02046nas a2200253   4500008004100000022001400041245018600055210006900241300001400310490000700324520116100331653002201492100002001514700001901534700001901553700002401572700002501596700001801621700001801639700002401657700002101681700001901702856007101721       2016                        eng d  a1616-504700aGenome-wide single nucleotide polymorphism (SNP) identification and characterization in a non-model organism, the African buffalo (Syncerus caffer), using next generation sequencing0 aGenomewide single nucleotide polymorphism SNP identification and  a595 - 6030 v813 a<p>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 İI\} 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.</p>
10aMolecular markers1 aSmitz, Nathalie1 aVan Hooft, Pim1 aHeller, Rasmus1 aCornÃ©lis, Daniel1 aChardonnet, Philippe1 aKraus, Robert1 aGreyling, Ben1 aCrooijmans, Richard1 aGroenen, Martien1 aMichaux, Johan  uhttp://www.sciencedirect.com/science/article/pii/S1616504716300982