Article (Scientific journals)
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 et al.
2016In Mammalian Biology, 81, p. 595-603
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Abstract :
[en] 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.
Disciplines :
Zoology
Author, co-author :
smitz, nathalie
Van Hooft, pim
Heller, Rasmus
Cornelis, Daniel
Chardonnet, Philippe
Kraus, Robert
Greyling, Ben
Crooijmans, Richard
Groenen, Martien
Michaux, Johan  ;  Université de Liège > Département des sciences de la vie > Génétique et physiologie des microalgues
Language :
English
Title :
Genome-wide single nucleotide polymorphism (SNP) identification and characterization in a non-model organism, the African buffalo (Syncerus caffer), using next generation sequencing
Publication date :
2016
Journal title :
Mammalian Biology
ISSN :
1616-5047
Publisher :
Elsevier GmbH, Urban & Fischer Verlag
Volume :
81
Pages :
595-603
Peer reviewed :
Peer Reviewed verified by ORBi
Available on ORBi :
since 03 October 2016

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