cc_byLanzl, TobiasMelchinger, Albrecht E.Schön, Chris-Carolin2025-08-152025-08-152023https://doi.org/10.1007/s00122-023-04447-2https://hohpublica.uni-hohenheim.de/handle/123456789/16992The additive genetic variance VAinherent to a breeding population is a major determinant of short- and long-term genetic gain. When estimated from experimental data, it is not only the additive variances at individual loci (QTL) but also covariances between QTL pairs that contribute to estimates of VA. Thus, estimates of VAdepend on the genetic structure of the data source and vary between population samples. Here, we provide a theoretical framework for calculating the expectation and variance of VAfrom genotypic data of a given population sample. In addition, we simulated breeding populations derived from different numbers of parents ( P  = 2, 4, 8, 16) and crossed according to three different mating designs (disjoint, factorial and half-diallel crosses). We calculated the variance of VAand of the parameter b reflecting the covariance component in VA,standardized by the genic variance. Our results show that mating designs resulting in large biparental families derived from few disjoint crosses carry a high risk of generating progenies exhibiting strong covariances between QTL pairs on different chromosomes. We discuss the consequences of the resulting deflated or inflated VAestimates for phenotypic and genome-based selection as well as for applying the usefulness criterion in selection. We show that already one round of recombination can effectively break negative and positive covariances between QTL pairs induced by the mating design. We suggest to obtain reliable estimates of VAand its components in a population sample by applying statistical methods differing in their treatment of QTL covariances.engBiological sciences630Article18704395112024-12-02