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Geographical structuring and low diversity of paternal lineages in Bahrain shown by analysis of 27 Y-STRs.

ABSTRACT: We have determined the distribution of Y-chromosomal haplotypes and predicted haplogroups in the ethnically diverse Kingdom of Bahrain, a small archipelago in the Arabian Gulf. Paternal population structure within Bahrain was investigated using the 27 Y-STRs (short tandem repeats) in the Yfiler Plus kit to generate haplotypes from 562 unrelated Bahraini males, sub-divided into four geographical regions-Northern, Capital, Southern and Muharraq. Yfiler Plus provided a significant improvement over the 17-locus Yfiler kit in discrimination capacity (from 77% to 87.5% overall), but discrimination capacity differed widely between regions from 98.4% in Muharraq to 75.2% in the Northern region, an unusually low value possibly resulting from recent rapid population expansion. Clusters of closely related male lineages were seen, with only 79.4% of donors displaying unique haplotypes and 59% of instances of shared haplotypes occurring within, rather than between, regions. Haplogroup prediction indicated diverse origins of the population with a predominance of haplogroups J2 and J1, both typical of the Arabian Peninsula, but also haplogroups such as B2 and E1b1a likely originating in Africa, and H, L and R2 likely indicative of migration from South Asia. Haplogroup frequencies differed significantly between regions, with J2 significantly more common in the Northern region compared with the Southern, possibly due to differential settlement by Baharna and Arabs. Our study shows that paternal lineage population structure can exist even over small geographical scales, and that highly discriminating genetic tools are required where rapid expansions have occurred within tightly bounded populations.

SUBMITTER: Al-Snan NR

PROVIDER: S-EPMC7524810 | biostudies-literature | 2020 Nov

REPOSITORIES: biostudies-literature

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Geographical structuring and low diversity of paternal lineages in Bahrain shown by analysis of 27 Y-STRs.

Al-Snan Noora R NR Messaoudi Safia A SA Khubrani Yahya M YM Wetton Jon H JH Jobling Mark A MA Bakhiet Moiz M

Molecular genetics and genomics : MGG 20200625 6

We have determined the distribution of Y-chromosomal haplotypes and predicted haplogroups in the ethnically diverse Kingdom of Bahrain, a small archipelago in the Arabian Gulf. Paternal population structure within Bahrain was investigated using the 27 Y-STRs (short tandem repeats) in the Yfiler Plus kit to generate haplotypes from 562 unrelated Bahraini males, sub-divided into four geographical regions-Northern, Capital, Southern and Muharraq. Yfiler Plus provided a significant improvement over ...[more]

PMID: 32588126

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Project description:Bahrain's population consists mainly of Arabs, Baharna and Persians leading Bahrain to become ethnically diverse. The exploration of the ethnic origin and genetic structure within the Bahraini population is fundamental mainly in the field of population genetics and forensic science. The purpose of the study was to investigate and conduct genetic studies in the population of Bahrain to assist in the interpretation of DNA-based forensic evidence and in the construction of appropriate databases. 24 short-tandem repeats in the GlobalFiler PCR Amplification kit including 21 autosomal STR loci and three gender determination loci were amplified to characterize different genetic and forensic population parameters in a cohort of 543 Bahraini unrelated healthy men. Samples were collected during the year 2017. The genotyping of the 21 autosomal STRs showed all of the loci were in Hardy-Weinberg Equilibrium (HWE) after applying Bonferroni's correction. We also found out no significant deviations from LD between pairwise STR loci in Bahraini population except when plotting for D3S1358-CSF1PO, CSF1PO-SE33, D19S433-D12S391, FGA-D2S1338, FGA-SE33, FGA-D7S820 and D7S820-SE33. The SE33 locus was the most polymorphic for the studied population and THO1 locus was the less polymorphic. The Allele 8 in TPOX scored the highest allele frequency of 0.496. The SE33 locus showed the highest power of discrimination (PD) in Bahraini population, whereas TPOX showed the lowest PD value. The 21 autosomal STRs showed a value of combined match probability (CMP) equal to 4.5633E-27, and a combined power of discrimination (CPD) of 99.99999999%. Off-ladders and tri-allelic variants were observed in various samples at D12S391, SE33 and D22S1045 loci. Additionally, pairwise genetic distances based on FST were calculated between Bahraini population and other populations extracted from the literature. Genetic distances were represented in a non-metric MDS plot and clustering of populations according to their geographic locations was detected. Phylogenetic tree was constructed to investigate the genetic relatedness between Bahraini population and the neighboring populations. Our study indicated that the twenty-one autosomal STRs are highly polymorphic in the Bahraini population and can be used as a powerful tool in forensics and population genetic analyses including paternity testing and familial DNA searching.

Project description:Maoming is located in the southwest region of Guangdong Province and is the cradle of Gaoliang culture, which is the representative branch of Lingnan cultures. Historical records showed that the amalgamations between Gaoliang aborigines and distinct ethnic minorities had some influences on the shaping of Gaoliang culture, especially for the local Tai-kadai language-speaking Baiyue and Han Chinese from Central China. However, there is still no exact genetic evidence for the influences on the genetic pool of Maoming Han, and the genetic relationships between Maoming Han and other Chinese populations are still unclear. Hence, in order to get a better understanding of the paternal genetic structures and characterize the forensic features of 27 Y-chromosomal short tandem repeats (Y-STRs) in Han Chinese from Guangdong Maoming, we firstly applied the AmpFLSTR® Yfiler® Plus PCR Amplification Kit (Thermo Fisher Scientific, Waltham, MA, United States) to genotype the haplotypes in 431 Han males residing in Maoming. A total of 263 different alleles were determined across all 27 Y-STRs with the corresponding allelic frequencies from 0.0004 to 0.7401, and the range of genetic diversity (GD) was 0.4027 (DYS391) to 0.9596 (DYS385a/b). In the first batch of 27 Yfiler data in Maoming Han, 417 distinct haplotypes were discovered, and nine off-ladder alleles were identified at six Y-STRs; in addition, no copy number variant or null allele was detected. The overall haplotype diversity (HD) and discrimination capacity (DC) of 27 Yfiler were 0.9997 and 0.9675, respectively, which demonstrated that the 6-dye and 27-plex system has sufficient system effectiveness for forensic applications in Maoming Han. What is more, the phylogenetic analyses indicated that Maoming Han, which is a Southern Han Chinese population, has a close relationship with Meizhou Kejia, which uncovered that the role of the gene flows from surrounding Han populations in shaping the genetic pool of Maoming Han cannot be ignored. From the perspectives of genetics, linguistics, and geographies, the genetic structures of Han populations correspond to the patterns of the geographical-scale spatial distributions and the relationships of language families. Nevertheless, no exact genetic evidence supports the intimate relationships between Maoming Han and Tai-Kadai language-speaking populations and Han populations of Central Plains in the present study.

Dataset Information

Geographical structuring and low diversity of paternal lineages in Bahrain shown by analysis of 27 Y-STRs.

Publications

Geographical structuring and low diversity of paternal lineages in Bahrain shown by analysis of 27 Y-STRs.

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