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. 2012;7(3):e34130.
doi: 10.1371/journal.pone.0034130. Epub 2012 Mar 28.

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

Didier Boichard  1 , Hoyoung Chung, Romain Dassonneville, Xavier David, André Eggen, Sébastien Fritz, Kimberly J Gietzen, Ben J Hayes, Cynthia T Lawley, Tad S Sonstegard, Curtis P Van Tassell, Paul M VanRaden, Karine A Viaud-Martinez, George R Wiggans; Bovine LD Consortium
Affiliations

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

Didier Boichard et al. PLoS One. 2012.

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 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.

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Conflict of interest statement

Competing Interests: André Eggen, Kimberly J. Gietzen, Cynthia T. Lawley, and Karine Viaud are employees of Illumina Inc. This study was partly funded by Apisgene. There are no patents, products in development, or marketed products to declare. This does not alter the authors' adherence to all the PLoS ONE policies on sharing data and materials.

Figures

Figure 1
Figure 1. BovineLD single-nucleotide polymorphism (SNP) gap distribution.
Figure 2
Figure 2. Imputation accuracy for Bovine3K and BovineLD genotypes.
Imputation was performed for A) Bovine3K and B) BovineLD genotypes using Beagle software (http://faculty.washington.edu/browning/beagle/beagle.html); imputation accuracy is reported by single-nucleotide polymorphism (SNP).
See this image and copyright information in PMC

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