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Title: Development and Characterization of a High Density SNP Genotyping Assay for Cattle

item Allan, Mark
item Heaton, Michael - Mike
item MOORE, STEPHEN - University Of Alberta
item Smith, Timothy - Tim
item Sonstegard, Tad
item Van Tassell, Curtis - Curt

Submitted to: PLOS ONE
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/23/2009
Publication Date: 4/24/2009
Citation: Matukumalli, L.K., Lawley, C.T., Schnabel, R.D., Taylor, J.F., Allan, M.F., Heaton, M.P., O'Connell, J., Moore, S.S., Smith, T.P., Sonstegard, T.S., Van Tassell, C.P. 2009. Development and Characterization of a High Density SNP Genotyping Assay for Cattle. PLoS One. 4(4):e5350. Available:

Interpretive Summary: The manuscript describes the planning and development of an Illumina iSelect assay having >50,000 informative SNP, with minor allele frequencies estimated for 21 breeds of cattle including the taurine and indicine subspecies. All of the incorporated SNP were from public domain sources to ensure that no IP issues would interfere with the broad public use of the assay. The remarkably uniform SNP spacing achieved throughout the genome (median inter-SNP gap of 37 kb, largest gap <300 kb) and simultaneous optimization of the minor allele frequency distribution demonstrate our success within the SNP identification and selection processes. The commercial availability of this assay has enabled its widespread use worldwide, and numerous manuscripts will soon begin to reference this design paper. Furthermore, we believe that the work is relevant far beyond the bovine research community and that other research communities will benefit from our approach. The authors are currently involved in similar SNP discovery and assay design projects for the international sheep and swine research communities.

Technical Abstract: The success of genomewide association (GWA) studies for the detection of sequence variation affecting complex traits in human has spurred interest in the use of large-scale high-density single nucleotide polymorphism (SNP) genotyping for the identification of quantitative trait loci (QTL) and for marker-assisted selection in model and agricultural species. We describe the development of a highly parallel custom genotyping assay interrogating 54,001 SNP loci to support these applications in cattle. This assay is made available to the community by Illumina as the BovineSNP50 BeadChip. The utility of the assay is substantially enhanced because of the use of high quality SNP from a SNP discovery method that simultaneously estimates minor allele frequencies (MAF) and by the implementation of a novel SNP selection algorithm to ensure genomewide coverage, compact gap distribution, and high average MAF. A panel of 576 animals from 21 cattle breeds and six outgroup species was genotyped to establish that from 39,765 to 46,492 SNP are polymorphic within individual breeds, with an average MAF ranging from 0.24 to 0.27. Genotype data were analyzed to discover 79 putative copy number variants in cattle, some of which were independently confirmed by arrayCGH and Q-PCR. The utility of the assay for GWA analysis was demonstrated by precisely localizing the QTL region for coat color in the Angus breed (Melanocortin 1 Receptor on chromosome 18) and the QTL region harboring the POLL locus in Hereford and Limousin to the centromere of chromosome 1.