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

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.

Download Full-text

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.

Download Full-text

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

Arab Journal of Forensic Sciences and Forensic Medicine ◽

10.26735/kjrv2063 ◽

2021 ◽

Vol 3 (2) ◽

pp. 216-230

Author(s):

Adelaja Akinlolu ◽

Nabila Sule ◽

Maryam Muhammed ◽

David Oyedepo ◽

Maryam Olawole ◽

...

Keyword(s):

Ethnic Groups ◽

Tandem Repeats ◽

Gene Diversity ◽

Haplotype Diversity ◽

Pcr Amplification ◽

Haplotype Frequency ◽

Dna Index ◽

North Central ◽

Hardy Weinberg Equilibrium ◽

Forensic Genotyping

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.

Download Full-text

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.

Download Full-text

Czechoslovakian Wolfdog Genomic Divergence from Its Ancestors Canis lupus, German Shepherd Dog, and Different Sheepdogs of European Origin

Genes ◽

10.3390/genes12060832 ◽

2021 ◽

Vol 12 (6) ◽

pp. 832

Author(s):

Nina Moravčíková ◽

Radovan Kasarda ◽

Radoslav Židek ◽

Luboš Vostrý ◽

Hana Vostrá-Vydrová ◽

...

Keyword(s):

Demographic History ◽

Genome Structure ◽

Principal Component ◽

Genetic Distances ◽

Nucleotide Polymorphisms ◽

German Shepherd ◽

German Shepherd Dog ◽

Genome Wide ◽

Scale Population ◽

History Effect

This study focused on the genomic differences between the Czechoslovakian wolfdog (CWD) and its ancestors, the Grey wolf (GW) and German Shepherd dog. The Saarloos wolfdog and Belgian Shepherd dog were also included to study the level of GW genetics retained in the genome of domesticated breeds. The dataset consisted of 131 animals and 143,593 single nucleotide polymorphisms (SNPs). The effects of demographic history on the overall genome structure were determined by screening the distribution of the homozygous segments. The genetic variance distributed within and between groups was quantified by genetic distances, the FST index, and discriminant analysis of principal components. Fine-scale population stratification due to specific morphological and behavioural traits was assessed by principal component and factorial analyses. In the CWD, a demographic history effect was manifested mainly in a high genome-wide proportion of short homozygous segments corresponding to a historical load of inbreeding derived from founders. The observed proportion of long homozygous segments indicated that the inbreeding events shaped the CWD genome relatively recently compared to other groups. Even if there was a significant increase in genetic similarity among wolf-like breeds, they were genetically separated from each other. Moreover, this study showed that the CWD genome carries private alleles that are not found in either wolves or other dog breeds analysed in this study.

Download Full-text

Genetic diversity and phylogeny analysis of Azolla based on DNA amplification by arbitrary primers

Genome ◽

10.1139/g93-092 ◽

1993 ◽

Vol 36 (4) ◽

pp. 686-693 ◽

Cited By ~ 23

Author(s):

Benoit Van Coppenolle ◽

Iwao Watanabe ◽

Charles Van Hove ◽

Gerard Second ◽

Ning Huang ◽

...

Keyword(s):

Principal Component Analysis ◽

Polymerase Chain Reaction ◽

Principal Component ◽

Dna Amplification ◽

Component Analysis ◽

Genetic Distances ◽

Group Method ◽

Chain Reaction ◽

Arbitrary Primers ◽

Polymerase Chain

The polymerase chain reaction was used to amplify random sequences of DNA from 25 accessions of Azolla to evaluate the usefulness of this technique for identification and phylogenetic analysis of this aquatic fern. Accessions were selected to represent all known species within the genus Azolla and to encompass the worldwide distribution of the fern. Primers of 10 nucleotides with 70% G + C content were used to generate randomly amplified polymorphic DNA from the symbiotic Azolla–Anabaena complex. Twenty-two primers were used and each primer gave 4–10 bands of different molecular weights for each accession. Bands were scored as present or absent for each accession and variation among accessions was quantified using Nei's genetic distances. A dendrogram summarizing phenetic relationships among the 25 accessions was generated using the unweighted pair-group method with arithmetic mean. Principal component analysis was also used to evaluate genetic similarities. Three distinct groups were identified: group 1 contains five species, group 2 contains the pinnata species, and group 3 contains the nilotica species. The analysis demonstrates that the major groups of Azolla species can be easily distinguished from one an other and, in addition, that closely related accessions within species can be identified. We further found that using 10 primers, a phylogeny that is essentially the same as that derived from 22 primers can be constructed. Our results suggest that total DNA extracted from the Azolla–Anabaena symbionts is useful for classification and phylogenetic studies of Azolla.Key words: Azolla–Anabaena symbiosis, genetic distances, polymerase chain reaction, principal component analysis.

Download Full-text

Association study of rs17782313 polymorphism near MC4R gene with obesity/overweight, BMI, and hedonic hunger among women from Northwestern Iran

Mediterranean Journal of Nutrition and Metabolism ◽

10.3233/mnm-200530 ◽

2021 ◽

pp. 1-12

Author(s):

Mahan Narjabadifam ◽

Morteza Bonyadi ◽

Seyed Abbas Rafat ◽

Reza Mahdavi ◽

Fereshteh Aliasghari

Keyword(s):

Medical Condition ◽

Sequencing Data ◽

Mc4r Gene ◽

Melanocortin 4 Receptor ◽

Group Methods ◽

Pcr Rflp ◽

Hedonic Hunger ◽

Hardy Weinberg Equilibrium ◽

Northwestern Iran ◽

Different Populations

BACKGROUND: Obesity, as a medical condition, results from interactions between environmental and genetic factors. The rs17782313 polymorphism, located 188kb downstream of the Melanocortin 4 Receptor (MC4R) gene, is one of the essential candidate genetic markers that has shown the highest association with obesity in different populations. OBJECTIVE: This study aimed to investigate the possible associations of rs17782313 polymorphism near the MC4R gene with obesity/overweight, body mass index (BMI), and hedonic hunger among women from the Iranian Azeri ethnic group. METHODS: Five hundred sixty-three women, composed of 396 patients with obesity/overweight and 167 unrelated healthy controls, were genotyped for the rs17782313 polymorphism by applying the polymerase chain reaction-restriction fragment length polymorphism (PCR–RFLP) method. RESULTS: This population was in Hardy-Weinberg equilibrium (P = 0.878). The study confirmed a significant association of rs17782313 with obesity, where subjects carrying the C/C genotype had higher odds of obesity (OR = 2.681, P = 0.005, 95%CI:1.340–5.365). Also, C allele carriers have statistically significantly higher BMI scores than those carrying the T allele (P = 0.029). However, no significant associations were found among PFS scores and genotypic/allelic groups of rs17782313 polymorphism (P = 0.368). CONCLUSIONS: Our findings suggest that rs17782313 polymorphism is strongly associated with obesity and BMI but not with hedonic hunger among Northwest Iran women. Moreover, the sequencing data analysis in several homozygous and heterozygous carriers of the C allele led to identifying a novel frameshift variant with TCT deletion (rs534212081) in the 166 upstream of rs17782313, which has not been reported so far.

Download Full-text

Genetic polymorphism of milk protein loci in Argentinian Holstein cattle

Genetics and Molecular Biology ◽

10.1590/s1415-47572000000400019 ◽

2000 ◽

Vol 23 (4) ◽

pp. 819-823 ◽

Cited By ~ 5

Author(s):

Adriana Gloria Bonvillani ◽

Miguel Angel Di Renzo ◽

Iván Nicolás Tiranti

Keyword(s):

Genetic Polymorphism ◽

Milk Protein ◽

Genotypic Diversity ◽

Genetic Distances ◽

Holstein Cattle ◽

Starch Gel Electrophoresis ◽

Beta Casein ◽

Hardy Weinberg Equilibrium ◽

Quality Of Milk ◽

Beta Lactoglobulin

Some alleles of milk protein loci are associated with superior cheese production characteristics. The genetic polymorphism of the milk protein loci alphas1-casein, beta-casein, k-casein and beta-lactoglobulin was examined in Argentinian Holstein cattle. Samples from 12 herds of four regions of Córdoba were analyzed by starch gel electrophoresis. The chi² test was used to assess whether the populations were in Hardy-Weinberg equilibrium. Genotypic diversity was analyzed by the Shannon-Weaver index. The observed genotypic frequencies were analyzed by Hedrick's genetic identity and the genetic distance of Balakrishnan and Sanghvi. The allelic and genotypic frequencies were similar to those of other Holstein populations. The genotypic frequencies of the alphas1-casein and beta-casein loci were in equilibrium, whereas in some populations the k-casein and beta-lactoglobulin loci were not. According to the Shannon-Weaver index the total genetic diversity within each herd was greater than 96%. The high values of identity agreed with the low genetic distances among populations. We conclude that there is extensive genetic homogeneity in Holstein cattle in Córdoba Province and that it would be feasible to select for B alleles at the k-casein and b-lactoglobulin loci in order to improve the quality of milk available for cheese manufacturing.

Download Full-text

Genetic diversity and population structure among goat genotypes in Kenya

10.1101/2020.07.06.189290 ◽

2020 ◽

Author(s):

Ruth W. Waineina ◽

Kiplangat Ngeno ◽

Tobias O. Otieno ◽

Evans D. Ilatsia

Keyword(s):

Population Structure ◽

Principal Component ◽

Genetic Distances ◽

Snp Markers ◽

Founder Population ◽

Good Opportunity ◽

Model Based Clustering ◽

Population Structuring ◽

Improvement Programs ◽

Genotype Clustering

AbstractPopulation structure and relationship information among goats is critical for genetic improvement, utilization and conservation. This study explored population structure and level of gene intermixing among four goat genotypes in Kenya: Alpine (n = 30), Toggenburg (n = 28), Saanen (n = 24) and Galla (n = 12). The population structuring and relatedness were estimated using principal component analysis utilizing allele frequencies of the SNP markers. Genotype relationships were evaluated based on the calculated Reynolds genetic distances. A phylogenetic tree was constructed to represent genotype clustering using iTOL software. Population structure was investigated using model-based clustering (ADMIXTURE) Genotypes relationships revealed four distinctive clusters: Alpine, Galla, Saanen and Toggenburg. The ADMIXTURE results revealed some level of gene intermixing among Alpine, Toggenburg and Saanen with Galla. Saanen goats were the most admixed genotype with 84%, 7% and 4% of its genome derived from Galla, Alpine and Toggenburg respectively. Alpine and Toggenburg goats shared some associations with the Galla goat; 10% and 1% respectively. The association of Galla with other genotypes was anticipated since Galla goat was used as the founder population for crossbreeding with Saanen, Alpine and Toggenburg breed. The genetic variations among the goat genotypes observed, will provide a good opportunity for sustainable utilization, conservation and future genetic resource improvement programs in goat genotypes in Kenya.

Download Full-text

Distribution Of Phenotypic And Genotypic Abo And Rhesus Blood Groups Among Bangladeshi Population

Ibrahim Medical College Journal ◽

10.3329/imcj.v5i2.10101 ◽

1970 ◽

Vol 5 (2) ◽

pp. 59-62

Author(s):

Tashmim Farhana Dipta ◽

Md Roushan Iqbal ◽

Ahmed Zahid Hossain ◽

Md Tahminur Rahman ◽

Subhagata Chowdhury

Keyword(s):

Blood Group ◽

Blood Donors ◽

Allelic Frequency ◽

Blood Groups ◽

Weinberg Equilibrium ◽

Changing Trend ◽

Hardy Weinberg Equilibrium ◽

Bangladeshi Population ◽

Group B ◽

Positive Groups

The present study is a retrospective analysis of allelic frequency of ABO and Rhesus (D) blood groups of donors attending the Deaprtment of Transfusion Medicine of Bangladesh Institute of Research and Rehabilitation in Diabetes, Endocrine and Metabolic Disorders (BIRDEM), Dhaka. BIRDEM IS a 625 bed hospital, where patients and blood donors come from all parts of Bangladesh. A total of 1, 28,506 blood donors of both genders were included in the study over fourteen years from June 1995 to June 2009 for analysis. Blood group was determined by performing the both tube and slide method blood grouping method. The distribution of blood groups in our population was B>O>A>AB in Rh positive groups donors and O>B>A>AB among Rh negative donors. Blood group B was more common among the males (37.42%) while O was predominant among female donors (33.83 %). On the other hand, blood group O negative was predominant in both genders (36.88%). In this study, Hardy- Weinberg equilibrium law was used to calculate the allelic frequency for ABO/ Rh system. Homozygous allelic frequency for Rh negative population was only 0.0007. Although phenotypically B group was dominant and AB was rare in our population, but according to Hardy- Weinberg equilibrium law the estimated allelic frequency of A (0.3694) and O (0.3040) showed higher frequency than B type (0.2300) in Bangladeshi population in both homozygous and heterozygous state. So, with increasing population of Bangladesh, this changing trend in estimated blood group in ABO system may play an important role in our genetic pattern. DOI: http://dx.doi.org/10.3329/imcj.v5i2.10101 IMCJ 2011; 5(2): 59-62

Download Full-text

An Immunocapture RT-PCR Procedure Using Apple stem grooving virus Antibodies Facilitates Analysis of Citrus tatter leaf virus from the Original Meyer Lemon Host

Plant Disease ◽

10.1094/pdis-92-5-0746 ◽

2008 ◽

Vol 92 (5) ◽

pp. 746-750 ◽

Cited By ~ 6

Author(s):

Mark E. Hilf

Keyword(s):

Pcr Amplification ◽

Pairwise Alignment ◽

Magnetic Bead ◽

Genetic Distances ◽

Polyclonal Antiserum ◽

Apple Stem Grooving Virus ◽

Apple Stem ◽

Genomic Regions ◽

Leaf Virus ◽

Citrus Tatter Leaf Virus

A magnetic bead-based immunocapture system using polyclonal antiserum against Apple stem grooving virus (ASGV) successfully facilitated polymerase chain reaction (PCR) amplification of sequences from three Citrus tatter leaf virus (CTLV) isolates originally isolated from the citrus host Meyer lemon. Primers designed from a pairwise alignment of genomic sequences of CTLV isolates from lily and from kumquat amplified two nonoverlapping genomic regions of 625 and 1,165 bp (approximately 28% of the CTLV genome) which were cloned and sequenced. Despite being propagated separately in the glasshouse for more than 40 years, the CTLV sequences from separate Meyer lemon sources were identical but had only approximately 80% nucleotide identity with the homologous regions of CTLV genomes of isolates from lily and kumquat. Neighbor-joining phylogenetic analysis indicated the CTLV isolates from Meyer lemon were distinct from but more closely related to CTLV from kumquat than from lily, and these CTLV sequences showed equivalent genetic distances from two ASGV isolates.

Download Full-text