Population data and genetic diversity analysis of 17 Y-STR loci in Saudi population

Abstract Background The Y chromosome polymorphism has been widely studied for human migrations, population genetics, forensic applications, and paternity analysis. However, studies regarding genetic lineage and population genetic structure of the Y chromosome in different regions of Saudi Arabia are limited. Aim This study aimed to analyze the distribution of Y chromosome haplotypes in a sample of 125 native Saudi males from different geographic regions of Saudi Arabia and compare to previously published Y chromosome haplotype data from Saudi Arabia and some neighboring Arab populations. Materials and methods Buccal swabs were collected from 125 healthy unrelated native Saudi males from different geographic regions of Saudi Arabia. Genomic DNA was extracted by Chelex®100; 17 Y-STR loci were amplified using the AmpFℓlSTR Yfiler PCR amplification kit and detected on the 3130 Genetic AnalyzerTM. Allele frequency and gene diversity were calculated with online tool STRAF. The Saudi population data were compared with the neighboring populations using pairwise genetic distances and associated probability values were calculated using the Y Chromosome Haplotype Reference Database Website (YHRD) software. Results and conclusion One hundred six YSTR haplotypes and 102 YSTR alleles (excluding 4 null alleles) were identified having a discrimination capacity (DC) of 85.8%. The highest haplotype diversity (HD) and gene diversity (GD) were observed at the loci DYS 458 (0.817) and DYS385b (0.807), respectively. According to our results, the Iraqi and Qena (Egypt) populations appeared to have closer relatedness to the Saudi population as compared with Yemen. The UAE and Kuwait populations showed the same degree of relatedness to the Saudi population followed by Bahrain. On the contrary, the Adnanit and Qahtanit populations of Jordan demonstrated low genetic distance from the Saudi population. In short, studying a population sample of pure Saudi ethnicity enabled us to identify a unique set of haplotypes which may help in establishing genetic relatedness between Saudi and the neighboring Arab populations. The present paper, therefore, highlights the importance of ensuring ethnic originality of the study sample while conducting population genetics studies.

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Population Data for Four Population Groups from the United States for the Eleven Y-Chromosome STR Loci Recommended by SWGDAM

Journal of Forensic Sciences ◽

10.1111/j.1556-4029.2006.00143.x ◽

2006 ◽

Vol 51 (3) ◽

pp. 700-702 ◽

Cited By ~ 3

Author(s):

Jaiprakash G. Shewale ◽

Anurag Bhushan ◽

Huma Nasir ◽

Elaine Schneida ◽

Brandi Washington ◽

...

Keyword(s):

United States ◽

Y Chromosome ◽

Population Data ◽

The United States ◽

Population Groups ◽

Str Loci ◽

Y Chromosome Str

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Population data for 12 Y-chromosome STR loci in a sample from El Salvador

Legal Medicine ◽

10.1016/j.legalmed.2009.10.003 ◽

2010 ◽

Vol 12 (1) ◽

pp. 46-51 ◽

Cited By ~ 2

Author(s):

Juan Carlos Monterrosa ◽

Josefina A. Morales ◽

Iñaki Yurrebaso ◽

Leonor Gusmão ◽

Oscar García

Keyword(s):

El Salvador ◽

Y Chromosome ◽

Population Data ◽

Str Loci ◽

Y Chromosome Str

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Population data for 48 ‘Non-Core’ Y chromosome STR loci

Legal Medicine ◽

10.1016/j.legalmed.2006.12.002 ◽

2007 ◽

Vol 9 (4) ◽

pp. 221-231 ◽

Cited By ~ 5

Author(s):

Erin K. Hanson ◽

Jack Ballantyne

Keyword(s):

Y Chromosome ◽

Population Data ◽

Str Loci ◽

Y Chromosome Str

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Evaluation and comparison of population genetics software in Rabari Tribe of Gujarat population

Egyptian Journal of Forensic Sciences ◽

10.1186/s41935-021-00239-1 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Aditi Mishra ◽

Archana Kumari ◽

Sumit Choudhary ◽

Ulhas Gondhali

Keyword(s):

Population Genetics ◽

Population Data ◽

Genomic Diversity ◽

Match Probability ◽

Statistical Software ◽

Str Loci ◽

Autosomal Str ◽

Forensic Practice ◽

Population Structures ◽

Dna Profiles

Abstract Background Today, when forensic experts talk about quantifiable hereditary traits, they do not just depend on the assessment and examination of DNA profiles but also relate them to the population structures. The use of high-throughput molecular marker technologies and advanced statistical and software tools have improved the accuracy of human genetic diversity analysis in many populations with limited time and resources. The present study aimed to investigate the genomic diversity in Gujarat’s Rabari population, using 20 autosomal genetic markers. Numerous bio-statistical software programs are available for the interpretation of population data in forensics. These statistics deal with the measurement of uncertainty and also provides a probability of a random match. The present paper aims to provide a practical guide to the analysis of population genetics data. Three statistical software packages named Cervus, Genepop, and Fstat are compared and contrasted. The comparison is performed on the profiles obtained from fifty unrelated blood samples of healthy male individuals. DNA was extracted using the organic extraction method, 20 autosomal STR loci were amplified using PowerPlex 21 kit (Promega, Madison, WI, USA) and detected on 3100 Genetic Analyser (Life Technologies Corporation, Carlsbad, CA, USA). Results A total of 170 alleles were observed in the Rabari Tribe of Gujarat population, and allele frequencies ranged from 0.010 to 0.480. The highest allele frequency detected was 0.480 for allele 9 at locus TH01. Based on heterozygosity and the polymorphism information content, FGA may be considered as the most informative markers. Both the combined power of discrimination (CPD) and the combined power of exclusion (CPE) for the 20 analyzed loci were higher than 0.999999. The combined match probability (CPM) for all 20 loci was 2.5 × 10−22. Conclusions With respect to the results, the 20 STR loci are highly polymorphic and discriminating in the Gujarat population and could be used for forensic practice and population genetics studies. However, Fstat demonstrated better genetic software for analysis of the demographic structure of a specific or set of populations.

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Forensic features and genetic legacy of the Baloch population of Pakistan and the Hazara population across Durand-line revealed by Y chromosomal STRs

10.1101/2020.11.21.392456 ◽

2020 ◽

Author(s):

Atif Adnan ◽

Shao-Qing Wen ◽

Allah Rakha ◽

Rashed Alghafri ◽

Shahid Nazir ◽

...

Keyword(s):

Gene Diversity ◽

Haplotype Diversity ◽

Pcr Amplification ◽

Null Alleles ◽

Str Loci ◽

Asian Populations ◽

The People ◽

Central Asian ◽

History Of ◽

Discriminatory Analysis

ABSTRACTHazara population across Durand-line has experienced extensive interaction with Central Asian and East Asian populations. Hazara individuals have typical Mongolian facial appearances and they called themselves descendants of Genghis Khan’s army. The people who speak the Balochi language are called Baloch. Previously, a worldwide analysis of Y-chromosomal haplotype diversity for rapidly mutating (RM) Y-STRs and with PowerPlex Y23 System (Promega Corporation Madison, USA) kit was created with collaborative efforts, but Baloch and Hazara population from Pakistan and Hazara population from Afghanistan were missing. A limited data with limited number of markers and samples is available which poorly define these populations. So, in the current study, Yfiler Plus PCR Amplification Kit loci were examined in 260 unrelated Hazara individuals from Afghanistan, 153 Hazara individuals, and 111 Balochi individuals from Baluchistan Pakistan. For the Hazara population from Afghanistan and Pakistan overall, 380 different haplotypes were observed on these 27 Y-STR loci, gene diversities ranged from 0.51288 (DYS389I) to 0.9257 (DYF387S1) and haplotype diversity was 0.9992 +/- 0.0004. For the Baloch population, every individual was unique at 27 Y-STR loci, gene diversity ranged from 0.5718 (DYS460) to 0.9371(DYF387S1). Twelve haplotypes shared between 178 individuals while only two haplotypes among these twelve were shared between 87 individuals in Hazara populations. Rst and Fst pairwise genetic distance analyses, multidimensional scaling (MDS) plot, Neighbor-joining (NJ) tree, linear discriminatory analysis (LDA), and median-joining network (MJNs) were performed, which shed light on the history of Hazara and Baloch populations. Interestingly null alleles were observed at DYS448 with specific mutation patterns in Hazara populations. The results of our study showed that the Yfiler Plus PCR Amplification Kit marker set provided substantially stronger discriminatory power in the Baloch population of Pakistan and the Hazara population across the Durand-line.

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