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ARS Home » Plains Area » Clay Center, Nebraska » U.S. Meat Animal Research Center » Genetics and Animal Breeding » Research » Publications at this Location » Publication #346668

Title: Evaluation of a functional variant assay for selecting beef cattle

item Snelling, Warren
item McDaneld, Tara
item Kuehn, Larry
item Dickey, Aaron
item Bennett, Gary

Submitted to: World Congress of Genetics Applied in Livestock Production
Publication Type: Proceedings
Publication Acceptance Date: 10/9/2017
Publication Date: 5/7/2018
Citation: Snelling, W.M., McDaneld, T.G., Kuehn, L.A., Dickey, A.M., Bennett, G.L. 2018. Evaluation of a functional variant assay for selecting beef cattle. In: Proceedings World Congress of Genetics Applied in Livestock Production. 11-16 Feb 2018. Auckland, New Zealand. Volume Technologies - Genotyping p.589. Available:

Interpretive Summary:

Technical Abstract: A commercially available genotyping assay for functional variants was chosen to obtain genotypes needed for a selection experiment in populations of pedigreed cattle that have not been extensively genotyped. The assay design included probes for coding sequence variation in 88% of annotated protein coding genes, and variants up- and downstream that may regulate 74% of genes, so function of 97% of genes may be affected by an assayed variant. Slightly more than half (54%) of the 221,115 probed variants were polymorphic in the 3,442 selection population animals genotyped. The low conversion was not unexpected, due to the assay including rare variants that might allow detecting lethal recessives in large populations. The informative variants include coding sequence variation in 63% of genes and variants that may affect regulation of 65%. Overall, 84% of annotated genes may be affected by a polymorphic variant on the functional variant assay. The commercial assay is sufficient to genotype many variants affecting gene function that are segregating in these populations. Strategies to couple this assay with targeted assays for additional functional variation may be needed for some applications.