UMR1313 Animal Genetics and Integrative Biology, National Institute for Agricultural Research (INRA), Jouy-en-Josas, France.
PLoS One. 2012;7(3):e34130. doi: 10.1371/journal.pone.0034130. Epub 2012 Mar 28.
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.
Illumina BovineLD BeadChip 旨在通过包含具有高次要等位基因频率的单核苷酸多态性（SNP）以及基因组中除染色体末端之外的均匀间隔来支持在奶牛和肉牛品种中向更高密度基因型的推断。该芯片还包括 Y 染色体和线粒体 DNA 基因座上的 SNP，这些 SNP 可用于确定亚种分类和某些父本和母本品种谱系。SNP 的总数为 6909 个。使用 BovineLD 芯片对 Illumina BovineSNP50 基因型进行推断的准确性在大多数奶牛和肉牛群体中超过 97%。在多个群体中，BovineLD 推断比来自 Illumina GoldenGate Bovine3K BeadChip 的推断准确约 3 个百分点。当父母双方都未进行基因分型时，改进最大。在牛磺酸肉牛和奶牛品种中，次要等位基因频率相似，多态性 SNP 的比例也相似。新的 BovineLD 芯片应有助于牛磺酸肉牛和奶牛的低成本基因组选择。
