Allele Diversity, Haplotype Frequency and Diversity, and Forensic Genotyping of Fulanis and Yorubas Population in North Central Region of Nigeria

Nigeria is the most populous African nation, comprising over 250 ethnic groups. The Yoruba and Fulani are the second and fourth largest ethnic groups in Nigeria, respectively. Forensic genotyping of short tandem repeats (STRs) is used in computation of Combined DNA Index System databases of individuals and ethnic groups. We examined allele diversity, haplotype frequency, haplotype diversity, and forensic genotyping data of autosomal STRs in Fulani and Yoruba residents in Ilorin, Kwara State, North Central Nigeria, in-order to further provide forensic genotyping data of these ethnic groups. Samples of 25 Fulani males and 23 Yoruba males whose ethnicity was confirmed by three generations (paternal and maternal) were collected with informed consent using purposive sampling. All individuals in the samples were unrelated. The samples were amplified and then genotyped using the SureID® 21G PCR Amplification Kit containing Amelogenin and 20 autosomal STR loci. Statistical analyses of forensic genotyping parameters confirmed no deviation from expectation of Hardy-Weinberg Equilibrium and no dependence of alleles between loci. All tested loci were polymorphic. Expected Heterozygosity and gene diversity parameters showed lower genetic diversity amongst Fulanis compared to Yorubas. This is possibly due to the prevalent custom of marriage between cousins amongst Fulanis, which is forbidden in Yoruba customs.

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

Frontiers in Genetics ◽

10.3389/fgene.2021.760760 ◽

2021 ◽

Vol 12 ◽

Author(s):

Atif Adnan ◽

Adeel Anwar ◽

Halimureti Simayijiang ◽

Noor Farrukh ◽

Sibte Hadi ◽

...

Keyword(s):

Ethnic Groups ◽

Tandem Repeats ◽

Pcr Amplification ◽

Principal Component ◽

Genetic Distances ◽

Allelic Frequency ◽

Sequential Bonferroni Correction ◽

Hardy Weinberg Equilibrium ◽

Different Populations ◽

Xinjiang Uyghur Autonomous Region

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.

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Forensic Value of Ten Short Tandem Repeat Loci in Turkey Compared to Other Ethnic Groups

Balkan Journal of Medical Genetics ◽

10.2478/v10034-009-0005-9 ◽

2009 ◽

Vol 12 (1) ◽

pp. 69-72

Author(s):

A Ozkorkmaz ◽

A Baransel Isir ◽

S Pehlivan ◽

E Özkorkmaz

Keyword(s):

Ethnic Groups ◽

Tandem Repeat ◽

Short Tandem Repeat ◽

Tandem Repeats ◽

Unrelated Individual ◽

Published Data ◽

Short Tandem Repeat Loci ◽

Hardy Weinberg Equilibrium ◽

Forensic Value ◽

Short Tandem

Forensic Value of Ten Short Tandem Repeat Loci in Turkey Compared to Other Ethnic GroupsAllele frequencies of the 10 short tandem repeats (STRs) loci (D16S539, D2S1338, D3S1358, vWA, D18S51, D21S11, D8S1179, D19S433, FGA, THO1) included in the AmpFISTR SGM Plus kit, were obtained from biological samples from 100 unrelated individual residing in different part of Turkey. The χ2 test showed that all these loci agreed with Hardy-Weinberg equilibrium, The results were compared with the previously published data from Turkish and other ethnic groups. Suggest that these loci with their high heterozygosity and combined power of discrimination (PD) values are useful for forensic identifications.

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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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Insights Into Forensic Features and Genetic Structures of Guangdong Maoming Han Based on 27 Y-STRs

Frontiers in Genetics ◽

10.3389/fgene.2021.690504 ◽

2021 ◽

Vol 12 ◽

Author(s):

Haoliang Fan ◽

Qiqian Xie ◽

Yanning Li ◽

Lingxiang Wang ◽

Shao-Qing Wen ◽

...

Keyword(s):

Tandem Repeats ◽

Genetic Relationships ◽

Phylogenetic Analyses ◽

Haplotype Diversity ◽

Pcr Amplification ◽

Han Chinese ◽

Genetic Evidence ◽

Central China ◽

Genetic Pool ◽

Genetic Structures

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.

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Population genetic portrait of Pakistani Lahore-Christians based on 32 STR loci

Scientific Reports ◽

10.1038/s41598-020-76016-2 ◽

2020 ◽

Vol 10 (1) ◽

Author(s):

Aqsa Rubab ◽

Muhammad Shafique ◽

Faqeeha Javed ◽

Samia Saleem ◽

Fatima Tuz Zahra ◽

...

Keyword(s):

Tandem Repeats ◽

Pcr Amplification ◽

Genetic Distances ◽

Cumulative Probability ◽

Christian Community ◽

Genetic Characteristics ◽

Pakistani Population ◽

Identifiler Plus ◽

Hardy Weinberg Equilibrium ◽

Christian Population

Abstract Phylogenetic relationship and the population structure of 500 individuals from the Christian community of Lahore, Pakistan, were examined based on 15 autosomal short tandem repeats (STRs) using the AmpFℓSTR Identifiler Plus PCR Amplification Kit and our previously published Y-filer kit data (17 Y-STRs) of same samples. A total of 147 alleles were observed in 15 loci and allele 11 at the TPOX locus was the most frequent with frequency value (0.464). The data revealed that the Christian population has unique genetic characteristics with respect to a few unusual alleles and their frequencies relative to the other Pakistani population. Significant deviations from Hardy–Weinberg equilibrium were found at two loci (D13S317, D18S51) after Boneferroni’s correction (p ≤ 0.003). The combined power of discrimination, combined power of exclusion and cumulative probability of matching were 0.999999999999999978430815060354, 0.999995039393942 and 2.15692 × 10−17, respectively. On the bases of genetic distances, PCA, phylogenetic and structure analysis Lahore-Christians appeared genetically more associated to south Asian particularly Indian populations like Tamil, Karnataka, Kerala and Andhra Pradesh than rest of global populations.

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GENETIC POLYMORPHISM OF 23 Y-CHROMOSOME SHORT TANDEM REPEAT LOCI IN THE KINH POPULATION OF VIETNAM

Vietnam Journal of Biotechnology ◽

10.15625/1811-4989/16/2/13431 ◽

2018 ◽

Vol 16 (2) ◽

pp. 223-229

Author(s):

Ha Huu Hao ◽

Nguyen Duc Nhu ◽

Chu Hoang Ha ◽

Le Van Son ◽

Le Tuan Anh ◽

...

Keyword(s):

Y Chromosome ◽

Tandem Repeats ◽

Gene Diversity ◽

Haplotype Diversity ◽

Genetic Distances ◽

Reference Database ◽

Sample Population ◽

Forensic Application ◽

Str Loci ◽

Short Tandem

Y-chromosome microsatellites or short tandem repeats (STRs) have been proved to be ideal markers to delineate the differences between individuals in human population. Nowadays, Y-STR testing using the PowerPlex® Y23 amplification kit is considered as an extremely sensitive analysis method and has the potential to be used to perform forensic caseworks, and to explore the complexity in population substructures. However, little is known about the forensic Y-chromosome databases in the Vietnam population. In this study, 23 Y-STR loci (DYS576, DYS389I, DYS389 II, DYS448, DYS19, DYS391, DYS481, DYS549, DYS533, DYS438, DYS437, DYS570, DYS635, DYS390, DYS439, DYS392, DYS393, DYS458 DYS456, DYS643, YGATAH4, and DYS385a/b) were investigated in 120 non-related males of the Kinh population in Northern Vietnam using PowerPlex® Y23 system kit (Promega). Our results showed that allele frequencies of 23 loci in the sample population, with the calculated average gene diversity (GD) for each locus, ranged from 0.24 (DYS438) to 0.92 (DYS385a/b). In addition, a total of 120 different haplotypes were found, all of them were unique. Therefore, we found that the haplotype diversity was 1 with a discrimination capacity of 100%, which serves as an essential prerequisite for using Y-chromosomal STR with PowerPlex® Y23 System kit in forensic application in Vietnam. We also compared genetic distances between Kinh population and 10 other neighboring populations from Y-chromosome haplotype reference database (YHRD). The Kinh population is significantly different from other populations. In conclusion, it was indicated that the 23 Y-STR loci were highly genetically polymorphic in the Kinh population in Vietnam and might be of great value in forensic application.

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Population genetic variation analysis of bitter gourd wilt caused by Fusarium oxysporum f. sp. momordicae in China using inter simple sequence repeats (ISSR) molecular markers

Journal of Plant Pathology ◽

10.1007/s42161-021-00759-8 ◽

2021 ◽

Author(s):

Rui Zang ◽

Ying Zhao ◽

Kangdi Guo ◽

Kunqi Hong ◽

Huijun Xi ◽

...

Keyword(s):

Genetic Variation ◽

Genetic Differentiation ◽

Fusarium Oxysporum ◽

Diversity Index ◽

Gene Diversity ◽

Pcr Amplification ◽

Bitter Gourd ◽

Diseased Plant ◽

Variation Analysis ◽

Group I

AbstractBitter gourd wilt caused by Fusarium oxysporum f. sp. momordicae (FOM) is a devastating crop disease in China. A total of 173 isolates characteristic of typical Fusarium oxysporum with abundant microconidia and macroconidia on white or ruby colonies were obtained from diseased plant tissues. BLASTn analysis of the rDNA-ITS of the isolates showed 99% identity with F. oxysporum species. Among the tested isolates, three were infectious toward tower gourd and five were pathogenic to bottle gourd. However, all of the isolates were pathogenic to bitter gourd. For genetic differences analysis, 40 ISSR primers were screened and 11 primers were used for ISSR-PCR amplification. In total, 127 loci were detected, of which 76 were polymorphic at a rate of 59.84%. POPGENE analysis showed that Nei’s gene diversity index (H) and Shannon’s information index (I) were 0.09 and 0.15, respectively, which indicated that the genetic diversity of the 173 isolates was low. The coefficient of gene differentiation (Gst = 0.33 > 0.15) indicated that genetic differentiation was mainly among populations. The strength of gene flow (Nm = 1.01 > 1.0) was weak, indicating that the population differentiation caused by gene drift was blocked to some degree. The dendrogram based on ISSR markers showed that the nine geographical populations were clustered into two groups at the threshold of genetic similarity coefficient of 0.96. The Shandong and Henan populations were clustered into Group I, while the Guangdong, Hainan, Guangxi, Fujian, Jiangxi, and Hubei populations constituted Group II. Results of the genetic variation analysis showed that the Hunan and Guangxi populations had the highest degree of genetic differentiation, while the Hubei population had the lowest genetic differentiation. Our findings enrich the knowledge of the genetic variation characteristics of FOM populations with the goal of developing effective disease-management programs and resistance breeding programs.

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Forensic application of Y-chromosomal STR analysis in Lithuanian population

Biologija ◽

10.6001/biologija.v61i2.3140 ◽

2015 ◽

Vol 61 (2) ◽

Author(s):

Giedrė Ruzgaitė ◽

Marija Čaplinskienė ◽

Rima Baranovienė ◽

Jūratė Jankauskienė ◽

Jolanta Kukienė ◽

...

Keyword(s):

Y Chromosome ◽

Gene Pool ◽

Haplotype Diversity ◽

Haplotype Frequency ◽

Reference Database ◽

Match Probability ◽

Str Analysis ◽

Str Markers ◽

Forensic Casework ◽

Chromosome Gene

This paper presents a comprehensive Y-chromosomal STR haplotype analysis in the Lithuanian population in order to evaluate Lithuanians’ Y chromosome diversity, to infer genetic relations between Lithuanian and other European neighbouring populations and to introduce population reference data for generation of reliable Y-STR haplotype frequency estimates to be used in the quantitative assessment of Y-STR haplotype match in the forensic casework. Data were collected from the peripheral blood samples of 194 unrelated males throughout various regions of Lithuania. The amplification of 17 Y-STRs was carried out in one multiplex PCR using an AmpFlSTR® Yfiler<sup>TM</sup> PCR Amplication Kit according to the supplier’s protocol. The results indicated that the Y-chromosomal haplotype diversity in the Lithuanian population rises as the number of the analyzed Y-STRs is increased. However, all additional Y-STR loci are not hypervariable and only their whole makes a large diversity of Y-STR haplotypes in Lithuanian males. The analysis of molecular variance revealed low but significant interpopulation differences except the pair of Lithuanian and Latvian populations. The phylogenetic analysis showed that the clustered Y chromosome gene pool of Lithuanians and Latvians has a closer phylogenetic relation to Russian and Estonian populations and is less genetically related to other neighbouring populations of Belarus and Poland. Yet Y-STRs alleles and haplotypes differentiate effectively inside the Lithuanian population and between Lithuanians and its geographical neighbours excluding the Latvian population. Comparison of the Y-STR data suggests that Lithuanian and Latvian populations are closely related not only by geography and language but also by the Y chromosome gene pool represented by forensic Y-STR markers. Consequently, more forensic Y-STR markers should be included in the Y-STR haplotype in order to achieve a resolution between the Y chromosomes of Lithuanian and Latvian males. Lithuanian Y-STR haplotype data were submitted to the 34th release of the Y-STR Haplotype Reference Database 3.0 for match probability calculations in the forensic casework.

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