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Title: Design of a bovine low-density SNP array optimized for imputation

Author
item BOICHARD, DIDIER - Institut National De La Recherche Agronomique (INRA)
item CHUNG, HOYOUNG - National Institute Of Animal Science
item DASSONNEVILLE, ROMAIN - Institut National De La Recherche Agronomique (INRA)
item DAVID, XAVIER - Collaborator
item EGGEN, ANDRE - Illumina, Inc
item FRITZ, SEBASTIEN - Collaborator
item GIETZEN, KIMBERLEY - Illumina, Inc
item HAYES, BEN - Department Of Primary Industries
item LAWLEY, CYNTHIA - Illumina, Inc
item Sonstegard, Tad
item Van Tassell, Curtis - Curt
item Vanraden, Paul
item VIAUD, KARINE - Illumina, Inc
item Wiggans, George

Submitted to: PLOS ONE
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/22/2012
Publication Date: 3/28/2012
Citation: Boichard, D., Chung, H., Dassonneville, R., David, X., Eggen, A., Fritz, S., Gietzen, K.J., Hayes, B.J., Lawley, C.T., Sonstegard, T.S., Van Tassell, C.P., Van Raden, P.M., Viaud, K., Wiggans, G.R. 2012. Design of a bovine low-density SNP array optimized for imputation. PLoS One. 7(3):e34130.

Interpretive Summary: A major challenge in implementing genomic selection in most species is the cost of genotyping. An appealing approach is to use an economical, reduced-density chip with markers optimized for predicting unknown genotypes for animals from observed genotypes (imputation). The Illumina Infinium BovineLD Genotyping Beadchip was developed to replace the Bovine3K chip and provide higher density genotypes in dairy and beef breeds by including markers with a high minor allele frequency as well as uniform spacing across the genome except at the ends of the chromosome where densities were increased. The chip also includes markers that are useful for determining subspecies classification and certain paternal and maternal breed lineages. Accuracy of imputation to BovineSNP50 genotypes using the BovineLD chip was over 99% when both parents were genotyped in the North American BovineSNP50 reference population. That high accuracy suggests that the design criteria for the BovineLD chip would be useful to consider in other species for which an “imputation chip” could dramatically lower the cost of implementing genomic selection. The new BovineLD BeadChip should facilitate low cost genomic selection in beef and dairy cattle.

Technical Abstract: The Illumina BovineLD BeadChip was designed to support imputation to higher density genotypes in dairy and beef breeds by including single-nucleotide polymorphisms (SNPs) that had a high minor allele frequency as well as uniform spacing across the genome except at the ends of the chromosome where densities were increased. The chip also includes SNPs on the Y chromosome and mitochondrial DNA loci that are useful for determining subspecies classification and certain paternal and maternal breed lineages. The total of number of SNPs was 6,909. Accuracy of imputation to Illumina BovineSNP50 genotypes using the BovineLD chip was over 97% for most dairy and beef populations. The BovineLD imputations were about 3 percentage points more accurate than those from the Illumina GoldenGate Bovine3K BeadChip across multiple populations. The improvement was greatest when neither parent was genotyped. The minor allele frequencies were similar across taurine beef and dairy breeds as was the proportion of SNPs that were polymorphic. The new BovineLD chip should facilitate low-cost genomic selection in taurine beef and dairy cattle.