scholarly journals Efficiency of Tetrameric Short Tandem Repeats in Prestice Black-Pied Pig for Traceability and Parentity Testing

2016 ◽  
Vol 64 (2) ◽  
pp. 557-565
Author(s):  
Irena Vrtková ◽  
Štěpán Vrtek ◽  
Lenka Falková
Keyword(s):  
Information Content ◽  
Polymorphism Information Content ◽  
Short Tandem Repeats ◽  
Tandem Repeats ◽  
Genetic Resource ◽  
Marker Panel ◽  
Str Loci ◽  
Related Individuals ◽  
Crossbred Pigs ◽  
Short Tandem

The main goal of the research was to evaluate suitability of 11 tetrameric STRs (Short Tandem Repeats) marker panel for the Prestice Black-Pied pig (PC) breed as the only genetic resource in the Czech Republic.The analysis was carried out in 522 breeding and slaughter PC individuals. We observed 94 alleles overall across whole 11 STR panel. The observed heterozygosityHOwas 0.677, the polymorphism information content (PIC) was in average 0.664 per locus. The probability of identity of two independent samples (PI) using all 11 STR loci was 4.037·10−11and the probability of identity related individuals (PISibs) was 8.315·10−5. The power of exclusion for loci combinations when both parents are known (P1), when only one of the parent is known (P2) and for two putative parents (P3) were 0.9996, 0.9899 and 0.9999. The efficiency of the 11 tetrameric STRs (Animaltype Pig kit) is higher in PC in comparison to commercial breeds and slaughter crossbred pigs. In genetic resource PC, the 11 STRs panel is usable for forensic purpose such parentity testing and traceability.

scholarly journals Genetic analysis of DXS101and DXS6807 short tandem repeat (X-STR) in samples of Iraqi Arab male population

2020 ◽  
Vol 14 (1) ◽  
pp. 34-38
Author(s):  
Hayder Allawi Khaleefah ◽  
Salwa Jaber Abdullah Al-Awadi ◽  
Zaid Nsaif Abbas Al-Tameemi
Keyword(s):  
Information Content ◽  
Polymorphism Information Content ◽  
Tandem Repeats ◽  
Forensic Application ◽  
Male Population ◽  
Forensic Efficiency ◽  
Back Ground ◽  
Forensic Markers ◽  
Short Tandem ◽  
Apparently Healthy

Back ground: X-chromosomal short tandem repeats (X-STRs) have assured to be informative and particular role in complex relationship testing. DXS6807 known as tetra nucleotides polymorphism representing eight alleles of 251-275 bp in length. DXS6807 is located in, at XP 22.2, at a genetic distance of more than 87 and 151 Cm of X-chromosome. DXS101 is located104.9–121 cM from the Xp-telomere (Xp-tel) corresponding to cytogenetic position in Xq21.33–Xq22.3.  Objective: The aim of this present study   investigates the allele frequency of two markers DXS101, DXS6807 and forensic efficiency parameters for sample of Arabic Iraqi males. Material and methods: The population of this study includes 200 males apparently healthy unrelated participants from different region of Baghdad city, their ages ranged between (20-50) years. The Genomic DNA extracted and purified successfully from blood samples.  Results: The forensic efficiency parameters result for these markers were following: polymorphism information content (PIC) of 0.834708, power of discrimination (PD) in male 0.851750, Power of exclusion (PE) 0.698316, MEC Krüger0.511679, MEC Kishida 0.694890. The forensic efficiency parameters analyzing from Arabic population were Power of discrimination (PD) = 0.73405, Polymorphism information content (PIC) =0.69489, Power of exclusion (PE) =0.482879.MEC Krüger =0.511679, MEC Kishida = 0.694890. Conclusions: The information provided establish this X-linked microsatellite marker as a valuable strategy for forensic application. DXS101is and DXS6807 recently consider more stable and suitable forensic markers for forensic application.

scholarly journals A New Viewpoint on Genetic Diversity in Prestice Black-Pied Pig: Did the Breed Suffer from a Bottleneck?

2020 ◽  
Vol 68 (2) ◽  
pp. 305-309
Author(s):  
Lenka Falková ◽  
Irena Vrtková ◽  
Štěpán Vrtek
Keyword(s):  
Genetic Diversity ◽  
Genetic Variability ◽  
Short Tandem Repeats ◽  
Tandem Repeats ◽  
Genetic Resource ◽  
Heterozygosity Excess ◽  
Rare Alleles ◽  
Recent Bottleneck ◽  
Short Tandem

The research was aimed at determination of genetic variability of Prestice Black-Pied (PC) pig breed (Czech national breed and genetic resource) and to evaluate possible presence of recent bottleneck in this closed small pig population. One hundred and eighty of breeding boars were analysed by eleven tetramer Short Tandem Repeats (STR) panel specifically developed for the genotyping of breeding livestock. Despite the fact that appearance of rare alleles, which may be relatively increased after recent bottleneck, was discovered, the heterozygosity excess was not significant. The PC breed has not undergone recent bottleneck and remained at mutation-drift equilibrium.

scholarly journals The ancient Yakuts: a population genetic enigma

2015 ◽  
Vol 370 (1660) ◽  
pp. 20130385 ◽  
Author(s):  
Christine Keyser ◽  
Clémence Hollard ◽  
Angela Gonzalez ◽  
Jean-Luc Fausser ◽  
Eric Rivals ◽  
...  
Keyword(s):  
Short Tandem Repeats ◽  
Tandem Repeats ◽  
Hypervariable Region ◽  
Dna Analyses ◽  
Autosomal Str ◽  
Region I ◽  
Related Individuals ◽  
Hypervariable Region I ◽  
Ongoing Project ◽  
Short Tandem

This study is part of an ongoing project aiming at determining the ethnogenesis of an eastern Siberian ethnic group, the Yakuts, on the basis of archaeological excavations carried out over a period of 10 years in three regions of Yakutia: Central Yakutia, the Vilyuy River basin and the Verkhoyansk area. In this study, genetic analyses were carried out on skeletal remains from 130 individuals of unknown ancestry dated mainly from the fifteenth to the nineteenth century AD. Kinship studies were conducted using sets of commercially available autosomal and Y-chromosomal short tandem repeats (STRs) along with hypervariable region I sequences of the mitochondrial DNA. An unexpected and intriguing finding of this work was that the uniparental marker systems did not always corroborate results from autosomal DNA analyses; in some cases, false-positive relationships were observed. These discrepancies revealed that 15 autosomal STR loci are not sufficient to discriminate between first degree relatives and more distantly related individuals in our ancient Yakut sample. The Y-STR analyses led to similar conclusions, because the current Y-STR panels provided the limited resolution of the paternal lineages.

scholarly journals Sibling Indices as Comparisons in Personal Identification Process through Short Tandem Repeats [STR] Loci CSF1PO, THOI, TPOX, vWA of Maduranese Ethnic in Surabaya

2021 ◽  
Vol 6 (2) ◽  
pp. 60318
Author(s):  
Ahmad Yudianto ◽  
Fery Setiawan ◽  
Simon Martin Manyanza Nzilibili
Keyword(s):  
Observational Study ◽  
Short Tandem Repeats ◽  
Tandem Repeats ◽  
Personal Identification ◽  
Allele Sharing ◽  
Blood Samples ◽  
Identification Process ◽  
Str Loci ◽  
Calculation Results ◽  
Short Tandem

Sibling indices can be used as a comparison through alleles Short Tandem Repeats [STR] loci. This is an observational study among Maduranese with 4 STR loci (CSF1PO, THOI, TPOX, vWA) obtained from their blood samples. The percentage of alleles shared: 82.5% [33 times] with 2 allele sharing, 12.5% [5 times] with 1 allele sharing, and 5 % [2 times] with 0 sharing alleles. Sibling indices (SI) calculation results: 65% of sibling indices pairs have SI greater than 100 and 15% of them were between 10-100 (strong and very strong). Sibling indices interpretation is supported; therefore, the claimed sibling indices relationships were indeed true among Maduranese ethnic group in Surabaya.

scholarly journals The Mutational Dynamics of Short Tandem Repeats in Large, Multigenerational Families

2021 ◽  
Author(s):  
Cody J Steely ◽  
Scott Watkins ◽  
Lisa Baird ◽  
Lynn Jorde
Keyword(s):  
Short Tandem Repeats ◽  
Tandem Repeats ◽  
De Novo ◽  
Friedreich Ataxia ◽  
Whole Genome Sequencing Data ◽  
Sequencing Data ◽  
Alu Elements ◽  
Str Loci ◽  
Genome Wide ◽  
Short Tandem

Short tandem repeats (STRs) are tandemly repeated sequences of 1-6 bp motifs. STRs compose approximately 3% of the genome, and mutations at STR loci have been linked to dozens of human diseases including amyotrophic lateral sclerosis, Friedreich ataxia, Huntington disease, and fragile X syndrome. Improving our understanding of these mutations would increase our knowledge of the mutational dynamics of the genome and may uncover additional loci that contribute to disease. Here, to estimate the genome-wide pattern of mutations at STR loci, we analyzed blood-derived whole-genome sequencing data for 544 individuals from 29 three-generation CEPH pedigrees. These pedigrees contain both sets of grandparents, the parents, and an average of 9 grandchildren per family. Using HipSTR we identified de novo STR mutations in the 2nd generation of these pedigrees. Analyzing ~1.6 million STR loci, we estimate the empircal de novo STR mutation rate to be 5.24*10-5 mutations per locus per generation. We find that perfect repeats mutate ~2x more often than imperfect repeats. De novo STRs are significantly enriched in Alu elements (p < 2.2e-16). Approximately 30% of STR mutations occur within Alu elements, which compose only ~11% of the genome, and ~10% are found in LINE-1 insertions, which compose ~17% of the genome. Phasing these de novo mutations to the parent of origin shows that parental transmission biases vary among families. We estimate the average number of de novo genome-wide STR mutations per individual to be ~85, which is similar to the average number of observed de novo single nucleotide variants.

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