Skip to main content
ARS Home » Plains Area » Clay Center, Nebraska » U.S. Meat Animal Research Center » Genetics and Animal Breeding » Research » Publications at this Location » Publication #359147
Research Project: Developing a Systems Biology Approach to Enhance Efficiency and Sustainability of Beef and Lamb Production

Location: Genetics and Animal Breeding

Title: Evaluating accuracy of DNA pool construction based on white blood cell counts versus two common DNA quantification methods

Author
item ABRAMS, AMY - South Dakota State University
item Keele, John
item McDaneld, Tara
item Chitko-Mckown, Carol
item GONDA, MICHAEL - South Dakota State University
item Kuehn, Larry

Submitted to: Annual International Plant & Animal Genome Conference
Publication Type: Abstract Only
Publication Acceptance Date: 11/12/2018
Publication Date: 1/2/2019
Citation: Abrams, A., Keele, J.W., McDaneld, T.G., Chitko-McKown, C.G., Gonda, M.G., Kuehn, L.A. 2019. Evaluating accuracy of DNA pool construction based on white blood cell counts versus two common DNA quantification methods [abstract]. International Plant & Animal Genome XXVII Conference, January 12-16, 2019, San Diego, California. Abstract PE0160. Available: https://plan.core-apps.com/pag_2019/abstracts

Interpretive Summary:

Technical Abstract: Pooling samples prior to DNA extraction could further mitigate the cost of genotyping if these methods can accurately generate equal representation within pools. The objective of this study was to determine accuracy of pool construction based on white blood cell counts compared to two common DNA quantification methods. Ten individual bovine blood samples were collected, and then pooled with two individuals represented in each pool. Pools were constructed based on equal amounts of whole blood volume, white blood cell counts, spectrophotometer determined DNA concentrations, spectrofluorometer determined DNA concentrations, and equal volumes of extracted DNA, for a total of 25 pools. Pools and each individual sample were genotyped using the Bovine GGP 50K SNP array. Representation of individuals in each pool was estimated by non-negative least squares. Each pool was tested against all 10 individuals to ensure that only the two individual animals represented in the pool had nonzero representation. Square root of mean square differences between observed and expected sample representations (mean and range of pools) were 0.013 and (0.008, 0.018) for white blood cell counts, 0.036 (0.016, 0.050) for spectrofluorometer DNA representation, and 0.022 (0.009, 0.044) for spectrophotometer DNA representation. White blood cell count was more predictive of sample representation than DNA concentration. Pools constructed using white blood cell count had more equal representation of DNA from each individual than pools constructed using DNA concentration. Constructing pools using white blood cell counts may reduce DNA extraction cost associated with genotyping.