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Sultan Qaboos University (2017)

Charaterization of genetic markers for Arabian Tahr (Arbitragus jayakari) and Nubian Ibex (Capra nubiana)

Al-Maashani, Khalifa Salim.

Titre : Charaterization of genetic markers for Arabian Tahr (Arbitragus jayakari) and Nubian Ibex (Capra nubiana)

Auteur : Al-Maashani, Khalifa Salim.

Université de soutenance : Sultan Qaboos University

Grade : Master of Science (MS) in Biology 2017

Résumé
Arabian tahr and Nubian ibex, wild goats, are endangered and vulnerable, respectively according to International Union for the Conservation of Nature ( IUCN). Poaching, illegal trade and their habitat degradation are collectively major threats to these species. Genetic studies using nuclear or mitochondrial DNA markers play a vital role in understanding not only population structure and forensic conservation, but the health status as well. In fact, sampling challenges could be a major limitations for evaluating the population status and developing reference databases. The aims of this study were optimizing extraction of DNA and amplification of non-invasive samples to study Arabian tahr and Nubian ibex and establishing molecular markers for conservation and forensic studies. Arabian tahr and Nubian ibex samples, tissue and scats, were collected from three different populations each. Chelex 100, Qiagen and Roche kits, were compared for DNA quality and quantity. Polymorphic nuclear (M1-M10 microsatellites, MHCII-DRB2) and mtDNA (D-loop) markers were optimized for PCR using different thermal conditions and additives. Based on fragment analysis of 8 microsatellite markers for tahr and 5 markers for ibex, different genetic diversity measures were calculated. The result of the DNA quality and quantity by Roche kit method found to be significantly higher than other methods. DRB2 was successfully amplified in tahr samples but failed for ibex samples. D-loop marker was not amplified probably because the complementary sequences of primer sites are not conserved. New degenerate primers that flanks highly variable short fragment of D-loop were designed for both species. The optimal amplifiable PCR size in scat sample was 200 bp. Relatively, high observed mean heterozygosity were observed for M2, M4, M6 and M8 for tahr but M4 and M6 for Nubian ibex. Marker 3 was excluded because of ambiguous peak results. Based on the characterization of nuclear markers using the samples collected from 3 different populations for Arabian tahr and Nubian ibex, the markers with high heterozygosity values can be used for demographic or population assignment in population genetics.

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