Accuracy of GEBV of sires based on pooled allele frequency of their progeny

Authors

Napoleón Vargas Jurado, University of Nebraska–LincolnFollow
Larry A. Kuehn, USDA ARS Roman L. Hruska U.S. Meat Animal Research Center
John W. Keele, USDA ARS Roman L. Hruska U.S. Meat Animal Research Center
Ronald M. Lewis, University of Nebraska–LincolnFollow

ORCID IDs

Napoleón Vargas Jurado https://orcid.org/0000-0001-8645-3753

Date of this Version

1-1-2021

Document Type

Article

Citation

G3, 2021, 11(11), jkab231

DOI: 10.1093/g3journal/jkab231

Comments

This work is written by US Government employees and is in the public domain in the US.

Abstract

Despite decreasing genotyping costs, in some cases individually genotyping animals is not economically feasible (e.g., in small ruminants). An alternative is to pool DNA, using the pooled allele frequency (PAF) to garner information on performance. Still, the use of PAF for prediction (estimation of genomic breeding values; GEBVs) has been limited. Two potential sources of error on accuracy of GEBV of sires, obtained from PAF of their progeny themselves lacking pedigree information, were tested: (i) pool construction error (unequal contribution of DNA from animals in pools), and (ii) technical error (variability when reading the array). Pooling design (random, extremes, K-means), pool size (5, 10, 25, 50, and 100 individuals), and selection scenario (random, phenotypic) also were considered. These factors were tested by simulating a sheep population. Accuracy of GEBV-the correlation between true and estimated values-was not substantially affected by pool construction or technical error, or selection scenario. A significant interaction, however, between pool size and design was found. Still, regardless of design, mean accuracy was higher for pools of 10 or less individuals. Mean accuracy of GEBV was 0.174 (SE 0.001) for random pooling, and 0.704 (SE 0.004) and 0.696 (SE 0.004) for extreme and K-means pooling, respectively. Non-random pooling resulted in moderate accuracy of GEBV. Overall, pooled genotypes can be used in conjunction with individual genotypes of sires for moderately accurate predictions of their genetic merit with little effect of pool construction or technical error.