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

By Lakshmi K. Matukumalli, Cynthia T. Lawley, Robert D. Schnabel, Jeremy F. Taylor, Mark F. Allan, Michael P. Heaton, Jeff O'Connell, Stephen S. Moore, Timothy P. L. Smith, Tad S. Sonstegard and Curtis P. Van Tassell


The success of genome-wide 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. A cost-effective and efficient approach for the development of a custom genotyping assay interrogating 54,001 SNP loci to support GWA applications in cattle is described. A novel algorithm for achieving a compressed inter-marker interval distribution proved remarkably successful, with median interval of 37 kb and maximum predicted gap of <350 kb. The assay was tested on a panel of 576 animals from 21 cattle breeds and six outgroup species and revealed that from 39,765 to 46,492 SNP are polymorphic within individual breeds (average minor allele frequency (MAF) ranging from 0.24 to 0.27). The assay also identified 79 putative copy number variants in cattle. Utility for GWA was demonstrated by localizing known variation for coat color and the presence/absence of horns to their correct genomic locations. The combination of SNP selection and the novel spacing algorithm allows an efficient approach for the development of high-density genotyping platforms in species having full or even moderate quality draft sequence. Aspects of the approach can be exploited in species which lack an available genome sequence. The BovineSNP50 assay described here is commercially available from Illumina and provides a robust platform for mapping disease genes and QTL in cattle

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Publisher: Public Library of Science
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    1. (2007). Genome-wide association scanning highlights two autophagy genes, ATG16L1 and IRGM, as being significantly associated with Crohn’s disease.
    2. (2007). Genome wide association (GWA) study for early onset extreme obesity supports the role of fat mass and obesity associated gene (FTO) variants.
    3. (2007). Framingham Heart Study genome-wide association: results for pulmonary function measures.
    4. (2007). Whole genome linkage disequilibrium maps in cattle.
    5. (2007). Recent human effective population size estimated from linkage disequilibrium.
    6. (2001). Linkage disequilibrium in humans: models and data.
    7. (2007). Power analysis for genome-wide association studies.
    8. (2001). Prediction of total genetic value using genome-wide dense marker maps.
    9. (2002). Selection and use of SNP markers for animal identification and paternity analysis in U.S. beef cattle.
    10. (2005). Use of bovine single nucleotide polymorphism markers to verify sample tracking in beef processing.
    11. (1996). Misidentification rate in the Israeli dairy cattle population and its implications for genetic improvement.
    12. (1986). Effect of misidentification on the estimation of breeding value and heritability in cattle.
    13. (2008). The influence of incorrect sireidentification on the estimates of genetic parameters and breeding values.
    14. (2000). Effect of misidentification on genetic gain and estimation of breeding value in dairy cattle populations.
    15. (2001). Impact of paternity errors in cow identification on genetic evaluations and international comparisons.
    16. (2008). SNP discovery and allele frequency estimation by deep sequencing of reduced representation libraries.
    17. Survey of SNP Variation Uncovers the Genetic Structure of Cattle Breeds. The Bovine HapMap Consortium.
    18. (2004). Ropiquet A
    19. (2009). Evol 33: 896–907. SNP Genotyping Assay PLoS
    20. (2007). PLINK: a tool set for whole-genome association and population-based linkage analyses.
    21. (1996). The polled locus maps to BTA1 in a Bos indicus6Bos taurus cross.
    22. (2000). Construction and characterization of a new bovine bacterial artificial chromosome library with 10 genome-equivalent coverage.
    23. (2007). Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome.
    24. (2000). An SNP map of the human genome generated by reduced representation shotgun sequencing.
    25. (2006). Measuring the extent of linkage disequilibrium in commercial pig populations.

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