Y chromosome valuable in anthropology, population genetics, molecular archaeology, and human evolution studies [4,5,6]. To date, over 65,000 genetic markers have been identified on the human Y chromosome [7]. These markers are broadly categorized into two classes: biallelic variants, such as single nucleotide polymorphisms (SNPs), and multiallelic loci, exemplified by short tandem repeats (STRs) [8–9]. Two primary genetic markers on the Y chromosome, Y-STRs and Y-SNPs, are widely used in forensic paternity testing, personal identification, and population structure analysis.

Y-STRs are highly polymorphic and can be readily detected using standard genetic analyzers, making them a preferred tool for forensic DNA analysis. They are instrumental in solving crimes, accurately determining paternity, and identifying kinship, even in the absence of maternal or other familial samples [10]. However, their relatively high mutation rates (3.95 × 10− 4-1.40 × 10− 2 per locus per generation, https://yhrd.org/) can complicate studies involving distant relatives or ancient DNA. In contrast, Y-SNPs have much lower mutation rates (~ 3 × 10− 8 mutations/generation), offering stability over generations [11–12]. This stability underpins their role in constructing the Y-chromosome haplogroup phylogenetic tree, which classifies global male populations into hierarchical clades.

Although less polymorphic than Y-STRs, Y-SNPs complement them by providing additional insights, enhancing the accuracy and reliability of forensic analyses. Together, Y-STRs and Y-SNPs form a robust dual-marker system, enabling precision paternity testing, kinship analysis, and a deeper understanding of population genetic structures [13–14].

The Han ethnic group, the largest in China, exhibits notable genetic diversity influenced by geography, historical migrations, and cultural exchanges. While broad genetic patterns among Southern and Northern Han populations are relatively well-studied [15], subgroups such as those in Jiangsu Province remain underexplored. Jiangsu, a critical province in eastern China, serves as a cultural and geographical bridge between south and north regions. As a hub for population and cultural exchanges, studying the Han population in Jiangsu offers an opportunity to uncover the genetic characteristics of this transitional zone and gain deeper insights into the genetic diversity and distribution within the Han ethnicity.

Despite the importance of Jiangsu’s Han population, previous studies have focused primarily on Y-STR markers, often analyzing an insufficient number of loci. While these studies have provided data on genetic polymorphisms and intergroup variations, they have not adequately addressed the distribution of Y-SNP haplogroups or the paternal genetic structure of the population. A more comprehensive approach that combines Y-STR and high-resolution Y-SNP data is essential to fill these gaps.

This study employs 29 Y-STR loci and a high-resolution haplogroup system comprising 183 Y-SNP markers to analyze genetic polymorphisms in the Han population of Jiangsu Province. The objectives are to elucidate the paternal genetic structure of this population, expand the genetic database of eastern China, and provide accurate data to advance forensic and human genetic research.

Materials and methods

Sample collection and DNA extraction

Blood samples were collected with the approval of the Ethics Committee of Academy of Forensic Science, Ministry of Justice, China (2014-3-3-5). Male participants were eligible if their ancestors had resided in Jiangsu Province for at least three generations. Peripheral blood was collected after receiving written informed consent. Finally, a total of 374 unrelated male individuals were collected. The geographic location of the Jiangsu Province is detailed in Supplementary Fig. S1. Genomic DNA was extracted using QIAamp DNA blood Mini Kit (Qiagen, Germany), following the manufacturer’s instructions, and quantified with NanoDrop 2000c (Thermo Fisher Scientific). DNA samples were stored at -20 °C until PCR amplification.

Y-STR typing via capillary electrophoresis

The Goldeneye 29Y kit (Peoplespot Technology Ltd., Beijing, China), referred to as Y29, was used to generate Y-chromosome haplotypes for 29 Y-STR loci. This kit includes all loci from the Yfiler kit, supplemented with the four rapidly mutating Y-STR loci and eight loci with low-medium mutation rates. Specifically, the 29 loci analyzed were: DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS385, DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, DYS635, Y-GATA-H4, DYS526a, DYS526b, DYS570, DYS576, DYS626, DYS388, DYS460, DYS481, DYS593, DYS596, DYS643, DYS645. PCR was performed on a GeneAmp 9700 thermal cycler (Thermo Fisher Scientific) in accordance with the manufacturer’s recommendations. Separation and detection of PCR products were carried out with the Applied Biosystems 3130XL Genetic Analyser (Applied Biosystems, CA, USA). STR profiles were analysed with the ORG-500 Size Standard and allelic ladder (Peoplespot Technology Ltd., Beijing, China) and the set of bins and panels provided by the manufacturer using GeneMapper ID v3.2 software (Applied Biosystems, CA, USA).

Y-SNP typing via MALDI-TOF MS platform

Y-SNPs typing employed a self-designed panel of 183 markers, developed based on DNA mass spectrometry (MALDI-TOF MS). The panel included 36 Y-SNPs from major world-wide haplogroups (A to R) and 147 additional markers specific to haplogroup O. Marker nomenclature followed the International Society of Genetic Genealogy (ISOGG2019) guidelines. Detailed information regarding the primers of 183 Y-SNP markers, the names and corresponding haplogroups of the 183 Y-SNPs, the chromosomal positions relative to human reference sequence hg19, dbSNP rs numbers, and mutation information is shown in the Supporting Information of our previous study [16].

Data analysis

Y-STR analytic methods

Allele and haplotype frequencies were estimated by the direct counting method. Haplotype diversity (HD) and gene diversity (GD) were calculated according to the formula of Nei and Tajima [17]: HD/GD = n (1- ∑Pi2)/ (n-1), where n is the total number of samples and Pi denotes the frequency of the i-th allele/haplotype. Match probability (MP) was computed as the sum of squared haplotype frequencies (MP =∑Pi2). Discrimination capacity (DC) was calculated as the ratio between the number of observed haplotypes and the number of total samples. The percentage of unique haplotype (PUH) was calculated by dividing the number of unique haplotypes by the total sample size.

The Y29 system encompasses all the STR loci present in the European minimal haplotype (MHT), extended haplotype (EXT), PowerPlex Y12 (PPY12), and Yfiler kits. In light of this comprehensive coverage, we partitioned the haplotypes generated by the Y29 system into five distinct haplotype systems, namely Y29 itself, MHT, EXT, PPY12, and Yfiler. Subsequently, we computed the relevant forensic efficiency parameters, specifically haplotype diversity (HD), discrimination capacity (DC), and the proportion of unique haplotypes (PUH), for each of these five systems separately.

Y-STR haplotypes from 24 published Chinese populations (comprising both Han Chinese and diverse ethnic minority groups) alongside 9 geographically distinct outgroups were curated as reference datasets [18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48]. Detailed group information was listed in Table S1. To characterize population genetic structure, pairwise Fst genetic distances were computed by Arlequin (version 3.5.2.2) software [49] and visualized via multidimensional scaling (MDS) analysis using IBM SPSS Statistics 23 software (IBM Corp., Armonk, NY, USA). Additionally, a neighbor-joining (NJ) phylogenetic tree [50] was inferred from these Fst matrices using MEGA X software (version 10.0.5), which incorporates bootstrapping (1,000 replicates) to assess branch robustness [51]. Samples carrying duplicated alleles (and triplicated alleles), null alleles, and microvariants were excluded during the Fst analysis. P-values were calculated at a significance level of 0.05 using 1,000 permutations.

Y-SNP analytic methods

Haplogroup frequencies were estimated by the direct counting method. The haplogroup diversity and DC value were calculated using the same method as Y-STR. A total of 36 representative reference populations were selected based on haplogroup frequency distributions derived from supplementary datasets encompassing both ancient and modern Chinese populations [15, 52,53,54,55,56,57,58]. Since the haplogroup classifications of each reference population were different, we pooled the haplogroup results of these reference populations together using the main haplogroups and calculated the haplogroup frequency. The reference populations were listed in Supplementary Table S2. Based on the results of haplogroup frequencies, a Reynold’s distance matrix was obtained with Arlequin (version 3.5.2.2) software [49], and used as input for MDS analysis. MDS plots were constructed using IBM SPSS Statistics 23 software (IBM Corp., Armonk, NY, USA).

Y- STR and Y-SNP joint analytic methods

Median-joining (MJ) networks of Y-STR haplotypes (comprising DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, and DYS393) for O-clade sub-haplogroups in the Jiangsu Han, Northern Han, and Southern Han populations [15] were constructed using NETWORK 10.2 software (Fluxus Technology, Suffolk, UK) [59]. Graphical representation of these networks was subsequently generated with Network Publisher software (Fluxus Technology, Suffolk, UK). Locus-specific weights were assigned based on empirical mutation rate estimates [57, 60].

An analysis of molecular variance (AMOVA) was conducted to assess the population structure between the Jiangsu Han, Northern Han, and Southern Han populations, employing the Arlequin software (version 3.5.2.2) [49]. Both Y-STRs and Y-SNPs were utilized in this analysis. The Y-STR dataset consisted of 17 loci, consistent with those included in the Yfiler kit. The Y-STR and Y-SNP data for the Northern and Southern Han populations were sourced from the literature [15]. The Southern Han group encompassed six populations, namely the Han populations from Guangdong, Guangxi, Fujian, Zhejiang, Jiangxi, and Hunan. The Northern Han group was composed of five populations, including the Han populations from Beijing, Shandong, Heilongjiang, Henan, and Shanxi.

Admixture analysis between the Jiangsu Han, Northern Han, and Southern Han populations was performed using the coalescent-based approach implemented in Admix 2.0 software [61–62]. This method infers genetic contributions from hypothetical parental source populations by modeling STR haplotype frequencies as alleles at a single locus. Specifically, the Northern and Southern Han populations were designated as the primary parental groups for admixture estimation. The analysis incorporated seven Y-STR loci (DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, and DYS393), selected based on their mutation rate parameters and forensic relevance [57].

Results

Y-STR haplotype analysis

In this study, 374 unique haplotypes were identified from 374 male samples (Supplementary Table S3), with a total of 206 alleles observed. Allele frequency distributions and gene diversity values for Y-STR loci were listed in Supplementary Table S4. The number of alleles at single-copy Y-STRs varied from 4 (DYS645, DYS393, DYS437 and DYS593) to 12 ( DYS458). For the multi-copy DYS385a/b, 17 alleles and 58 haplotypes were identified.

Additionally, one null allele was observed at DYS438 and six intermediate alleles [DYS460 (7.2), DYS576 (18.3), DYS645 (7.1), DYS448 (19.2) and DYS458 (18.2/19.2)] were detected in seven samples. Of these, microvariants (except DYS645) were observed in YHRD. DYS645 (7.1) was reported for the first time.

The GD values exceeded 0.5 for 25 of the 29 loci, with the lowest being 0.0628 (DYS645) and the highest 0.9598 (DYS385). Key forensic parameters showed robust discriminative power: HD and DC values were both 1, while the MP value was 0.0027 (Supplementary Table S5).

Further analysis of forensic parameters across five Y-STR typing systems-MHT, EXT, PPY12, Yfiler, and Y29-highlighted significant differences in discriminative power as the number of Y-STR loci increased (Table 1). In the MHT system (9 Y-STRs), the DC was only 0.8021 and HD was 0.9983, including 300 different haplotypes. While in the Yfiler system (17 Y-STRs), the DC was 0.9786 and HD was 0.9999, including 366 different haplotypes. After the addition of 12 Y-STR markers, the DC and HD values were significantly increased to 1 in the Y29 system with 374 different haplotypes. The value of the PUH ranged from 66.84% (MHT) to 100% (Y29).

Table 1 The number of haplotypes and the forensic parameters estimated for different combinations of Y-STR loci (N = 374)
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Comparison of Jiangsu Han with other populations based on Y-STR

To better reveal the genetic relationship between Jiangsu Han and 24 other Chinese populations, pairwise genetic distance (Fst) and p values based on 17 Y-STRs (Yfiler kit) among 25 Chinese populations were summarized in Supplementary Table S6. The closest genetic distance was observed between the Jiangsu Han and Changzhou Han (Fst = 0.0033, p = 0.2295), while the furthest genetic distance was found with the Xinjiang Kazak (Fst = 0.550, p = 0.4337).

These genetic distances were visualized using a multidimensional scaling (MDS) plot (Fig. 1a) and a neighbor-joining (NJ) phylogenetic tree (Fig. 1b). The MDS plot revealed that the Jiangsu Han population showed no significant genetic differentiation from other Han subgroups across China but displayed clear distinctions when compared to certain ethnic minority groups. The Jiangsu Han clustered closely with the Southern Han groups in the central-right region of the MDS plot and maintained proximity to the Northern Han populations, indicating a transitional genetic structure. Ethnic minority groups were more dispersed around these clusters.

Similar patterns were reflected in the NJ phylogenetic tree, where the Jiangsu Han and other Han populations formed distinct branches separated from ethnic minorities, consistent with their geographic and genetic backgrounds. However, notable exceptions included the Hainan Li and Liangshan Yi groups, which appeared closer to the Han populations. This could be attributed to historical intermarriage between these groups and the Han population in recent decades, influencing their genetic composition.

Population comparisons of the Jiangsu Han with the other 9 populations from the outgroups were also conducted based on 17 Y-STRs (Supplementary Figure S2). The results revealed that Jiangsu Han had a close relationship with East Asian and Southeast Asian populations.

Fig. 1
figure 1

Jiangsu Han and other reference populations based on Fst value of 17 Y-STRs. (a) MDS plot. (b) N-J phylogenetic tree. Jiangsu Han marked with a red box

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Y-SNP haplogroup distribution

A total of seven major haplogroups O (85.03%), C (9.09%), K (4.01%), D (0.53%), Q (0.8%), J (0.27%), and R (0.27% ) were observed in the Jiangsu Han (Fig. 2). Within these, 83 unique terminal haplogroups were detected, and their frequencies were listed in Supplementary Table S7. Forensic parameters revealed a HD of 0.9480 and a DC value of 0.2219 (Table S5).

To investigate the frequency distributions of haplogroups across Chinese populations and other East Asian and Southeast Asian populations, comparative analyses were conducted. Haplogroup frequency data for Southern Han, Northern Han [15], other East Asian nations (Japan and Korea) [56], and Southeast Asian populations (Thailand, Vietnam, Indonesia, and the Philippines) [57]were systematically retrieved from the literature. The outcomes of these inter-population comparisons are visually depicted in Fig. 2, enabling a clear assessment of haplogroup distribution patterns among the studied groups.

A comprehensive analysis of nine East Asian and Southeast Asian populations revealed the presence of a total of fourteen major haplogroups (C, D, F, G, H, J, K, L, N, NO1, O1, O2, Q, and R). Evidently, the O haplogroup emerged as the predominant lineage across all populations under investigation. The O haplogroup can be further classified into O1 and O2 sub-haplogroups. In Chinese Han populations, Korea and Vietnam, the frequency of the O2 sub-haplogroup exceeded that of the O1 sub-haplogroup. Conversely, in Japan and three Southeast Asian countries (Thailand, Indonesia, and the Philippines), the O1 sub-haplogroup was more prevalent than the O2 sub-haplogroup.

In the Jiangsu Han population, the frequency of the O1 haplogroup was 26.20%, which is consistent with the characteristics of Southern Han populations, where the O1 haplogroup typically accounts for over 25%. In contrast, in Northern Han populations, the frequency of the O1 haplogroup usually remains below 20%. The frequency of the O2 haplogroup in the Jiangsu Han population was 58.82%, and it was further subdivided into four subgroups: O2a1 (17.11%), O2a2a (10.16%), O2a2b (30.75%), and O2b1a (0.8%).

In East Asian populations, excluding Japan, the C haplogroup was the second-most frequent haplogroup. In Japan, the D haplogroup held this position. In Southeast Asian countries, haplogroups such as F, K, and Q were among the second-largest haplogroups, yet their distribution was relatively scarce in East Asian populations. These findings contribute to an in-depth understanding of the genetic structure and diversity within East Asian and Southeast Asian populations, providing valuable insights into the complex genetic history and population dynamics of these regions.

Fig. 2
figure 2

The major haplogroup frequency distribution in Jiangsu Han and East/Southeast Asian populations

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Comparison of Jiangsu Han with other populations based on Y-SNP

To further elucidate the genetic relationships among diverse populations, an MDS plot was constructed using haplogroup frequencies from the Jiangsu Han and 36 reference populations. As depicted in Fig. 3, Chinese Han populations (excluding the Guangxi Han) clustered closely on the right side of the MDS plot. This concentrated distribution underscores substantial genetic similarities among Han groups, likely stemming from shared ancestral origins or recent genetic exchanges. Furthermore, the Jiangsu Han population exhibited tight clustering with Southern Han groups (e.g., Guangdong, Fujian, Zhejiang, Hunan, and Jiangxi populations), exemplifying genetic proximity. In contrast, it demonstrated distinct separation from Chinese Hui populations (e.g., Yunnan Hui, Gansu Hui) and Chinese ethnic minority groups (e.g., Li, Dai). Additionally, the Jiangsu Han population was genetically distanced from Southeast Asian populations (Vietnam, Thailand), South Asian populations (Pakistani), and East Asian populations (Korea, Japan), highlighting its unique genetic positioning within the Han ethnic framework. We collected a dataset of the ancient Taiwan population (TW), dating from approximately 6000 BCE to 1000 CE. As visualized in the MDS plot, the ancient Taiwan population was distinctly positioned apart from most modern populations.

Fig. 3
figure 3

MDS based on the frequencies of Y-SNP haplogroups. Jiangsu Han marked with a red box

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Network analysis

To investigate the genetic structure among Jiangsu Han, Northern and Southern Han in detail, we carried out a series of analyses. We used the median joining (MJ) method to create the STR haplotype network within the O sub-haplogroup. The median-joining network based on 7 Y-STRs for haplogroups O1, O2a1, O2a2a, and O2a2b revealed distinct clustering patterns among Jiangsu Han, Southern Han, and Northern Han populations (Fig. 4). As depicted in Fig. 4, for Jiangsu Han, within each haplogroup network, Jiangsu Han individuals were interspersed with Southern Han and Northern Han, indicating shared haplotype connections. In the O1 network, Jiangsu Han clustered centrally, suggesting a core contribution to the haplotype diversity. Similarly, in the O2a1, O2a2a, and O2a2b networks, Jiangsu Han nodes were distributed across various branches, with some forming prominent sub-clusters. The network topology showed a central star-like structure dominated by O2a2a, which suggested a founder effect or recent population expansion. Subclusters of O1 and O2a2b displayed closer genetic proximity to Southern Han populations, while O2a1 exhibited partial overlap with Northern Han haplotypes. Notably, Jiangsu Han occupied an intermediate position between Southern and Northern Han in the network, indicating bidirectional genetic influences.

Fig. 4
figure 4

Median-joining network based on 7 Y-STRs

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AMOVA and admixture

To estimate the ancestry proportion, AMOVA was conducted between the Jiangsu Han population and the groupings of Northern Han and Southern Han Chinese populations, as shown in Table 2. For Y-SNP data, as expected, the majority of variance (93.84%, p < 0.001) originated from within-population differences. Moderate variance (3.08%, p < 0.001) was observed within groups, while significant differences (3.08%, p = 0.027) were detected among groups. Regarding Y-STR data, the vast majority of variance (98.90%, p < 0.001) resided within populations. Slight variance (1.22%, p < 0.001) occurred within groups, and no significant differences were identified among groups. For both Y-SNPs and Y-STRs, intraspecific variation within populations served as the dominant contributor to genetic variance. Notably, Y-SNPs exhibit the capability to unravel differentiation patterns at both the intergroup level and the intragroup population level, thereby highlighting their superior sensitivity in dissecting interpopulation genetic structures.

Table 2 Analysis of molecular variance (AMOVA) using Y-SNPs and Y-STRs
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Using Admix 2.0, the contributions of the two hypothetical parental groups “Southern Han” and “Northern Han” to the hybrid population (Jiangsu Han) were estimated, with results presented in Table 3. The findings reveal that Jiangsu Han derived approximately 11% of its ancestry from Northern Han and 89% from Southern Han, thus supporting the hypothesis that Jiangsu Han predominantly originated from Southern Han.

Table 3 Gene contribution estimates using 7 Y-STR
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Discussion

In forensic genetics practice, Y-STRs and Y-SNPs serve as crucial genetic marker systems, demonstrating unique research value and application potential. Y-SNPs, characterized by extremely low mutation rates, effectively elucidate the paternal genetic history of populations by identifying haplogroup distribution patterns in specific geographic regions, providing molecular evidence for reconstructing ancient population migration routes. Conversely, Y-STRs exhibit significant advantages in studying genetic relationships among closely related populations and short-term evolutionary events due to their high mutation rates. This study systematically analyzed the genetic polymorphism characteristics and paternal genetic structure of the Jiangsu Han population through integration of 29 Y-STR loci and 183 Y-SNP markers. Among the five Y-STR systems, the Y29 system demonstrated the highest discriminatory power (DC = 1), with its exceptional haplotype resolution (HD = 1) proving ideal for forensic applications in the Jiangsu Han population.

The global Y-chromosomal phylogenetic tree reveals that East Asian populations primarily consist of four major haplogroups: C-M130, D-M174, N-M231, and O-M175 [63]. Notably, the O-M175-derived O1-F265 and O2-M122 haplogroup (formerly O3-M122) show high-frequency distribution in East Asian populations. The two principal subgroups of O1 haplogroup (O1a and O1b) predominantly distribute in Southern East Asia/Southeast Asia. Our findings align with previous studies [64], demonstrating higher O1 frequencies in Southeast Asian populations compared to O2, with O1 being more prevalent in Southern Chinese Han populations than their Northern counterparts.

The O2 haplogroup is dominant in East Asian populations and accounts for 58.82% of the Jiangsu Han population. O2 in Jiangsu Han is further classified into four main sub-haplogroups: O2a1, O2a2a, O2a2b, and O2b1a. According to the research records of Yan et al., O2a1 exhibits a relatively uniform distribution pattern in the Han Chinese population across the geographical regions of the east, north, and south [64]. O2a2b is also widely distributed in China, and its proportion is much higher among the Han population in the Northern region than that in the Southern region (Northern region: 34.11% vs. Southern region: 21.54%) [65].

The C haplogroup ranks as the second most frequent in East Asian populations (excluding Japan) in our study and primarily distributes in Northern Mongolia, Korea, and Northeastern China. The D haplogroup shows a high frequency among the Japanese population. Additionally, it has a notable prevalence in the populations of Tibet and the Andaman Islands. Specifically, haplogroup D1a1 is extensively spread among the Tibetan, Sichuan Yi, Yunnan Yi (Tangut-Qiang), and Lolo populations, as noted in [66]. In contrast, D1a2 is most commonly found in Tibetans, as reported in [67]. The distribution of the N haplogroup in our study primarily occurs in Korea (12%) and Northern Chinese Han (8.31%), with previous research indicating that East Asian N1a1 and N1a2 sub-haplogroups mainly distribute in Mongolia and Northern China, occasionally appearing in Manchu, Xibe, and Ewenki populations [68].

Median-joining network analysis based on Y-STR data revealed Jiangsu Han occupying central nodal positions in O1 haplogroup networks, suggesting their potential role as a genetic radiation center. In O2a sub-haplogroup networks, Jiangsu Han displayed multi-branch divergent distributions, consistent with gene flow models between Northern and Southern Han populations, reflecting the complex historical processes of Central Plains population southward migration and Baiyue ethnic integration [69]. MDS analysis demonstrated significant genetic clustering between Jiangsu Han and Southern Han populations, with substantially smaller genetic distances compared to Northern Han and minority groups. AMOVA and admixture analysis clearly revealed Jiangsu Han’s genetic admixture patterns from both Northern and Southern Han populations. Admixture analysis indicated 89% Southern Han contribution and 11% Northern Han component in Jiangsu Han’s genetic composition, robustly confirming their close genetic affinity with Southern Han populations. This pattern likely results from historical large-scale southward migrations and sustained regional gene flow. While Northern Han contributions remain relatively minor, they indicate ongoing genetic exchanges potentially attributable to early Northern Han migrations or inter-ethnic interactions.

Conclusions

This study systematically characterizes the paternal genetic architecture of the Jiangsu Han population through integrated Y-STR and Y-SNP analysis, offering novel insights into their evolutionary history and forensic relevance. Genetic admixture results reveal Jiangsu Han population derive 89% of their ancestry from Southern Han populations, consistent with historical southward migrations, while retaining 11% Northern Han contributions, reflecting long-term regional gene flow. Median-joining network analysis further highlights Jiangsu Han as a central node in the O1 haplogroup radiation, underscoring their role in shaping Southern East Asian genetic diversity. Forensic applications are advanced by the Y29 multiplex system, which exhibits exceptional discriminative power (DC = 1) and haplotype diversity (HD = 1), providing a robust tool for individual identification in this population. These findings establish a critical foundation for constructing population-specific forensic databases and refining kinship inference models in East Asia. While this research enhances understanding of Jiangsu Han genetics, limitations include restricted sub-regional sampling and reliance on Y-chromosomal markers. Future studies integrating autosomal and mitochondrial data will further resolve fine-scale population structure. Collectively, this work contributes to the genetic characterization of Han subgroups, advancing both anthropological knowledge and forensic practice.

Data availability

Data is provided within the manuscript or supplementary information files.

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Funding

This research was funded by Natural Science Foundation of Shandong Province(No. ZR2022QH337), the Visiting Research Fund for Teachers of Ordinary Undergraduate Universities in Shandong Province, National Natural Science Foundation of China (No. 82002006) and Qingchuang Talents Induction Program of Shandong Higher Education Institution (2022 Forensic medicine innovation team).

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Author notes

  1. Min Li and Han Zhang contributed equally to this work.

Authors and Affiliations

  1. Department of Forensic Medicine, School of Clinical and Basic Medical Sciences, Shandong First Medical University& Shandong Academy of Medical Sciences, Jinan, 250117, China

    Min Li, Peng Zhou, Chunjiang Yu & Chen Fang

  2. Institute of Forensic Science, Fudan University, Shanghai, 200032, China

    Han Zhang, Anqi Chen, Suhua Zhang & Chengtao Li

  3. Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Key Laboratory of Forensic Science, Academy of Forensic Sciences, Ministry of Justice, Shanghai, 200063, China

    Ruiyang Tao, Yingnan Bian & Chengtao Li

Authors
  1. Min Li
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Contributions

CF and CL proposed the initial idea. SZ and YB developed the methodology. ML carried out experiments and mainly wrote the manuscript. CF and CL supervised and administrated the project, HZ composed and drew figures. RT and AC investigated resulting data and validated results. PZ and CY made formal analysis. CF and ML acquired the funding. All authors read and approved the final manuscript.

Corresponding authors

Correspondence to Chen Fang or Chengtao Li.

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Ethics approval and consent to participate

The study was conducted in accordance with the Declaration of Helsinki, and approved by the Ethics Committee of Academy of Forensic Science, Ministry of Justice, China (2014-3-3-5). Informed consent was obtained from all subjects involved in the study. Written informed consent has been obtained from the samples to publish this paper.

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The authors declare no competing interests.

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Li, M., Zhang, H., Tao, R. et al. Exploring Y-chromosomal STRs and SNPs for forensic and genetic insights in the Jiangsu Han population. BMC Genomics 26, 440 (2025). https://doiorg.publicaciones.saludcastillayleon.es/10.1186/s12864-025-11634-6

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BMC Genomics

ISSN: 1471-2164

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