Inferring population structures of African buffalo (Syncerus caffer) by means of Single Nucleotide Polymorphism (SNP) markers

Initiatives to establish transboundary conservation areas have been expanding in Southern Africa, intending to allow free movements of wild species across the fences in order to restock previously depleted areas. Nevertheless, these initiatives are increasing disease transfer risks at the wildlife-livestock interface, which is likely to have a significant long lasting impact on conservation, economics and sanitation. Among wild species, the African buffalo (Syncerus caffer) is known to be one of the main species responsible for the maintenance and potential spread of diseases. To fully understand the buffalo population dynamics, we aimed to generate a library of SNPs with high accuracy in population screening, that would permit to determine dispersal rate and environmental barriers that can slow down or completely stop spread of diseases. 18.5 million sequences of 76bp were generated on an Illumina Genome Analyzer from DNA of 13 buffalos. We identifi ed 3,000 putative SNPs by aligning the reads with the cattle genome (Bos taurus). Out of this set, an assay of 384 SNPs was designed taking care of each SNP's quality scores, minor allele frequencies, design scores and position in the genome. The use of those markers is completely innovative, as most of the time, they have only been developed on human model or domestic organisms. They are one of the most powerful tools and are becoming the marker of choice in genetic analyses. (Texte intégral)

Bibliographic Details

Main Authors:	Smitz, Nathalie, Van Hooft, Pim, Heller, Rasmus, Chardonnet, Philippe, Cornélis, Daniel, Kraus, R., Crooijmans, Richard, Groenen, M., Michaux, Johan
Format:	article biblioteca
Language:	eng
Subjects:	L10 - Génétique et amélioration des animaux, P01 - Conservation de la nature et ressources foncières, U30 - Méthodes de recherche, L73 - Maladies des animaux, buffle africain, génétique des populations, marqueur génétique, polymorphisme génétique, dynamique des populations, conservation des ressources génétiques, contrôle de maladies, http://aims.fao.org/aos/agrovoc/c_167, http://aims.fao.org/aos/agrovoc/c_34326, http://aims.fao.org/aos/agrovoc/c_24030, http://aims.fao.org/aos/agrovoc/c_24031, http://aims.fao.org/aos/agrovoc/c_6111, http://aims.fao.org/aos/agrovoc/c_37280, http://aims.fao.org/aos/agrovoc/c_2327, http://aims.fao.org/aos/agrovoc/c_165,
Online Access:	http://agritrop.cirad.fr/564171/ http://agritrop.cirad.fr/564171/1/document_564171.pdf
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