Genetic polymorphism and phylogenetic differentiation of the Huaxia Platinum System in three Chinese minority ethnicities

Forensic efficiency and population genetic construction of Guizhou Gelao minority from Southwest China revealed by a panel of 23 autosomal STR loci

Short tandem repeats (STRs) are the most common genetic markers in forensic and human population genetics due to their high polymorphism, rapid detection, and reliable genotyping. To adapt the rapid growth of forensic DNA database and solve problems in disputed cases, a panel of 23 autosomal STR loci with high discriminating ability was constructed recently. The Tai-Kadai-speaking Gelao is the most ancient indigenous minority in Guizhou province, however, the forensic efficiency and population genetic structure remain poorly explored. Here, 490 Guizhou Gelao individuals from Southwest China were genotyped with the panel of 23 STRs using the Huaxia Platinum Kit. A total of 265 alleles were screened. The combined discrimination power and the combined probability of paternity were 0.9999 and 0.9999, respectively. This indicated the 23 loci had higher discrimination power in Guizhou Gelao and could be applied to forensic practice. Comprehensive population structures with reference populations from China and abroad using the neighbour-joining phylogenetic tree (N-J tree), multidimensional scaling, principal component analysis and heatmap demonstrated that Guizhou Gelao was genetically closer to Guizhou Han than other populations. Moreover, our results showed that a complex phylogenetic model was influenced by ethnic, geographic, and linguistic factors.

Key points

The first batch of genetic data for 23 autosomal STRs in 490 Geolao individuals from Guizhou was provided.The 23 STR panel can afford high genetic polymorphisms and discrimination power and can be efficiently applied to forensic practice in Guizhou Gelao population.A complex phylogenetic model influenced by ethnic, geographic, and linguistic factors was uncovered.

A proof-of-principle study: The potential application of MiniHap biomarkers in ancestry inference based on the QNome nanopore sequencing

Haplotyped SNPs convey forensic-related information, and microhaplotypes (MHs), as the most representative of this kind of marker, have proved the potential value for human forensics. In recent years, nanopore sequencing technology has developed rapidly, with its outstanding ability to sequence long continuous DNA fragments and obtain phase information, making the detection of longer haplotype marker possible. In this proof-of-principle study, we proposed a new type of forensic marker, MiniHap, based on five or more SNPs within a molecular distance less than 800 bp, and investigated the haplotype data of 56 selected MiniHaps in five Chinese populations using the QNome nanopore sequencing. The sequencing performance, allele (haplotype) frequencies, forensic parameters, effective number of alleles (Ae), and informativeness (In) were subsequently calculated. In addition, we performed principal component analysis (PCA), phylogenetic tree, and structure analysis to investigate the population genetic relationships and ancestry components among the five investigated populations and 26 worldwide populations. MiniHap-04 exhibited remarkable forensic efficacy, with 148 haplotypes reported and the Ae was 66.9268. In addition, the power of discrimination (PD) was 0.9934, the probability of exclusion (PE) was 0.9898, and the In value was 0.7893. Of the 56 loci, 85.71% had PD values above 0.85, 66.07% had PE values above 0.54, 67.86% had Ae values over 7.0%, and 55.36% were with In values above 0.2 across all samples, indicating that most of the MiniHaps are suitable for individual identification, paternity testing, mixture deconvolution, and ancestry inference. Moreover, the results of PCA, phylogenetic tree and structure analysis demonstrated that this MiniHap panel had the competency in continental population ancestry inference, but the differentiation within intracontinental/linguistically restricted subpopulations was not ideal. Such findings suggested that the QNome device for MiniHap detection was feasible and this novel marker has the potential in ancestry inference. Yet, the establishment of a more comprehensive database with sufficient reference population data remains necessary to screen more suitable MiniHaps.

A Tibetan group from Ngawa Tibetan and Qiang Autonomous Prefecture, southwest China, is rich in genetic polymorphisms at 36 autosomal STR loci and shares a complex genetic structure with other Chinese populations

The Tibetan people are ancient and populous, constituting the seventh-largest of the fifty-five ethnic minority groups in China. The Ngawa Tibetan and Qiang Autonomous Prefecture (NTQAP), situated on the border of northwest and southwest China, has its distinct group relationships. Short tandem repeat (STR) is extremely polymorphic and extensively used in the application of forensic medicine and population genetics. However, it is not clear the genetic information including linkage disequilibrium (LD) by 36 autosomal STR (A-STR) markers in the Tibetan group from NTQAP. The Tibetan population from NTQAP of southwest China was examined for 36 A-STR loci in the research. Every marker across the 36 A-STR loci was consistent with Hardy-Weinberg equilibrium (HWE). The results of the calculation revealed that the total discrimination power (TDP) is 1-2.2552 × 10-42 and the cumulative probability of exclusion (CPE) is 1-1.3031 × 10-16. Subsequently, a total of 345 alleles with allelic frequencies ranging from 0.00382 to 0.55343 were identified, and the allelic numbers varied from 5 in both the TH01 and TPOX markers to 28 in the SE33 locus. The Ngawa Tibetan population, along with other Chinese populations, exhibited influences from historical factors and regional distribution, as indicated by the results of population genetics analysis. We thus first explored the genetic characteristics and correlated forensic parameters of the 36 A-STR markers in NTQAP to fill the gap in the Tibetan population. It was discovered that these 36 autosomal STR markers supplemented forensic STR databases and offered extremely valuable polymorphisms for Chinese forensic applications, such as parentage testing and personal identification. Moreover, the study would contribute additional information regarding the substructure and diversity in the Chinese population.

A forensic population database of autosomal STR and X-STR markers in the Qiang ethnic minority of China

The Qiang ethnic group is one of the oldest ethnic groups in China and is the most active ethnic group among all the populations along the Tibetan-Yi corridor. They have had a profound impact nationally and internationally. The paternal and maternal genetic feature of the Qiang ethnic group has been revealed, leaving the question of the genetic characteristics from autosomes and X chromosome not answered. The aim of this study was to explore the potential of 36 A-STR (Microreader™ 36A ID System) and 19 X-STR (Microreader™ 19X System) for application in the Qiang population and to elucidate their genetic diversity in southwest China. The cumulative probability of exclusion (CPE) for autosomal STRs is 1-1.3814 × 10-15 and the mean paternity exclusion chance (MEC) for X-STRs is 1-1.7323 × 10-6. Forensic parameters suggest that the STRs analyzed here are well-suited for forensic applications. The results of phylogenetic, interpopulation differentiation, and principal coordinates analysis (PCoA) indicate that the Qiang people have extensive connections with ethnic minorities in China, supporting the view that the Qiang people are the oldest group in the entire Sino-Tibetan language family. The Qiang appeared genetically more associated with most ethnic groups in China, especially the Han. The calculation of random matching probability (RMP) was improved by Fst correction of allele frequencies to make RMP more accurate and reasonable. This study can fill in the gaps in the Qiang STR reference database, providing valuable frequency data for forensic applications and evidence for the Qiang's genetic pattern as an important ancestral position in the Sino-Tibetan populations.

The Heart of Silk Road "Xinjiang," Its Genetic Portray, and Forensic Parameters Inferred From Autosomal STRs

The Xinjiang Uyghur Autonomous Region of China (XUARC) harbors almost 50 ethnic groups including the Uyghur (UGR: 45.84%), Han (HAN: 40.48%), Kazakh (KZK: 6.50%), Hui (HUI: 4.51%), Kyrgyz (KGZ: 0.86%), Mongol (MGL: 0.81%), Manchu (MCH: 0.11%), and Uzbek (UZK: 0.066%), which make it one of the most colorful regions with abundant cultural and genetic diversities. In our previous study, we established allelic frequency databases for 14 autosomal short tandem repeats (STRs) for four minority populations from XUARC (MCH, KGZ, MGL, and UZK) using the AmpFlSTR® Identifiler PCR Amplification Kit. In this study, we genotyped 2,121 samples using the GoldenEye™ 20A Kit (Beijing PeopleSpot Inc., Beijing, China) amplifying 19 autosomal STR loci for four major ethnic groups (UGR, HAN, KZK, and HUI). These groups make up 97.33% of the total XUARC population. The total number of alleles for all the 19 STRs in these populations ranged from 232 (HAN) to 224 (KZK). We did not observe any departures from the Hardy-Weinberg equilibrium (HWE) in these populations after sequential Bonferroni correction. We did find minimal departure from linkage equilibrium (LE) for a small number of pairwise combinations of loci. The match probabilities for the different populations ranged from 1 in 1.66 × 1023 (HAN) to 6.05 × 1024 (HUI), the combined power of exclusion ranged from 0.999 999 988 (HUI) to 0.999 999 993 (UGR), and the combined power of discrimination ranged from 0.999 999 999 999 999 999 999 983 (HAN) to 0.999 999 999 999 999 999 999 997 (UGR). Genetic distances, principal component analysis (PCA), STRUCTURE analysis, and the phylogenetic tree showed that genetic affinity among studied populations is consistent with linguistic, ethnic, and geographical classifications.

New insights into the fine-scale history of western-eastern admixture of the northwestern Chinese population in the Hexi Corridor via genome-wide genetic legacy

Trans-Eurasian cultural and genetic exchanges have significantly influenced the demographic dynamics of Eurasian populations. The Hexi Corridor, located along the southeastern edge of the Eurasian steppe, served as an important passage of the ancient Silk Road in Northwest China and intensified the transcontinental exchange and interaction between populations on the Central Plain and in Western Eurasia. Historical and archeological records indicate that the Western Eurasian cultural elements were largely brought into North China via this geographical corridor, but there is debate on the extent to which the spread of barley/wheat agriculture into North China and subsequent Bronze Age cultural and technological mixture/shifts were achieved by the movement of people or dissemination of ideas. Here, we presented higher-resolution genome-wide autosomal and uniparental Y/mtDNA SNP or STR data for 599 northwestern Han Chinese individuals and conducted 2 different comprehensive genetic studies among Neolithic-to-present-day Eurasians. Genetic studies based on lower-resolution STR markers via PCA, STRUCTURE, and phylogenetic trees showed that northwestern Han Chinese individuals had increased genetic homogeneity relative to northern Mongolic/Turkic/Tungusic speakers and Tibeto-Burman groups. The genomic signature constructed based on modern/ancient DNA further illustrated that the primary ancestry of the northwestern Han was derived from northern millet farmer ancestors, which was consistent with the hypothesis of Han origin in North China and more recent northwestward population expansion. This was subsequently confirmed via excess shared derived alleles in f₃/f₄ statistical analyses and by more northern East Asian-related ancestry in the qpAdm/qpGraph models. Interestingly, we identified one western Eurasian admixture signature that was present in northwestern Han but absent from southern Han, with an admixture time dated to approximately 1000 CE (Tang and Song dynasties). Generally, we provided supporting evidence that historic Trans-Eurasian communication was primarily maintained through population movement, not simply cultural diffusion. The observed population dynamics in northwestern Han Chinese not only support the North China origin hypothesis but also reflect the multiple sources of the genetic diversity observed in this population.

Population genetic analysis of Shaanxi male Han Chinese population reveals genetic differentiation and homogenization of East Asians

BACKGROUND

Shaanxi province, located in the upper Yellow River, has been evidenced as the geographic origin of Chinese civilization, Sino-Tibetan-speaking language, and foxtail or broomcorn millet farmers via the linguistic phylogenetic spectrum, archeological documents, and genetic evidence. Nowadays, Han Chinese is the dominant population in this area. The formation process of modern Shaanxi Han population reconstructed via the ancient DNA is on the way, however, the patterns of genetic relationships of modern Shaanxi Han, allele frequency distributions of high mutated short tandem repeats (STRs) and corresponding forensic parameters are remained to be explored.

METHODS

Here, we successfully genotyped 23 autosomal STRs in 630 unrelated Shaanxi male Han individuals using the recently updated Huaxia Platinum PCR amplification system. Forensic allele frequency and parameters of all autosomal STRs were assessed. And comprehensive population genetic structure was explored via various typical statistical technologies.

RESULTS

Population genetic analysis based on the raw-genotype dataset among 15,803 Eurasian individuals and frequency datasets among 56 populations generally illustrated that linguistic stratification is significantly associated with the genetic substructure of the East Asian population. Principal component analysis, multidimensional scaling plots and phylogenetic tree further demonstrated that Shaanxi Han has a close genetic relationship with geographically close Shanxi Han, and showed that Han Chinese is a homogeneous population during the historic and recent admixture from the STR variations. Except for Sinitic-speaking populations, Shaanxi Han harbored more alleles sharing with Tibeto-Burman-speaking populations than with other reference populations. Focused on the allele frequency correlation and forensic parameters, all loci are in accordance with the minimum requirements of HWE and LD. The observed combined probability of discrimination of 8.2201E-28 and the cumulative power of exclusion of 0.9999999995 in Shaanxi Han demonstrated that the studied STR loci are informative and polymorphic, and this system can be used as a powerful routine forensic tool in personal identification and parentage testing.

CONCLUSION

Both the geographical and linguistic divisions have shaped the genetic structure of modern East Asian. And more forensic reference data should be obtained for ethnically, culturally, geographically and linguistically different populations for better routine forensic practice and population genetic studies.

Genetic variation and population structure analysis of Chinese Wuzhong Hui population using 30 Indels

Background: Insertions and deletions (Indels) have been used in routine forensic studies, archaeology, and population genetics. They have certain advantages, such as absence of stutter, small amplicon lengths, and low mutation rates. The genetic variations and forensic features of Indels in the Wuzhong Hui population are, as yet, unclear.Aim: To investigate the genetic polymorphisms of 30 Indels in Wuzhong Hui people and explore their genetic relationship with 48 reference populations from all over the world.Subjects and methods: We genotyped 30 Indels included in the Investigator DIPplex Kit in 156 Wuzhong Hui individuals. The genetic polymorphisms and population genetic relationships were analysed and explored via pairwise Fst, principal component analysis, multidimensional scaling plots, phylogenetic tree, and structure.Results: The combined power of discrimination (CPD) and the combined probability of exclusion (CPE) were 0.9999999999899 and 0.9880, respectively. Population genetic diversity and affinity were associated with geographic origin and linguistic affiliation.Conclusions: The 30 Indels can be utilised as an important tool in forensic personal identification and as a supplementary method in paternity testing in Wuzhong Hui. The Wuzhong Hui people have a close genetic relationship with populations of geographical proximity and Sinitic-speaking populations, while they are different from other continental populations and Turkic-speaking populations.

Population Genetic Analysis of Modern and Ancient DNA Variations Yields New Insights Into the Formation, Genetic Structure, and Phylogenetic Relationship of Northern Han Chinese

Modern East Asians derived from the admixture of aborigines and incoming farmers expanding from Yellow and Yangtze River Basins. Distinct genetic differentiation and subsequent admixture between Northeast Asians and Southeast Asians subsequently evidenced by the mitochondrial DNA, Y-chromosomal variations, and autosomal SNPs. Recently, population geneticists have paid more attention to the genetic polymorphisms and background of southern-Han Chinese and southern native populations. The genetic legacy of northern-Han remains uncharacterized. Thus, we performed this comprehensive population genetic analyses of modern and ancient genetic variations aiming to yield new insight into the formation of modern Han, and the genetic ancestry and phylogenetic relationship of the northern-Han Chinese population. We first genotyped 25 forensic associated markers in 3,089 northern-Han Chinese individuals using the new-generation of the Huaxia Platinum System. And then we performed the first meta-analysis focused on the genetic affinity between Asian Neolithic∼Iron Age ancients and modern northern-Han Chinese by combining mitochondrial variations in 417 ancient individuals from 13 different archeological sites and 812 modern individuals, as well as Y-chromosomal variations in 114 ancient individuals from 12 Neolithic∼Iron Age sites and 2,810 modern subjects. We finally genotyped 643,897 genome-wide nucleotide polymorphisms (SNPs) in 20 Shanxi Han individuals and combined with 1,927 modern humans and 40 Eurasian ancient genomes to explore the genetic structure and admixture of northern-Han Chinese. We addressed genetic legacy, population structure and phylogenetic relationship of northern-Han Chinese via various analyses. Our population genetic results from five different reference datasets indicated that Shanxi Han shares a closer phylogenetic relationship with northern-neighbors and southern ethnically close groups than with Uyghur and Tibetan. Genome-wide variations revealed that modern northern-Han derived their ancestry from Yakut-related population (25.2%) and She-related population (74.8%). Summarily, the genetic mixing that led to the emergence of a Han Chinese ethnicity occurred at a very early period, probably in Neolithic times, and this mixing involved an ancient Tibeto-Burman population and a local pre-Sinitic population, which may have been linguistically Altaic.

Population background exploration and genetic distribution analysis of Pakistan Hazara via 23 autosomal STRs

Background: Short tandem repeats (STRs) have gained considerable attention in family search (Y-chromosomal STRs), complex paternity identification (X-chromosomal STRs), routine forensic personal identification (autosomal STRs) and population genetics.Aim: To explore the forensic characteristics of 23 autosomal STRs included in the Huaxia Platinum system in the South Pakistan Hazara population and investigate the genetic similarities and differences between Hazara and 54 worldwide reference populations.Subjects and methods: Variation of the 23 autosomal STRs included in the Huaxia Platinum system was first investigated and reported in a sample of 261 Quetta Hazara in Balochistan Province, Southwest Pakistan.Results: The combined power of discrimination is 0.999999999999999999999999999 and combined power of exclusion is 0.99999999989596 in Quetta Hazara. Comprehensive population comparisons between Hazara and another 13 Eurasian populations based on genotype data, as well as between Hazara and 54 worldwide populations based on the allele frequency distribution, were conducted. Multidimensional scaling plots, principal component analysis, and neighbour-joining phylogenetic trees consistently demonstrated that Pakistan Hazara harbours close affinities with neighbouring Turkic-speaking populations. Model-based genetic structure analysis further suggests that Quetta Hazara derives about half its ancestry directly from the East Asians.Conclusion: Twenty-five forensic-related markers included in the Huaxia Platinum system can be used for forensic practice in the Central Asia Hazara population. Quetta Hazara has a close genetic relationship with the Turkic-speaking populations of Uyghur and Kazakh. Further whole-genome sequencing of Hazara needs to be conducted to validate the observed genetic structure and reconstruct the fine-scale population history of Hazara.