Improving genetic monitoring of the northern hairy-nosed wombat (Lasiorhinus krefftii)

2014 ◽  
Vol 62 (3) ◽  
pp. 246 ◽  
Author(s):  
Lauren C. White ◽  
Alan Horsup ◽  
Andrea C. Taylor ◽  
Jeremy J. Austin
Keyword(s):  
Microsatellite Markers ◽  
Dna Analysis ◽  
Genotype Frequencies ◽  
Abundance Estimates ◽  
Multiplex Reaction ◽  
Hardy Weinberg Equilibrium ◽  
Genetic Techniques ◽  
Polymerase Chain ◽  
Future Population

The endangered northern hairy-nosed wombat (Lasiorhinus krefftii) has been monitored via remote sampling and genetic techniques since 2000, thus avoiding the detrimental effects on the animals of trapping and increasing the precision of abundance estimates. The currently available dinucleotide microsatellite markers used for this task are prone to stutter and other polymerase chain reaction artefacts, making allele calling difficult, and requiring costly duplication to ensure accuracy. To remedy this we have developed eight new tri- and tetranucleotide microsatellite markers that reduce the problem of stutter in DNA analysis. These new markers, along with three of the existing markers (two microsatellites and the SRY gender marker) were optimised in a single multiplex reaction that will reduce the time and cost of future northern hairy-nosed wombat hair censuses. We tested this new multiplex on 277 non-invasively collected hairs. One locus was rejected due to null-allele issues. The remaining nine microsatellite loci had two or three alleles. Genotype frequencies in the sample of detected individuals did not differ significantly from Hardy–Weinberg equilibrium and there was no evidence of linkage disequilibrium. This new multiplex provides comparable power to distinguish individuals, fewer issues with stutter artefacts and a reduced time and cost of analysis. It will be useful for future population censuses and long-term monitoring of individuals once they have been scored in previously genotyped and assigned samples.

scholarly journals Transferability of Microsatellite Markers Developed in Oenothera spp. to the Invasive Species Oenothera drummondii Hook. (Onagraceae)

Diversity ◽  
2020 ◽  
Vol 12 (10) ◽  
pp. 387
Author(s):  
Raquel Hernández-Espinosa ◽  
Jorge González-Astorga ◽  
Alejandro Espinosa de los Monteros ◽  
Dánae Cabrera-Toledo ◽  
Juan B. Gallego-Fernández
Keyword(s):  
Invasive Species ◽  
North Carolina ◽  
Microsatellite Markers ◽  
Coastal Dunes ◽  
The United States ◽  
Null Alleles ◽  
Genetic Studies ◽  
Native Populations ◽  
Hardy Weinberg Equilibrium ◽  
Future Population

Oenothera drummondii Hook. (Onagraceae) has life-history traits that make it an invasive species. Native populations are distributed along the coastal dunes from North Carolina in the United States to Tabasco in the Gulf of Mexico. It has been reported as an invasive species in Spain, Israel, and China, where this species can successfully colonize and dominate if the environmental conditions are appropriate. In South Africa, Australia, New Zealand, and France, it is reported to be naturalized. In this study, 28 microsatellite markers developed for other Oenothera species were evaluated for cross-amplification in O. drummondii. Nine primers showed consistent amplification and were polymorphic. Polymorphism was assessed in three populations from both native and invaded areas. Results indicated generalized low genetic variability. Three loci showed significant deviations from the Hardy Weinberg equilibrium, associated with null alleles’ presence. The observed heterozygosity and inbreeding coefficient reflected a generalized excess of homozygotes, particularly in the invaded population “El Dique”, likely due to allele fixation. High genetic differentiation was found between the three populations. These results highlight the accuracy of these markers for future population genetic studies in O. drummondii.

scholarly journals Polymorphisms in the Leptin and SCD genes in Buffaloes of the Amazon

2021 ◽  
Vol 10 (13) ◽  
pp. e233101321222
Author(s):  
Caio Santos Silva ◽  
Ednaldo da Silva Filho ◽  
Lorena Keyse Nery da Silva ◽  
Rafaella Sousa Ferraz ◽  
Amanda de Sousa Matos ◽  
...  
Keyword(s):  
Milk Production ◽  
Bubalus Bubalis ◽  
Shannon Index ◽  
Inbreeding Coefficients ◽  
Genotype Frequencies ◽  
Mixed Breed ◽  
Pcr Rflp ◽  
Hardy Weinberg Equilibrium ◽  
Polymerase Chain ◽  
Amazonian Region

The objective this work was to evaluate genetically the buffaloes populations using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) in the leptin and stearoyl-CoA desaturase (SCD) genes, and associate the genotypes with milk production. Sixty-nine samples of Bubalus bubalis - 38 Murrah breed, 18 Mediterranean and 13 mixed-breed of the Murrah with Mediterranean - were evaluated. Allele and genotype frequencies, the heterozygosity observed and expected, the inbreeding coefficients (FIS), the probabilities of the Hardy-Weinberg equilibrium, the F statistic for population differentiation and Shannon index were calculated using GENEPOP and GenALEx programs. The associations of the different genotypes with a role in milk production were tested by Analysis of Variance (ANOVA) and t-test. We reported the leptin and SCD allele contribution to genetic variability in buffaloes herds in the Brazilian Amazonian region. The A allele was more representative in leptin and SCD genes for all breed groups. No significant effects between genotypes and milk production were found in the present study, but there is an indicative that AA genotype in leptin gene affects milk production in Murrah breed.

Glucose-6-phosphate dehydrogenase deficiency genotypes and allele frequencies in the Kavango and Zambezi regions of northern Namibia

2019 ◽  
Vol 113 (8) ◽  
pp. 483-488
Author(s):  
Daniel H Haiyambo ◽  
Alex Ilunga ◽  
Ruth Nangombe ◽  
Grace Ababio ◽  
Toini Hatuikulipi ◽  
...  
Keyword(s):  
G6pd Deficiency ◽  
Allele Frequencies ◽  
Cross Sectional ◽  
Plasmodium Ovale Curtisi ◽  
Genotype Frequencies ◽  
Female Genotype ◽  
Hardy Weinberg Equilibrium ◽  
Polymerase Chain ◽  
Glucose 6 Phosphate Dehydrogenase ◽  
Genotype And Allele Frequencies

AbstractBackgroundNamibia has made significant gains in the fight against malaria, with a target of elimination by 2023. We examined the genotype and allele frequencies of glucose-6-phosphate dehydrogenase (G6PD) deficiency to inform decisions on primaquine use, as we recently detected clusters of Plasmodium ovale curtisi in Kavango.MethodsA multistaged cross-sectional sampling method was used to enrol 212 children 2–9 y of age from schools and clinics in the Okavango and Zambezi regions of northern Namibia. Genotypes for the 202 G→A and 376 A→G mutations were assigned by polymerase chain reaction restriction fragment length polymorphism.ResultsOf the 212 subjects enrolled, genotypes were available for 210, made up of 61 males and 149 females. G6PD-deficient males (hemizygotes) and females (homozygotes) constituted 3.27% (2/61) and 0.0% (0/149), respectively. Female heterozygotes (AA− and BA−) constituted 10.07% (15/149), while G6PD wild-type males (with A or B haplotype) and females (with AA, BB or AB haplotypes) consisted of 96.72% (59/61) and 89.93% (134/149), respectively. The A−, A and B allele frequencies were 0.0474, 0.3036 and 0.6490, respectively. Hardy–Weinberg equilibrium tests for female genotype frequencies did not show deviation (p=0.29).ConclusionsThe frequency of G6PD deficiency alleles in males in the Kavango and Zambezi regions of northern Namibia constitute 3.27%, a first report to inform policy on primaquine role out.

scholarly journals The geographic distribution of the ACE II genotype: a novel finding

2007 ◽  
Vol 89 (4) ◽  
pp. 259-267 ◽  
Author(s):  
Y. B. Saab ◽  
P. R. Gard ◽  
A. D. J. Overall
Keyword(s):  
Geographic Location ◽  
Reaction Products ◽  
Buccal Cells ◽  
Population Genomic ◽  
Genotype Frequencies ◽  
Lebanese Population ◽  
Hardy Weinberg Equilibrium ◽  
Different Populations ◽  
Polymerase Chain ◽  
The Relationship

SummaryAngiotensin converting enzyme (ACE) gene polymorphism insertion (I) or deletion (D) has been widely studied in different populations, and linked to various functional effects and associated with common diseases. The purpose of the present study was to investigate the relationship between the ACE I/D frequency in different populations and geographic location; ACE I/D allele frequency in the Lebanese population and ACE II genotype contribution to the geographic trend were also identified. Five hundred and seventy healthy volunteers were recruited from the Lebanese population. Genomic DNA was extracted from buccal cells, and amplified by polymerase chain reaction; products were then identified by gel electrophoresis. The frequencies of the different ACE I/D genotypes were determined and tested for Hardy–Weinberg equilibrium (HWE). To assess the relationship between ACE I/D frequency and geographic location, and to identify how the Lebanese population contributes to the geographic trend in ACE I/D frequencies, Eurasian population samples and Asians were incorporated in the analyses from the literature. The frequency of the I allele in the Lebanese population was 27% and the corresponding II genotype was at a frequency of 7·37% (in HWE;P=0·979). The ACE I allele and genotype frequencies show an association with longitude, with frequencies increasing eastwards and westwards from the Middle East.

Isolation and Characterisation of Novel Polymorphic Microsatellite Markers for the Wedge-Billed Woodcreeper Glyphorynchus Spirurus

2017 ◽  
Vol 10 (1) ◽  
pp. 24-26 ◽  
Author(s):  
Jasmin Unrein ◽  
Juliana Menger ◽  
Anne Weigert ◽  
Klaus Henle ◽  
Martin Schlegel
Keyword(s):  
Population Genetics ◽  
Linkage Disequilibrium ◽  
Microsatellite Markers ◽  
Population Genetic ◽  
Ecological Studies ◽  
Central Amazonia ◽  
Hardy Weinberg Equilibrium ◽  
Polymorphic Microsatellite ◽  
Generation Sequencing ◽  
Future Population

In order to study the population genetic structure of the Amazonian understorey bird Glyphorynchus spirurus, we have isolated eight polymorphic microsatellite loci using next-generation sequencing. All loci were screened using 40 samples from central Amazonia. The number of alleles varied from five to 22. The observed heterozygosities ranged from 0.475 to 0.875. No linkage disequilibrium was found among the loci. None of the loci showed significant deviation from Hardy–Weinberg equilibrium. These novel microsatellite markers will be a useful tool for future population genetics and ecological studies of the Wedge-billed Woodcreeper.

scholarly journals Acceptance of a Symptom-Based Approach for COVID-19 rtRT-PCR Testing to Conserve Resources in a Lower Middle-Income Setting

2021 ◽  
Vol 12 ◽  
pp. 215013272098771
Author(s):  
S. M. Rashed Ul Islam ◽  
Tahmina Akther ◽  
Md. Abdullah Omar Nasif ◽  
Sharmin Sultana ◽  
Saif Ullah Munshi
Keyword(s):  
Primary Method ◽  
Chain Reaction ◽  
Middle Income ◽  
Clinical Recovery ◽  
Clinical Presentations ◽  
Long Time ◽  
Nasopharyngeal Secretion ◽  
Polymerase Chain ◽  
Set Up

SARS-CoV-2 initially emerged in Wuhan, China in late 2019. It has since been recognized as a pandemic and has led to great social and economic disruption globally. The Reverse Transcriptase Real-Time Polymerase Chain Reaction (rtRT-PCR) has become the primary method for COVID-19 testing worldwide. The method requires a specialized laboratory set up. Long-term persistence of SARS-CoV-2 RNA in nasopharyngeal secretion after full clinical recovery of the patient is regularly observed nowadays. This forces the patients to spend a longer period in isolation and test repeatedly to obtain evidence of viral clearance. Repeated COVID-19 testing in asymptomatic or mildly symptomatic cases often leads to extra workload for laboratories that are already struggling with a high specimen turnover. Here, we present 5 purposively selected cases with different patterns of clinical presentations in which nasopharyngeal shedding of SARS-CoV-2 RNA was observed in patients for a long time. From these case studies, we emphasized the adoption of a symptom-based approach for discontinuing transmission-based precautions over a test-based strategy to reduce the time spent by asymptomatic and mildly symptomatic COVID-19 patients in isolation. A symptom-based approach will also help reduce laboratory burden for COVID-19 testing as well as conserve valuable resources and supplies utilized for rtRT-PCR testing in an emerging lower-middle-income setting. Most importantly, it will also make room for critically ill COVID-19 patients to visit or avail COVID-19 testing at their convenience.

Genomic fingerprinting ofFrankiamicrosymbionts fromCeanothuscopopulations using repetitive sequences and polymerase chain reactions

1999 ◽  
Vol 77 (9) ◽  
pp. 1220-1230 ◽  
Author(s):  
Soon-Chun Jeong ◽  
David D Myrold
Keyword(s):  
Dna Sequencing ◽  
Dna Analysis ◽  
Repetitive Sequences ◽  
Intergenic Spacer ◽  
Rrna Genes ◽  
23S Rrna ◽  
Genomic Fingerprinting ◽  
Chain Reactions ◽  
Intergenic Spacer Region ◽  
Polymerase Chain

Specificity between Ceanothus species and their microsymbionts, Frankia, were investigated with nodules collected from three geographically separated copopulations of Ceanothus species. Nodules were analyzed using DNA sequencing and repetitive sequence polymerase chain reaction (rep-PCR) techniques. DNA sequencing of the intergenic spacer region between 16S and 23S rRNA genes suggested that Ceanothus-microsymbiotic Frankia are closely related at the intraspecific level. Diversity of the microsymbionts was further analyzed by genomic fingerprinting using repetitive sequences and PCR. A newly designed direct repeat (DR) sequence and a BOX sequence were used as PCR primers after justification that these primers can generate Frankia-specific fingerprints from nodule DNA. Analysis of the nodules using BOX- and DR-PCR showed that Ceanothus-microsymbiotic Frankia exhibited less diversity within each copopulation than among copopulations. These data suggested that geographic separation plays a more important role for divergence of Ceanothus-microsymbiotic Frankia than host plant.Key words: Frankia, Ceanothus, rep-PCR, diversity.

scholarly journals Microsatellite-Based Genetic Structure and Hybrid Detection in Alpacas Bred in Poland

Animals ◽  
2021 ◽  
Vol 11 (8) ◽  
pp. 2193
Author(s):  
Angelika Podbielska ◽  
Katarzyna Piórkowska ◽  
Tomasz Szmatoła
Keyword(s):  
Genetic Diversity ◽  
Microsatellite Markers ◽  
First Generation ◽  
Expected Heterozygosity ◽  
Hybrid Detection ◽  
Average Coefficient ◽  
Mixed Origin ◽  
Generation Hybrid

This study aimed to characterize the population structure and genetic diversity of alpacas maintained in Poland using 17 microsatellite markers recommended by the International Society for Animal Genetics. The classification of llamas, alpacas, and hybrids of both based on phenotype is often difficult due to long-term admixture. Our results showed that microsatellite markers can distinguish alpacas from llamas and provide information about the level of admixture of one species in another. Alpacas admixed with llamas constituted 8.8% of the tested individuals, with the first-generation hybrid displaying only 7.4% of llama admixture. The results showed that Poland hosts a high alpaca genetic diversity as a consequence of their mixed origin. More than 200 different alleles were identified and the average observed heterozygosity and expected heterozygosity values were 0.745 and 0.768, respectively, the average coefficient of inbreeding was 0.034, and the average polymorphism information content value was 0.741. The probability of exclusion for one parent was estimated at 0.99995 and for two parents at 0.99999.

Genetic Characterization of Indigenous Duck of North-East Region using Microsatellite Markers

2021 ◽  
Author(s):  
Purabi Kaushik ◽  
Jnyanashree Saikia ◽  
Kabitabala Kalita ◽  
Rajjyoti Deka ◽  
J. Saharia
Keyword(s):  
Microsatellite Markers ◽  
Genetic Characterization ◽  
The Other ◽  
North East India ◽  
North East ◽  
Brahmaputra Valley ◽  
East Region ◽  
Hardy Weinberg Equilibrium ◽  
Common Variety

Background: Duck farming plays a significant role, next to chicken in the socio-economic uplift men of the rural farmers of North-East India. Pati duck is the most common duck breed in the Brahmaputra valley of Assam and the other common variety reared in North-East India is Chara-Chambeli, however it originatein Kerala. Genetic characterization plays a significant role for formulation of breeding strategies for improvement of any breed. Microsatellites are codominant in nature and are highly polymorphic. High level of allelic variation, co-dominant mode of inheritance and potential for automated analysis make them an excellent tool for genotyping, mapping and genetic characterization. Pati duck is the most common duck breed in the Brahmaputra valley of Assam and the other common variety reared in North-East India is Chara-Chambeli however its origin in Kerela. Therefore, the present investigation was carried out to characterize these two duck breeds using microsatellite markers to evaluate the genetic diversity in these two duck population. Methods: For the present study, Blood sample were collected from 50 Patiducks and 50 Chara-Chambeli ducks from different parts of North-East India. Assessment of genetic characterization of duck breeds of north-east region were carried out using 16 microsatellite markers and population genetics analysis were done by POPGENE software. Result: In the present study, all the studied loci were highly polymorphic. Analysis generated a total of 41 microsatellite alleles. The number of observed alleles (Na) with an overall mean of 1.93±0.258. However, the effective number of alleles (Ne) with a mean of 1.6933±0.2712. The Shannon’s information index was found to a mean value of 0.5685±0.1693. The overall means for observed (HO) and expected (He) heterozygosities were 0.2889±0.2477 and 0.5289±0.0853, respectively. The chi-square (χ2) test for Hardy-Weinberg equilibrium revealed that all the loci are in within Hardy-Weinberg equilibrium.

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