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Mammalian Biology

, Volume 81, Issue 6, pp 595–603 | Cite as

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

  • Nathalie SmitzEmail author
  • Pim Van Hooft
  • Rasmus Heller
  • Daniel Cornélis
  • Philippe Chardonnet
  • Robert Kraus
  • Ben Greyling
  • Richard Crooijmans
  • Martien Groenen
  • Johan Michaux
Original investigation

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.

Keywords

Population genomics Conservation Disease ecology Molecular markers 

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Copyright information

© Deutsche Gesellschaft für Säugetierkunde 2016

Authors and Affiliations

  • Nathalie Smitz
    • 1
    • 2
    Email author
  • Pim Van Hooft
    • 3
  • Rasmus Heller
    • 4
  • Daniel Cornélis
    • 5
    • 6
  • Philippe Chardonnet
    • 7
  • Robert Kraus
    • 8
    • 9
  • Ben Greyling
    • 10
  • Richard Crooijmans
    • 11
  • Martien Groenen
    • 11
  • Johan Michaux
    • 1
    • 5
  1. 1.Conservation GeneticsUniversity of LiègeLiègeBelgium
  2. 2.Joint Experimental Molecular UnitRoyal Museum for Central AfricaTervurenBelgium
  3. 3.Resource Ecology GroupWageningen UniversityWageningenThe Netherlands
  4. 4.Bioinformatics, Department of BiologyUniversity of CopenhagenCopenhagenDenmark
  5. 5.Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), UPR AGIRSCampus International de BaillarguetMontpellierFrance
  6. 6.Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD)-RP-PCPUniversity of ZimbabweHarareZimbabwe
  7. 7.International Foundation for the Conservation of Wildlife (IGF)ParisFrance
  8. 8.Department of BiologyUniversity of KonstanzKonstanzGermany
  9. 9.Department of Migration and Immuno-EcologyMax Planck Institute for OrnithologyRadolfzellGermany
  10. 10.Agricultural Research CouncilIrene CenturionSouth Africa
  11. 11.Animal Breeding and Genomics CentreWageningen UniversityWageningenThe Netherlands

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