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

Boichard, Didier, Chung, Hoyoung, Dassonneville, Romain, David, Xavier, Eggen, Andre, Fritz, Sebastien, Gietzen, Kimberly J., Hayes, Ben J., Lawley, Cynthia T., Sonstegard, Tad S., Van Tassell, Curtis P., VanRaden, Paul M., Viaud-Martinez, Karine A. and Wiggans, George R. (2012) Design of a bovine low-density snp array optimized for imputation. PLoS One, 7 3: . doi:10.1371/journal.pone.0034130

Author Boichard, Didier
Chung, Hoyoung
Dassonneville, Romain
David, Xavier
Eggen, Andre
Fritz, Sebastien
Gietzen, Kimberly J.
Hayes, Ben J.
Lawley, Cynthia T.
Sonstegard, Tad S.
Van Tassell, Curtis P.
VanRaden, Paul M.
Viaud-Martinez, Karine A.
Wiggans, George R.
Title Design of a bovine low-density snp array optimized for imputation
Journal name PLoS One   Check publisher's open access policy
ISSN 1932-6203
Publication date 2012-03-28
Sub-type Article (original research)
DOI 10.1371/journal.pone.0034130
Open Access Status DOI
Volume 7
Issue 3
Total pages 10
Place of publication San Francisco, United States
Publisher Public Library of Science
Language eng
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.
Q-Index Code C1
Q-Index Status Provisional Code
Institutional Status Non-UQ
Additional Notes Article number e34130

Document type: Journal Article
Sub-type: Article (original research)
Collection: Queensland Alliance for Agriculture and Food Innovation
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