The statistical theory of linear selection indices from phenotypic to genomic selection

Abstract

A linear selection index (LSI) can be a linear combination of phenotypic values, marker scores, and genomic estimated breeding values (GEBVs); phenotypic values and marker scores; or phenotypic values and GEBVs jointly. The main objective of the LSI is to predict the net genetic merit ( H), which is a linear combination of unobservable individual traits’ breeding values, weighted by the trait economic values; thus, the target of LSI is not a parameter but rather the unobserved random H values. The LSI can be single‐stage or multi‐stage, where the latter are methods for selecting one or more individual traits available at different times or stages of development in both plants and animals. Likewise, LSIs can be either constrained or unconstrained. A constrained LSI imposes predetermined genetic gain on expected genetic gain per trait and includes the unconstrained LSI as particular cases. The main LSI parameters are the selection response, the expected genetic gain per trait, and its correlation with H. When the population mean is zero, the selection response and expected genetic gain per trait are, respectively, the conditional mean of H and the genotypic values, given the LSI values. The application of LSI theory is rapidly diversifying; however, because LSIs are based on the best linear predictor and on the canonical correlation theory, the LSI theory can be explained in a simple form. We provided a review of the statistical theory of the LSI from phenotypic to genomic selection showing their relationships, advantages, and limitations, which should allow breeders to use the LSI theory confidently in breeding programs.

Core Ideas

• Linear selection indices (LSIs) are useful in plant and animal breeding.

• The main LSI objective is to predict the net genetic merit of individuals.

• We did a complete review of the statistical theory of LSIs.

• We described the bases of genomic LSIs.