Genetic polymorphism of 24 Y-STR loci in Altay Hui and Kazakh populations from northwest China

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

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.

A machine learning approach for estimating Eastern Asian origins from massive screening of Y chromosomal short tandem repeats polymorphisms

Inferring the ancestral origin of DNA evidence recovered from crime scenes is crucial in forensic investigations, especially in the absence of a direct suspect match. Ancestry informative markers (AIMs) have been widely researched and commercially developed into panels targeting multiple continental regions. However, existing forensic ancestry inference panels typically group East Asian individuals into a homogenous category without further differentiation. In this study, we screened Y chromosomal short tandem repeat (Y-STR) haplotypes from 10,154 Asian individuals to explore their genetic structure and generate an ancestry inference tool through a machine learning (ML) approach. Our research identified distinct genetic separations between East Asians and their neighboring Southwest Asians, with tendencies of northern and southern differentiation observed within East Asian populations. All machine learning models developed in this study demonstrated high accuracy, with the Asian classification model achieving an optimal performance of 82.92% and the East Asian classification model reaching 84.98% accuracy. This work not only deepens the understanding of genetic substructures within Asian populations but also showcases the potential of ML in forensic ancestry inference using extensive Y-STR data. By employing computational methods to analyze intricate genetic datasets, we can enhance the resolution of ancestry in forensic contexts involving Asian populations.

Population data and phylogenetic analysis of 37 Y-STR loci in the Hui population from Yunnan Province, Southwest China

Background: Previous studies of the genetic polymorphism of the Y-chromosomal short tandem repeat (Y-STR) of Huis were focused on the northwest of China. However, the population genetic characteristics of Chinese Hui residing in Yunnan province, Southwest China, remain unclear.Aim: To provide genetic data for 37 Y-STRs in the Chinese Hui population of Yunnan province, as well as to investigate population genetic relationships between the Chinese Hui and another 26 populations from China and neighbouring countries.Subjects and methods: 326 unrelated healthy male individuals were genotyped using the Goldeneye^TM Y Plus PCR Amplification Kit. Genetic relationships between different populations were analysed using YHRD's AMOVA tools.Results: A total of 279 haplotypes were detected, out of which 244 were unique. The overall haplotype diversity (HD) and discrimination capacity (DC) were 0.9989 and 0.8611, respectively. The gene diversity (GD) ranged from 0.0544 (DYS645) to 0.9656 (DYS385).Conclusions:  The population comparison indicated that Muslim populations (Hui, Salar, and Uighur) showed significant genetic affinity than other populations. Our results could be applied in forensic practice and population genetic studies.

Genetic polymorphism of 27 Y-STR loci in Kazakh populations from Eastern Kazakhstan

BACKGROUND

The establishment of a national haplotype database is important for forensic and genetic applications and requires studying genetic polymorphisms at Y-STR sites. However, the genetic structure of the Eastern Kazakhstan population is poorly characterised.

AIM

To investigate the genetic polymorphisms of 27 Y-STR loci in the Kazakh population from Eastern Kazakhstan and analyse the population genetic relationships of the Eastern Kazakhs with other populations.

SUBJECTS AND METHODS

The Yfiler Plus kit was utilised to genotype 246 healthy, unrelated males from Eastern Kazakhstan. Based on the raw data, haplotype and allele frequencies along with forensic parameters were calculated, and an MDS plot was constructed.

RESULTS

A total of 207 haplotypes were detected, of which 186 were unique. The haplotype diversity and discrimination capacity were 0.997 and 0.841, respectively. Population comparisons showed that Eastern Kazakhs have close genetic relationships with Kazakhs from Xinjiang, China. At the same time, a difference was found between the studied population and the previous one in the same part of Kazakhstan.

CONCLUSIONS

The obtained haplotypes will help to expand the Kazakhstan Y-chromosome reference database and will be useful for future genetic research and forensic applications.

Genetic polymorphism of 27 Y-STR loci in Kazakh populations from Northern Kazakhstan

BACKGROUND

Previous studies of the genetic polymorphism of the Y-chromosome of Kazakhs were focused on the Eastern, Central, Southern, and Western regions of Kazakhstan. In addition, many of these studies were limited to 17 Y-STR loci from the Yfiler.

AIM

To enrich the existing Kazakhstan Y-chromosome Haplotype Reference Database from the Northern Kazakh population data by a wide set of 27 Y-STR and investigate the population genetic relationships with previously published data.

SUBJECTS AND METHODS

27 Y-STR loci from the Yfiler Plus PCR Amplification Kit were analysed in 382 healthy unrelated Kazakh males from Northern Kazakhstan. Genetic polymorphism was analysed using Arlequin software.

RESULTS

A total of 326 distinct haplotypes of the 27 Y-STR loci were observed in 382 individuals. The discrimination capacity (0.9982) and haplotype diversity (0.8534) were computed. A total of 168 alleles at single-copy loci were observed, and their frequencies ranged from 0.003 to 0.843. The pairwise genetic distance (R_ST) showed that the Northern Kazakh population is genetically distinct from the Chinese Kazakh population.

CONCLUSIONS

Genetic polymorphism shows that the potential value of 27 Y-STR loci for forensic casework in the Northern Kazakh population, and the current findings, might be beneficial for paternal lineages in the study of population genetics.