Interpretation of electrophoretograms of seven microsatellite loci to determine the genetic diversity of the Arabian Oryx

Arif, Ibrahim A.; Khan, Haseeb A.; Shobrak, Mohammad; Homaidan, Ali A. Al; Sadoon, Mohammad Al; Farhan, Ahmad H. Al; Bahkali, Ali H.

doi:10.4238/vol9-1gmr714

Cited by 34 publications

(25 citation statements)

References 12 publications

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“…All PCRs were carried out in singleplexes using a T1 Thermocycler (Biometra GmbH, Göttingen, Germany) under the following conditions: initial denaturation at 94°C for 3 min; 30 cycles of 94°C for 30 s, 55°C for 45 s, and 72°C for 1 min; eight cycles of 94°C for 30 s, 53°C for 45 s, and 72°C for 1 min; and a final extension step of 72°C for 5 min. The resulting fluorescently labeled PCR products were run in multiplexes on an ABI 3130xl Genetic Analyzer (Applied Biosystems, Foster City, California, USA) using GeneScan 500 LIZ Size Standard (Applied Biosystems) as a size standard and scored using GeneMapper 4.1 (Applied Biosystems), following the recommendations given by Arif et al (2010).…”

Section: Methods and Resultsmentioning

confidence: 99%

Development of 13 microsatellite markers in the endangered Sinai primrose (Primula boveana, Primulaceae)

et al. 2013

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• Premise of the study: We developed microsatellite markers for the endangered plant Primula boveana, the Sinai primrose, and assessed the cross-transferability of these markers to six related taxa.• Methods and Results: DNA sequences containing microsatellites were isolated from a microsatellite-enriched library. We obtained successful amplification of 13 microsatellite primer pairs, seven of which were polymorphic in P. boveana. Eleven of these primers successfully cross-amplified to related taxa.• Conclusions: The markers reported herein will be useful to characterize the genetic diversity of the endangered P. boveana and to evaluate its mating system, and have the potential to be useful for similar studies in close relatives.

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Section: Methods and Resultsmentioning

confidence: 99%

Development of 13 microsatellite markers in the endangered Sinai primrose (Primula boveana, Primulaceae)

et al. 2013

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“…We carried out allele identification (Arif et al 2010) to identify microsatellites that were reliably genotyped and also tested for the ability to multiplex loci (Chamberlain et al 1988). To perform the allele identification, all microsatellite candidates were fluorescently labeled on forward primers (5′-FAM, TAMRA, HEX, ROX; Invitrogen, Paisley, UK) and tested using high quality DNA from a blood sample in PCRs with an annealing temperature of 60 °C (all other PCR conditions were the same as those described above).…”

Section: Establishment Of a Microsatellite Marker Systemmentioning

confidence: 99%

Integrated tool for microsatellite isolation and validation from the reference genome and their application in the study of breeding turnover in an endangered avian population

Hou

Lin

et al. 2018

Integrative Zoology

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Accurate individual identification is required to estimate survival rates in avian populations. For endangered species, non-invasive methods of obtaining individual identification, such as using molted feathers as a source of DNA for microsatellite markers, are preferred because of less disturbance, easy sample preparation and high efficiency. With the availability of many avian genomes, a few pipelines isolating genome-wide microsatellites have been published, but it is still a challenge to isolate microsatellites from the reference genome efficiently. Here, we have developed an integrated tool comprising a bioinformatic pipeline and experimental procedures for microsatellite isolation and validation based on the reference genome. We have identified over 95 000 microsatellite loci and established a system comprising 10 highly polymorphic markers (PIC value: 0.49-0.93, mean: 0.79) for an endangered species, saker falcon (Falco cherrug). These markers (except 1) were successfully amplified in 126 molted feathers, exhibiting high amplification success rates (83.9-99.7%), high quality index (0.90-0.97) and low allelic dropout rates (1-9.5%). To further assess the efficiency of this marker system in a population study, we identified individual sakers using these molted feathers (adult) and 146 plucked feathers (offspring). The use of parent and offspring samples enabled us to infer the genotype of missing samples (N = 28), and all adult genotypes were used to ascertain that breeding turnover is a useful proxy for survival estimation in sakers. Our study presents a cost-effective tool for microsatellite isolation based on publicly available reference genomes and demonstrates the power of this tool in estimating key parameters of avian population dynamics.

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“…Microsatellite markers are highly polymorphic, abundant and fairly evenly distributed throughout eukaryotic genomes (ARIF et al, 2010). There are numerous reports suggesting the usefulness of microsatellite markers for measuring the genetic variability in a wider taxonomic range (CHAN et al, 2008;BANHOS et al, 2008;AZEEM et al, 2012;SPANIC et al, 2012).…”

Section: Introductionmentioning

confidence: 99%

Diversity of tunisian bread wheat genotypes revealed by morpho-agronomical and microsatellite markers

Babay¹,

Chaabane²,

Mzid-Abdmouleh³

et al. 2015

Biosci. J.

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ABSTRACT:The genetic diversity of a set of 21 hexaploid wheat germplasm from the National Agronomic Institute of Tunisia were investigated by applying 26 agro morphological traits and 10 wheat microsatellites molecular markers (Simple Sequence Repeat). The morphological variability was analyzed using the Principal Component Analysis (PCA) and the cluster analysis based on ward's method and square Euclidean distance. Eighteen microsatellites primer pairs were tested for all genotypes, among them 10 primers generated polymorphic and reproducible profiles. They revealed a total of 414 reducible bands among which 373 were polymorphic. The polymorphic information content (PIC) values per locus varied from 0,33 to 0,94 with an average of 0,72. Genetic similarity values between genotypes, calculated by the molecular derived data, were used to produce a dendrogram. The genotypes were clustered in four clear groups according to their origin, pedigree and in some cases to phenotypic characters similarities.

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Interpretation of electrophoretograms of seven microsatellite loci to determine the genetic diversity of the Arabian Oryx

Cited by 34 publications

References 12 publications

Development of 13 microsatellite markers in the endangered Sinai primrose (Primula boveana, Primulaceae)

Development of 13 microsatellite markers in the endangered Sinai primrose (Primula boveana, Primulaceae)

Integrated tool for microsatellite isolation and validation from the reference genome and their application in the study of breeding turnover in an endangered avian population

Diversity of tunisian bread wheat genotypes revealed by morpho-agronomical and microsatellite markers

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