Mapping quantitative trait loci in outcross populations via residual maximum likelihood .2. A simulation study

Position and variance contribution of a single QTL together with additive polygenic and residual variance components were estimated using a residual maximum likelihood method and a derivative-free algorithm. The variance-covariance matrix of QTL effects and its inverse were computed conditional on incomplete information from multiple-linked markers. Simulation was employed to investigate the accuracy of parameter estimates and likelihood ratio tests. The design was a granddaughter design with 2 000 sons, 20 sires of sons and 9 ancestors of sires. Designs with 1 000 and 600 sons were also investigated. Data were simulated under three different genetic models for the QTL, a biallelic model, a multiallelic model with ten alleles at equal frequencies, and a model with normally and independently distributed QTL allelic effects for base individuals. The trait analyzed was daughter yield deviation or the daughter average adjusted for environmental effects and merits of mates of the sons. Genotypes for five markers situated on the same chromosome were generated for all sons and their ancestors. Data were analyzed with and without relationships among sires. Parameters were estimated with good accuracy under all three simulation models. The REML method was fairly robust to the number of alleles at the QTL for the designs studied.