scholarly journals Population genetic analysis of 12 X-STRs in a Bahraini population sample (Allele and haplotype frequencies of 12 X-STRs in Bahraini population)

2019 ◽  
Author(s):  
Noora R. Al-Snan ◽  
Safia A. Messaoudi ◽  
Moiz Bakhiet ◽  
Latifa A. Mansoor
Keyword(s):  
Population Sample ◽  
Arabian Gulf ◽  
Social Background ◽  
Population Genetic Analysis ◽  
Kinship Analysis ◽  
Genetic Studies ◽  
Buccal Swabs ◽  
Haplotype Frequencies ◽  
Bahraini Population ◽  
Genetic Analyzer

AbstractTo date, there are very limited genetic studies conducted on the Kingdom of Bahrain and this is one of the first studies conducted to evaluate the 12 X-STRs included in the Investigator X-12 QS kit. Bahrain is a small archipelago located in the Arabian Gulf. X-STRs are very informative in population genetics studies, human identification and complex kinship analysis. One hundred and fifty-six (156) buccal swabs were collected using cotton from non-relatives’ Bahraini males from four different regions of Bahrain. DNA was processed using QIAsymphony SP instrument following quantification with Investigator Quantiplex HYres Kit in the 7500 Real-Time PCR System and detected in ABI 3500xl Genetic Analyzer. Analysis was done using different statistical softwares to obtain allele frequencies and haplotype frequencies-based upon the available four clusters of Linkage Groups (LGs)- and the forensic parameters.. Results indicated the diversity of the Bahraini population in terms of high Power of Discrimination (PD) and Probability of Match (PM) values obtained. The combined values of each forensic parameter such as cPDM, Mean exclusion chance (CMEC) Krüger, CMEC Kishida, and CMEC Desmarais as well as CMEC Desmarais Duo, were 0.9999983, 9999979, 0.9999939, 0.9999996 and 0.9999514 respectively based on the allele and haplotype frequencies. No shared profiles were observed. Number of non-standard alleles and null samples were obtained with more profoundly in locus DXS10148. We have conducted phylogenetic tree as well as multidimensional scale to analyze the Interpopulation diversity between Bahraini population and nine other populations and found out they reflect the geographical and social background of the region. Overall, the results confirm the importance of X-STRs in discriminating between individuals among Bahraini population and in establishing DNA databases for forensic and kinship studies.

HLA-A, -B, -C, -DRB1 and -DQB1 allele and haplotype frequencies and phylogenetic analysis of Bahraini population

Gene ◽  
2020 ◽  
Vol 735 ◽  
pp. 144399
Author(s):  
Abdelhafidh Hajjej ◽  
F. Lisa Saldhana ◽  
Rana Dajani ◽  
Wassim Y. Almawi
Keyword(s):  
Phylogenetic Analysis ◽  
Haplotype Frequencies ◽  
Dqb1 Allele ◽  
Bahraini Population

Evaluation of an extended set of 15 candidate STR loci for paternity and kinship analysis in an Austrian population sample

2006 ◽  
Vol 121 (2) ◽  
pp. 85-89 ◽  
Author(s):  
P. Grubwieser ◽  
B. Zimmermann ◽  
H. Niederstätter ◽  
M. Pavlic ◽  
M. Steinlechner ◽  
...  
Keyword(s):  
Population Sample ◽  
Kinship Analysis ◽  
Str Loci ◽  
Austrian Population

Haplotype frequencies for 17 Y-STR loci (AmpFlSTR®Y-filer™) in a Moroccan population sample

2010 ◽  
Vol 4 (3) ◽  
pp. e73-e74 ◽  
Author(s):  
Rachid Aboukhalid ◽  
Mehdi Bouabdellah ◽  
Meriame Abbassi ◽  
Kaoutar Bentayebi ◽  
Mohammed Elmzibri ◽  
...  
Keyword(s):  
Population Sample ◽  
Moroccan Population ◽  
Str Loci ◽  
Haplotype Frequencies

scholarly journals Parental contribution in a cultivated stock for the spotted rose snapper Lutjanus guttatus (Steindachner, 1869) estimated by newly developed microsatellite markers

2020 ◽  
Vol 48 (2) ◽  
pp. 247-256
Author(s):  
Ricardo Perez-Enriquez ◽  
Janeth A. Valadez-Rodríguez ◽  
Adriana Max-Aguilar ◽  
Silvie Dumas ◽  
Noé Diaz-Viloria
Keyword(s):  
Wild Population ◽  
Management Strategies ◽  
Population Sample ◽  
Genetic Studies ◽  
Hardy Weinberg Equilibrium ◽  
Parental Couple ◽  
Cultivated Populations ◽  
Species Specific ◽  
Generation Sequencing

The spotted rose snapper Lutjanus guttatus is a fishery relevant species from the eastern Pacific Ocean, with aquaculture potential. Species-specific genetic markers are needed for the genetic characterization of wild and cultivated populations to help management strategies. Eighteen hypervariable microsatellites were developed by Next Generation Sequencing and characterized in a wild population sample. Genetic diversity was high (observed heterozygosity = 0.88 ± 0.050; the number of alleles per locus = 13.4 ± 1.3) and few loci departed from the Hardy-Weinberg Equilibrium, leaving 14 loci potentially suitable for population genetic studies. A reduced panel of five loci was tested in a cultivated stock to determine the parentage of progeny (embryonated eggs; n = 413), to estimate the temporal contribution of each parental broodstock. The above resulted in the successful assignment of 95.6% of the progeny to its parental couple, representing 17 out of the 24 possible families. Two of the four females produced most of those progeny (97.3%). These females, which reproduced throughout the season, did not spawn on consecutive days. The contribution of males was evenly distributed during the season and occurred on successive days. Some microsatellites can be used in other lutjanids (L. peru, L. argentiventris, and Hoplopagrus guentherii).

scholarly journals Development of microsatellite markers for the house cricket, Acheta domesticus (Orthoptera: Gryllidae)

2020 ◽  
Vol 21 (9) ◽  
Author(s):  
Yash Munnalal Gupta ◽  
SUPATCHAREE TANASARNPAIBOON ◽  
KITTISAK BUDDHACHAT ◽  
SURIN PEYACHOKNAGUL ◽  
PHATTHARAPORN INTHIM ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Genetic Analysis ◽  
Microsatellite Markers ◽  
Population Genetic ◽  
Acheta Domesticus ◽  
House Cricket ◽  
Population Genetic Analysis ◽  
Closely Related Species ◽  
Genetic Studies ◽  
Future Population

Abstract. Gupta YM, Tanasarnpaiboon S, Buddhachat K, Peyachoknagul S, Inthim P, Homchan S. 2020. Development of microsatellite markers for the house cricket, Acheta domesticus (Orthoptera: Gryllidae). Biodiversitas 21: 4094-4099. The house cricket, Acheta domesticus, is one of the species of crickets commonly found in Thailand. Insect breeders in Thailand prefer to breed house cricket as food due to its better taste and popularity among local people. Moreover, largescale breeding industries also breed house cricket to produce cricket-based edible products. Insect breeding industry is growing rapidly and requires primary precaution for sustainable production. To facilitate breeding system to maintain genetic variation in the captive population, we have sequenced the whole genome of A. domesticus to search for simple sequence repeats (SSRs) in order to develop polymorphic microsatellite markers for preliminary population genetic analysis. A total of 112,157 SSRs with primer pairs were identified in our analysis.  Of these, 91 were randomly selected to check for amplification of microsatellite polymorphisms. From these, nine microsatellites were used to check genetic variation in forty-five individuals of A. domesticus from the Phitsanulok population (Thailand).  These microsatellite markers also showed cross-amplification with other three species of edible crickets, specifically Gryllus bimaculatus, Gryllus testaceus, and Brachytrupes portentosus. The microsatellite markers presented herein will facilitate future population genetic analysis of A. domesticus populations. Moreover, the transferability of these makers would also enable researchers to conduct genetic studies for other closely related species.

scholarly journals Development and Use of Single Sequence Repeats (SSRs) Markers for Sugarcane Breeding and Genetic Studies

Agronomy ◽  
2018 ◽  
Vol 8 (11) ◽  
pp. 260 ◽  
Author(s):  
Ali Ahmad ◽  
Jin-Da Wang ◽  
Yong-Bao Pan ◽  
Rahat Sharif ◽  
San-Ji Gao
Keyword(s):  
Ssr Markers ◽  
Genome Mapping ◽  
Genetic Research ◽  
Paternity Analysis ◽  
Kinship Analysis ◽  
Genetic Studies ◽  
Advantages And Disadvantages ◽  
Crop Genetics ◽  
Ssrs Markers ◽  
Simple Sequence

Recently-developed molecular markers are becoming powerful tools, with applications in crop genetics and improvement. Microsatellites, or simple sequence repeats (SSRs), are widely used in genetic fingerprinting, kinship analysis, and population genetics, because of the advantages of high variability from co-dominant and multi-allelic polymorphisms, and accurate and rapid detection. However, more recent evidence suggests they may play an important role in genome evolution and provide hotspots of recombination. This review describes the development of SSR markers through different techniques, and the detection of SSR markers and applications for sugarcane genetic research and breeding, such as cultivar identification, genetic diversity, genome mapping, quantitative trait loci (QTL) analysis, paternity analysis, cross-species transferability, segregation analysis, phylogenetic relationships, and identification of wild cross hybrids. We also discuss the advantages and disadvantages of SSR markers and highlight some future perspectives.

scholarly journals The Discovery of the “Skipping Generations” Phenomenon

2018 ◽  
Vol 1 (1) ◽  
Keyword(s):  
Mitochondrial Dna ◽  
Nuclear Dna ◽  
Theoretical Orientation ◽  
Cycle Sequencing ◽  
Real Time Quantitative Pcr ◽  
Buccal Swabs ◽  
Colleges Of Technology ◽  
Haplotype Data ◽  
Dna Profiles ◽  
Genetic Analyzer

Statement of the Problem: The demanding need to discover someone’s identity is not possible with the nuclear DNA especially when the traces are highly degraded, since the nuclear DNA is destroyed in these conditions. Only the mitochondrial DNA that is inherited maternally can survive in these compromised conditions. The purpose of this study is to find a genetic commonality between UAE nationals. Methodology and Theoretical Orientation: 150 buccal swabs of unrelated UAE female students (approved by the UAE ID) of Sharjah Higher Colleges of Technology were collected and kept at room temperature for a period of three months or longer; to destroy the nuclear DNA, so only the mtDNA is present. mtDNA testing was performed on these buccal swabs, and it’s consisting of DNA Extraction, Real-Time quantitative PCR, Cycle sequencing and Capillary electrophoresis. The ABI PRISM®310 Genetic Analyzer capillary autosequencer [ABI PRISM® SeqScape® Soft-ware Version 2.6] was used to generate the mitochondrial DNA profiles. Findings: From these haplotype data, a total of 229 polymorphisms were observed carefully. 106 different polymorphisms were identified out of them, and classified into unique and common polymorphisms. Interestingly, two individuals from the study subjects lacked unique polymorphisms. Conclusion and Significance: It’s impossible for anyone to preserve their mtDNA from their great ancestors till now. The discovery of the remains of the Romanov family back in 1991 concluded that the comparison of mtDNA that is more than three generations old is more likely to get at least one mutation in the current generation. Therefore, if a vertical study is done on those two individuals with their older generations, definitely they will have unique polymorphisms compared to their older generations. Those two individuals are the effect of “Skipping Generations” phenomenon, the term that I have invented to solve the mystery of having two individuals with no unique polymorphisms.

scholarly journals Implications of HLA linkage disequilibrium phenomenon in finding unrelated volunteer bone marrow donors

2007 ◽  
Vol 60 (3-4) ◽  
pp. 178-182
Author(s):  
Svetlana Vojvodic ◽  
Stevan Popovic ◽  
Lana Macukanovic-Golubovic
Keyword(s):  
Bone Marrow ◽  
Linkage Disequilibrium ◽  
Normal Population ◽  
Unrelated Donor ◽  
Strong Linkage Disequilibrium ◽  
Genetic Studies ◽  
Haplotype Frequencies ◽  
Unrelated Donors ◽  
Hla Phenotype ◽  
Hla Haplotypes

Introduction. The distribution of HLA genes and haplotypes in the normal population is of considerable importance in disease susceptability studies, population and genetic studies and tissue and organ transplantation. The HLA phenotype frequencies can be used for the estimation of the probability of finding phenotypically identical unrelated volunteer bone marrow donors. It has been presumed that patients with HLA haplotypes in strong linkage disequilibrium, a have higher probability of finding HLA identical unrelated donors than others. Material and methods. HLA gene and haplotype frequencies were calculated, as well as delta values and their significance. The implications of HLA disequilibrium phenomenon in unrelated donor search, was investigated by calculating the correlation coefficient between frequencies of haplotypes showing significant delta values and the linkage disequilibrium coefficient, as well as between the average number of donors necessary for research. Results. Haplotypes showing the highest delta values are at the same time the most frequent haplotypes (A1B8:0,1188 and 0,145; A3B35:0,0722 and 0,1;A2B12:0,055 and 0,105). In patients who have both haplotypes showing significant delta values (e.g. A2B5/A3B35), the number of donors necessary for research is clearly lower than in patients who have only one given haplotype, or have no such haplotypes. Conclusion. Our results showed that patients with HLA haplotypes showing significant delta values have a higher probability of finding HLA identical unrelated donors. .

scholarly journals Population genetic analysis of 12 X-chromosomal STRs in a Swiss sample

2021 ◽  
Author(s):  
Michel Bottinelli ◽  
Alexandre Gouy ◽  
Silvia Utz ◽  
Martin Zieger
Keyword(s):  
Linkage Disequilibrium ◽  
Genetic Analysis ◽  
Population Genetic ◽  
Genetic Parameters ◽  
Population Substructure ◽  
Linkage Groups ◽  
Population Genetic Analysis ◽  
Haplotype Frequencies ◽  
Broad Variety ◽  
Population Genetic Parameters

AbstractX-chromosomal STRs are a powerful tool to assess a broad variety of complex kinship scenarios. We introduce herewith the first Swiss X-STR dataset based on 1198 individuals (592 female, 606 male), characterized with the Qiagen Investigator® Argus X-12 QS multiplex kit. Anomalous allele patterns, allele and haplotype frequencies, and forensic and population genetic parameters are presented. We detected linkage disequilibrium within three out of the four designated linkage groups and no apparent intra-national population substructure. We compared the dataset to a global panel of X-STR datasets and it fits well in the European context, as expected.

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