Abstract
Using advanced intermated populations has been proposed as a way to increase the accuracy of mapping experiments. An F3 population of 300 lines and an advanced intermated F3 population of 322 lines, both derived from the same parental maize inbred lines, were jointly evaluated for dry grain yield (DGY), grain moisture (GM), and silking date (SD). Genetic variance for dry grain yield was significantly lower in the intermated population compared to the F3 population. The confidence interval around a QTL was on average 2.31 times smaller in the intermated population compared to the F3 population. One controversy surrounding QTL mapping is whether QTL identified in fact represent single loci. This study identifies two distinct loci for dry grain yield in the intermated population in coupling phase, while the F3 identifies only a single locus. Surprisingly, fewer QTL were detected in the intermated population than the F3 (21 vs. 30) and ,50% of the detected QTL were shared among the two populations. Crossvalidation showed that selection bias was more important in the intermated population than in the F3 and that each detected QTL explained a lower percentage of the variance. This finding supports the hypothesis that QTL detected in conventional populations correspond mainly to clusters of linked QTL. The actual number of QTL involved in the genetic architecture of complex traits may be substantially larger, with effect sizes substantially smaller than in conventional populations.