SNP ascertainment bias plays an important role in population genetics. This study aims at elucidating the impact of the different steps in the array design on its magnitude. For this purpose, the design of the Axiom™ Genome-Wide Chicken Array has been remodeled using a set of 46 sequenced chicken populations. Estimates for the allele frequency spectra and the expected heterozygosity have been contrasted against the estimates from whole genome sequences and the original array. Major influences by the number of populations used for the discovery of SNPs and the equal spacing of SNPs over the genome by genetic distances could be demonstrated. It could also be shown, that there is more pronounced ascertainment bias within populations used for SNP discovery, compared to other populations. Keywords: SNP array, whole genome sequencing, population genetics, chickens

Johannes Geibel, Steffen Weigend, Anett Weigend, Christian Reimer, Torsten Pook, Henner Simianer

Proceedings of the World Congress on Genetics Applied to Livestock Production, Volume Electronic Poster Session - Molecular Genetics 2, , 650, 2018
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