Genetic profile of 17 Y-chromosome STR haplotypes in East of Iran

Haplotype diversity of 17 Y-STR in the Iranian population

The current study aimed to evaluate Y chromosome haplotypes obtained from 1353 unrelated Iranian males using the AmpFlSTRTM YfilerTM kit; 1353 out of the 1353 identified haplotypes were unique. The haplotype diversity (HD) and discriminating capacity (DC) values were 1.00000 and 0.997, respectively. Analysis of genetic distance was performed using molecular variance (AMOVA) and multidimensional scaling plots (MDS), revealing a statistically significant difference between the study population and previous data reported for other Iranian populations and other neighboring countries. The present findings are likely to be useful for forensic casework analyses and kinship investigations.

Genetic Analysis of 27 Y-STR Haplotypes in 11 Iranian Ethnic Groups

BACKGROUND

The study of Y-chromosomal variations provides valuable insights into male susceptibility in certain diseases like cardiovascular disease (CVD). In this study, we analyzed paternal lineage in different Iranian ethnic groups, not only to identify developing medical etiology, but also to pave the way for gender-specific targeted strategies and personalized medicine in medical genetic research studies.

METHODS

The diversity of eleven Iranian ethnic groups was studied using 27 Y-chromosomal short tandem repeat (Y-STR) haplotypes from Y-filer® Plus kit. Analysis of molecular variance (AMOVA) based on pair-wise RST along with multidimensional scaling (MDS) calculation and Network phylogenic analysis was employed to quantify the differences between 503 unrelated individuals from each ethnicity.

RESULTS

Results from AMOVA calculation confirmed that Gilaks and Azeris showed the largest genetic distance (RST=0.35434); however, Sistanis and Lurs had the smallest considerable genetic distance (RST=0.00483) compared to other ethnicities. Although Azeris had a considerable distance from other ethnicities, they were still close to Turkmens. MDS analysis of ethnic groups gave the indication of lack of similarity between different ethnicities. Besides, network phylogenic analysis demonstrated insignificant clustering between samples.

CONCLUSION

The AMOVA analysis results explain that the close distance of Azeris and Turkmens may be the effect of male-dominant expansions across Central Asia that contributed to historical and demographics of populations in the region. Insignificant differences in network analysis could be the consequence of high mutation events that happened in the Y-STR regions over the years. Considering the ethnic group affiliations in medical research, our results provided an understanding and characterization of Iranian male population for future medical and population genetics studies.

The Qatari population's genetic structure and gene flow as revealed by the Y chromosome

The Y-chromosome has been widely used in forensic genetic applications and human population genetic studies due to its uniparental origins. A large database on the Qatari population was created for comparison with other databases from the Arabian Peninsula, the Middle East, and Africa. We provide a study of 23 Y-STR loci included in PowerPlex Y23 (Promega, USA) that were genotyped to produce haplotypes in 379 unrelated males from Qatar, a country at the crossroads of migration patterns. Overall, the most polymorphic locus provided by the Promega kit was DYS458, with a genetic diversity value of 0.85 and a haplotype diversity of 0.998924. Athey's Haplogroup Predictor tool was used to predict haplogroups from Y-STR haplotypes in the Qatari population. In a median-joining network, the haplogroup J1 predominance (49%) in Qatar generated a star-like expansion cluster. The graph of population Q-matrix was developed using Y-STR data from 38 Middle Eastern and 97 African populations (11,305 individuals), and it demonstrated a stronger sub-grouping of countries within each ethnic group and showed the effect of Arabs on the indigenous Berbers of North Africa. The estimated migration rate between the Qatari and other Arabian populations was inferred using Bayesian coalescence theory in the Migrate-n program. According to the Gene Flow study, the main migration route was from Yemen to Kuwait through Qatar. Our research, using the PowerPlex Y23 database, shows the importance of gene diversity, as well as regional and social structuring, in determining the utility of demographic and forensic databases.

Profiling of 17 Y-STR loci in Mazandaran and Gilan provinces of Iran

Background/aim

The Y-chromosome mainly consists of heterochromatin regions that have a father-to-son inheritance. Short tandem repeat polymorphic (STRP) markers distributed all over the chromosome provide the opportunity for investigations in forensic medicine and ancestral lineage studies. Due to the existence of wide varieties of geographical and ethnic groups in Iran, studying Y-STRP markers is necessary for further applications. Here we investigated the provinces of Mazandaran and Gilan for the first time.

Materials and methods

Samples included 119 and 90 unrelated males from Mazandaran and Gilan, respectively. Using a PCR amplification kit, 17 Y-STRP markers were amplified and genotyping was conducted by capillary electrophoresis. Allele frequency, haplotype diversity (HD), and haplotype discrimination capacity (DC) were calculated. The populations were compared together and to neighboring countries including Afghanistan and Azerbaijan by F_ST index.

Results

A total of 204 unique haplotypes were observed. No uniqueness was observed between the two provinces. HD was 0.9993 and 0.9998 in Mazandaran and Gilan, respectively. DC was 0.9666 and 0.9888 for Mazandaran and Gilan, respectively. DYS385b and DYS391 had the most and least polymorphic content in both provinces, respectively. There was not a significant difference between these two provinces (F_ST = 0.0006 and P = 0.00) and neighboring countries.

Conclusion

The results highlight the effectiveness of these Y-STRP markers for male discrimination in the north of Iran. Using additional markers along with extended sample size would provide a better opportunity for removing matched haplotypes and introducing the best polymorphic markers in this specific population.

Polymorphism of 11 Y Chromosome Short Tandem Repeat Markers among Malaysian Aborigines

The conventional technique such as patrilocality suggests some substantial effects on population diversity. With that, this particular study investigated the paternal line, specifically Scientific Working Group on DNA Analysis Methods (SWGDAM)-recommended Y-STR markers, namely, DYS19, DYS385, DYS389I/II, DYS390, DYS391, DYS392, DYS393, DYS438, and DYS439. These markers were tested to compare 184 Orang Asli individuals from 3 tribes found in Peninsular Malaysia. As a result, the haplotype diversity and the discrimination capacity obtained were 0.9987 and 0.9076, respectively. Besides, the most diverse marker was DYS385b, whereas the least was DYS391. Furthermore, the Senoi and Proto-Malay tribes were found to be the most distant, whereas the Senoi and Negrito clans were almost similar to each other. In addition, the analysis of molecular variance analysis revealed 82% of variance within the population, but only 18% of difference between the tribes. Finally, the phylogenetic trees constructed using Neighbour Joining and UPGMA (Unweighted Pair Group Method with Arithmetic Mean) displayed several clusters that were tribe specific. With that, future studies are projected to analyse individuals based on more specific sub-tribes.