SNP origin bias on population structure analysis: an Australian beef cattle case study.

TL;DRAbstract

The use of single nucleotide polymorphism (SNP) in cattle molecular genetics studies has increased in the last few years by several factors including the identification of new markers and the development of new genotyping technologies. Most of the cattle SNP markers were developed by comparison of a Hereford genome sequence to a sequence of an animal of a different breed, leading to different breed of origin of the SNP markers. In this Australian case study we analysed 302 SNP markers of two different origins (Brahman and Holstein) in a population study including eight cattle breeds. We demonstrate that the breed of origin of the marker can potentially bias this analysis, showing that it is important to find a balance between the origin of the markers and the composition of the population being studied.

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