scholarly journals Genetic polymorphism and phylogenetic analysis of 15 autosomal STR markers in the Santal indigenous population of Bangladesh

2021 ◽  
Vol 7 (2) ◽  
pp. 1004-1009
Author(s):  
Md Mahamud Hasan ◽  
Md Hadisur Rahman ◽  
Sharif Akhteruzzaman
Keyword(s):  
Pcr Amplification ◽  
Population Data ◽  
Bonferroni Correction ◽  
Str Markers ◽  
Autosomal Str ◽  
Expected Heterozygosity ◽  
Paternity Index ◽  
Hardy Weinberg Equilibrium ◽  
Matching Probability ◽  
Nei's Genetic Distance

Fifteen autosomal STR markers, namely D8S1179, D21S11, D7S820, CSF1PO, D3S1358, TH01, D13S317, D16S539, D2S1338, D19S433, vWA, TPOX, D18S51, D5S818, and FGA were typed using AmpFlSTR® Identifiler® Plus PCR amplification systems in 132 unrelated Santal individuals of Bangladesh. Forensic efficiency parameters like, matching probability (MP), power of discrimination (PD), polymorphism information content (PIC), power of exclusion (PE), typical paternity index (TPI), observed heterozygosity (Hobs), and expected heterozygosity (Hexp) were calculated for all the loci. No deviations from Hardy-Weinberg equilibrium were detected for the loci after Bonferroni correction. The combined matching probability (MP), combined power of discrimination (PD) and combined power of exclusion (PE) for the 15 tested STR markers were 8.38 x 10-17, 0.999999998 and 0.0.999993866, respectively. A comparison of the locus wise allele frequencies of autosomal STR data of the Santal population with the published geographically close population data based on Nei’s genetic distance revealed that the Santal population is closely related to Munda population from Jharkhand, India. Bioresearch Commu. 7(2): 1004-1009, 2021 (June)

scholarly journals Development And Identification of 131 SNP Markers In Sthenoteuthis Pteropus (Steenstrup)

2021 ◽  
Author(s):  
Yan Zhao ◽  
Congcong Wang ◽  
Bilin Liu ◽  
Gang Li ◽  
Hao Xu
Keyword(s):  
Molecular Markers ◽  
Snp Markers ◽  
Scientific Management ◽  
Sustainable Utilization ◽  
Bonferroni Correction ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Polymorphic Snps ◽  
Expected Heterozygosity ◽  
Hardy Weinberg Equilibrium

Abstract The orangeback flying squid, Sthenoteuthis pteropus, is a species of significant potential value that is widely distributed in the tropical and temperate waters of the Atlantic Ocean. There have been no reports of the population genetics and effective molecular markers for this species due to a lack of reliable information regarding its genetic structure and its many individual differences, as well as its complex and changeable life history. Therefore, the development of auxiliary molecular markers would contribute to the development, sustainable utilization, and protection of the species. In this study, 131 novel single nucleotide polymorphism (SNP) markers were developed by double digest restriction-site associated DNA sequencing (dd-RAD). The observed heterozygosity (Ho) and expected heterozygosity (He) ranged from 0.00 to 0.80 and 0.18 to 0.50, respectively. The polymorphism information content (PIC) value ranged from 0.18 to 0.50. None of the marker locations significantly deviated from the Hardy-Weinberg equilibrium (p >0.05) after a Bonferroni correction. These polymorphic SNPs will be important in the further analysis of the population heredity of S. pteropus and its scientific management.

scholarly journals Allele Frequencies of 10 Autosomal STR Loci from Chakma and Tripura Tribal Populations in Bangladesh

2010 ◽  
Vol 2010 ◽  
pp. 1-5 ◽  
Author(s):  
Ahmad Ferdous ◽  
Mohammad Eunus Ali ◽  
Shafiul Alam ◽  
Mahamud Hasan ◽  
Tania Hossain ◽  
...  
Keyword(s):  
Allele Frequency ◽  
Population Data ◽  
Allele Frequencies ◽  
Published Data ◽  
Allele Frequency Distribution ◽  
Str Loci ◽  
Autosomal Str ◽  
Significant Difference ◽  
Tribal Populations ◽  
Hardy Weinberg Equilibrium

Allele frequencies of ten autosomal STR loci, D3S1358, vWA, D16S539, D2S1338, D8S1179, D21S11, D18S51, D19S433, TH01, and FGA were investigated in Chakma and Tripura tribal populations of Bangladesh. In both the populations, all loci were in Hardy-Weinberg equilibrium except for FGA locus in Chakma and D21S11 in Tripura. All the loci were highly polymorphic in Chakma population with an observed heterozygosity (Ho) of >0.7 and moderately polymorphic in Tripura population (Ho>0.6). However, both the population showed least polymorphism at TH01 locus (Ho<0.6). A comparison between Chakma and Tripura population data revealed statistically significant differences in allele frequency distribution for most of the loci. A similar comparison with the mainstream Bengali population using previously published data from this lab also showed significant difference in allele frequency with these two tribal populations.

Population data of 15 autosomal STR markers from Afro-Bolivians of Nor Yungas Province (Bolivia)

2014 ◽  
Vol 129 (3) ◽  
pp. 463-464
Author(s):  
María Laura Parolin ◽  
Celia Estela Iudica ◽  
Julio Lucio Lancelotti ◽  
Lorena Andrea Sambuco ◽  
Stella Maris Jaureguiberry ◽  
...  
Keyword(s):  
Population Data ◽  
Str Markers ◽  
Autosomal Str

scholarly journals Development and Characterization of 123 SNP Markers in Neotrypaea Japonica (Ortmann 1891)

2021 ◽  
Author(s):  
Xiaoyue Sun ◽  
Jirui Zhang ◽  
Zhiwei Che
Keyword(s):  
Theoretical Basis ◽  
Species Conservation ◽  
Snp Markers ◽  
Bonferroni Correction ◽  
Frequency Range ◽  
Polymorphic Snps ◽  
Expected Heterozygosity ◽  
Minor Alleles ◽  
Hardy Weinberg Equilibrium

Abstract Neotrypaea japonica (Ortmann 1891) is a burrowing shrimp that lives in tidal flats. In this study, 123 SNP markers were isolated and characterized from N. japonica. The frequency range of minor alleles varied from 0.2500 to 0.4833, the observed heterozygosity ranged from 0.4333 to 0.9000, and the expected heterozygosity ranged from 0.4944 to 0.6503. The polymorphic parameter and inbreeding value varied from 0.3680 to 0.5651 and -0.2768 to 0.1045, respectively. Significant departures from Hardy-Weinberg equilibrium after Bonferroni correction (P < 0.05) were observed for 16 loci. The study of polymorphic SNPs will provide an important theoretical basis for further population genetic diversity analysis and species conservation of N. japonica.

scholarly journals Assessment of QIAGEN™ Investigator® 24plex GO! kit workflow for autosomal STR profiling of forensic reference samples

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Hashom Mohd Hakim ◽  
Hussein Omar Khan ◽  
Siti Afifah Ismail ◽  
Nurul Hazirah Mat Lazim ◽  
Japareng Lalung ◽  
...  
Keyword(s):  
Pcr Amplification ◽  
Dna Profiling ◽  
Buccal Swab ◽  
Forensic Dna ◽  
Str Typing ◽  
Str Analysis ◽  
Dna Database ◽  
Autosomal Str ◽  
Dna Template ◽  
Reference Samples

Abstract Background DNA profiling has proven to be a valuable technique for identification of individuals in crime. Currently, the technique targets several short tandem repeat (STR) regions in human genome. However, increasing number of samples submitted for STR analysis may lead to delays due to the limited number of experienced analysts who might be available at any given moment and the time taken to complete lengthy DNA profiling procedures. This study was conducted to test the specificity, repeatability, reproducibility and robustness of Investigator® 24plex GO! kit for genotyping of reference samples submitted to the Royal Malaysian Police Forensic DNA Laboratory for DNA database. Material and methods In this study, Investigator® 24plex GO! kit was used to directly amplify STR loci from buccal swab cell of reference samples that had previously been STR typed using GlobalFiler™ Express kit. Capillary electrophoresis was carried out on a 3500xL Genetic Analyser using POP-4® Polymer. Amplified products were assigned to particular STR alleles using the GeneMapper ID-X version 1.4 software. Results Our study shows that STR profiles generated using Investigator® 24plex GO! gave concordance results with those previously obtained using the GlobalFiler™ Express kit. In addition, quality sensors included in the kit are of particular importance for determining the effectiveness of the PCR reaction and help to indicate the nature and quantity of DNA template for PCR amplification. Conclusion The Investigator® 24plex GO! kit is reliable for STR typing of reference samples.

Genetic study with autosomal STR markers in people of the Peruvian jungle for human identification purposes

2021 ◽  
pp. 1-22
Author(s):  
Neyra-Rivera Carlos David ◽  
Delgado Ramos Edgardo ◽  
Díaz Soria Fabiola ◽  
Quispe Ramírez José Santos ◽  
Ge Jianye ◽  
...  
Keyword(s):  
Genetic Study ◽  
Human Identification ◽  
Str Markers ◽  
Autosomal Str

scholarly journals ISOLATION AND CHARACTERIZATION OF NEW MICROSATELLITE MARKERS FOR THE CORTÉS GEODUCK (Panopea globosa)

2016 ◽  
Vol 31 (1) ◽  
pp. 17
Author(s):  
Celia Isabel Bisbal -Pardo ◽  
Miguel Ángel Del Río -Portilla ◽  
Ana Yonori Castillo -Paéz ◽  
Axayácatl Rocha-Olivares
Keyword(s):  
Fishery Management ◽  
Genetic Research ◽  
Isolation And Characterization ◽  
Expected Heterozygosity ◽  
Tetranucleotide Repeats ◽  
Hardy Weinberg Equilibrium ◽  
Increasing Demand ◽  
Sustainable Fishery ◽  
Generation Technology

The geoduck Panopea globosa is a long-lived and large endemic infaunal clam sustaining a growing fishery in the Northwest coast of México that, in spite of its increasing demand in Asian markets very little is known about its biology. In order to provide genetic markers to support genetic research of wild populations, nine novel microsatellite loci (di-, tri-, and tetranucleotide repeats) were developed using shotgun sequencing with next generation technology (Illumina). The number of alleles per locus ranged from 3 to 16 and the observed and expected heterozygosity ranged from 0.286 to 0.650 and 0.504 to 0.906, respectively. Five loci were found to be significantly deviated from the Hardy-Weinberg equilibrium and three pairs showed evidence of linkage disequilibrium. Most loci are highly informative for population genetics and linkage analyses according to their polymorphism information content (> 0.5) and will be useful for increasing our understanding of the wild population structure and developing a sustainable fishery management. Aislamiento y caracterización de nuevos marcadores microsatelitales en la almeja generosa (Panopea globosa) La almeja generosa Panopea globosa es una especie infáunica longeva y de gran tamaño que mantiene una pesquería creciente en la costa del Noroeste de México. A pesar de su demanda creciente en los mercados asiáticos, se conoce muy poco acerca de su biología. Con la finalidad de proveer nuevos marcadores genéticos para la caracterización de poblaciones silvestres, se desarrollaron nueve marcadores microsatelitales nuevos (con patrones repetidos de di-, tri-, y tetranucleotídicos) utilizando secuenciación genómica aleatoria con tecnología de secuenciación de siguiente generación (Illumina). El número de alelos por locus varió de 3 a 16 y los valores de heterocigosidad observada y esperada variaron de 0.286 a 0.650 y 0.504 a 0.906, respectivamente. Cinco microsatelites se desvían del equilibrio de Hardy-Weinberg y tres pares de microsatélites mostraron evidencia de desequilibrio de ligamiento. La mayoría de los loci son altamente informativos para estudios poblacionales y análisis de ligamiento de acuerdo con su contenido de información de polimorfismos (> 0.5) y serán útiles para incrementar el conocimiento de la estructura genética de las poblaciones silvestres de esta almeja y para coadyuvar en su pesquería sustentable.

Belgian population data for 15 STR loci (AmpFlSTR® SGM Plus and AmpFlSTR™ profiler PCR amplification kit)

2004 ◽  
Vol 139 (2-3) ◽  
pp. 211-213 ◽  
Author(s):  
Ronny Decorte ◽  
Mireille Engelen ◽  
Lucie Larno ◽  
Karolien Nelissen ◽  
Anja Gilissen ◽  
...  
Keyword(s):  
Pcr Amplification ◽  
Population Data ◽  
Str Loci ◽  
Belgian Population

scholarly journals Population genetic data for 21 autosomal STR loci for the Saudi Arabian population using the GlobalFiler ® PCR amplification kit

2017 ◽  
Vol 31 ◽  
pp. e59-e61 ◽  
Author(s):  
Hussain M. Alsafiah ◽  
William H. Goodwin ◽  
Sibte Hadi ◽  
Mohammed A. Alshaikhi ◽  
Pet-Paul Wepeba
Keyword(s):  
Population Genetic ◽  
Pcr Amplification ◽  
Saudi Arabian ◽  
Genetic Data ◽  
Population Genetic Data ◽  
Str Loci ◽  
Autosomal Str ◽  
Arabian Population
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