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Genome-wide single nucleotide polymorphism (SNP) identification and characterization in a non-model organism, the African buffalo (Syncerus caffer), using next generation sequencing

Smitz Nathalie, Van Hooft Pim, Heller Rasmus, Cornélis Daniel, Chardonnet Philippe, Kraus R., Greyling B.J., Crooijmans Richard, Groenen M., Michaux Johan. 2016. Genome-wide single nucleotide polymorphism (SNP) identification and characterization in a non-model organism, the African buffalo (Syncerus caffer), using next generation sequencing. Mammalian Biology, 81 (6) : pp. 595-603.

Journal article ; Article de recherche ; Article de revue à facteur d'impact
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Quartile : Q2, Sujet : ZOOLOGY

Abstract : This study aimed to develop a set of SNP markers with high resolution and accuracy within the African buffalo. Such a set can be used, among others, to depict subtle population genetic structure for a better understanding of buffalo population dynamics. In total, 18.5 million DNA sequences of 76 bp were generated by next generation sequencing on an Illumina Genome Analyzer II from a reduced representation library using DNA from a panel of 13 African buffalo representative of the four subspecies. We identified 2534 SNPs with high confidence within the panel by aligning the short sequences to the cattle genome (Bos taurus). The average sequencing depth of the complete aligned set of reads was estimated at 5x, and at 13x when only considering the final set of putative SNPs that passed the filtering criterion. Our set of SNPs was validated by PCR amplification and Sanger sequencing of 15 SNPs. Of these 15 SNPs, 14 amplified successfully and 13 were shown to be polymorphic (success rate: 87%). The fidelity of the identified set of SNPs and potential future applications are finally discussed. (Résumé d'auteur)

Mots-clés géographiques Agrovoc : Afrique occidentale, Afrique australe, Afrique centrale

Classification Agris : L10 - Animal genetics and breeding

Champ stratégique Cirad : Axe 6 (2014-2018) - Sociétés, natures et territoires

Auteurs et affiliations

  • Smitz Nathalie, Université de Liège (BEL)
  • Van Hooft Pim, Wageningen University (NLD)
  • Heller Rasmus, University of Copenhagen (DNK)
  • Cornélis Daniel, CIRAD-ES-UPR AGIRs (ZWE)
  • Chardonnet Philippe, International Foundation for the Conservation of the Wildlife (FRA)
  • Kraus R., Wageningen University (NLD)
  • Greyling B.J., ARC (ZAF)
  • Crooijmans Richard, Wageningen University (NLD)
  • Groenen M., Wageningen University (NLD)
  • Michaux Johan, CIRAD-ES-UPR AGIRs (FRA)

Source : Cirad-Agritrop (https://agritrop.cirad.fr/581311/)

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