A Genomic Selection Index Applied to Simulated and Real Data

Abstract

A genomic selection index (GSI) is a linear combination of genomic estimated breeding values that uses genomic markers to predict the net genetic merit and select parents from a nonphenotyped testing population. Some authors have proposed a GSI; however, they have not used simulated or real data to validate the GSI theory and have not explained how to estimate the GSI selection response and the GSI expected genetic gain per selection cycle for the unobserved traits after the first selection cycle to obtain information about the genetic gains in each subsequent selection cycle. In this paper, we develop the theory of a GSI and apply it to two simulated and four real data sets with four traits. Also, we numerically compare its efficiency with that of the phenotypic selection index (PSI) by using the ratio of the GSI response over the PSI response, and the PSI and GSI expected genetic gain per selection cycle for observed and unobserved traits, respectively. In addition, we used the Technow inequality to compare GSI vs. PSI efficiency. Results from the simulated data were confirmed by the real data, indicating that GSI was more efficient than PSI per unit of time.

Keywords: GenPred; genomic estimated breeding value; genomic selection; net genetic merit; selection index; selection response; shared data resource.

Figure 1

Schematic illustration of the steps followed to generate data sets 1 and 2 for the selection process using the phenotypic selection index and the genomic selection index. Dotted lines indicate the process used to simulate the phenotypic data.

Figure 2

Correlation between the genomic estimated breeding values (GEBVs) and the true breeding values for four traits in seven selection cycles. For each cycle of selection, the four columns correspond to the correlation between the GEBV and the true breeding values for traits T1, T2, T3, and T4, respectively.

Figure 3

Correlation between the genomic selection index (GSI), the phenotypic selection index (PSI), and the true net genetic merit (H) values in seven selection cycles. For each cycle of selection, the first column corresponds to the correlation between the GSI estimated values and the H true values (blue), whereas the second column corresponds to the correlation between the PSI estimated values and the H true values (red).