Genomic Prediction of Complex Traits, Principles, Overview of Factors Affecting the Reliability of Genomic Prediction, and Algebra of the Reliability.

The quality of the predictions of genetic values based on the genotyping of neutral markers (GEBVs) is a key information to decide whether or not to implement genomic selection. This quality depends on the part of the genetic variability captured by the markers and on the precision of the estimate of their effects. Selection index theory provided the framework for evaluating the accuracy of GEBVs once the information had been gathered, with the genomic relationship matrix (GRM) playing a central role. When this accuracy must be known a priori, the theory of quantitative genetics gives clues to calculate the expectation of this GRM. This chapter makes a critical inventory of the methods developed to calculate these accuracies a posteriori and a priori. The most significant factors affecting this accuracy are described (size of the reference population, number of markers, linkage disequilibrium, heritability).