Editing Quantitative trait locus (section)

===Analysis of variance===
The simplest method for QTL mapping is analysis of variance ([[ANOVA]], sometimes called "marker regression") at the marker loci. In this method, in a backcross, one may calculate a [[t-statistic]] to compare the averages of the two marker [[genotype]] groups. For other types of
crosses (such as the intercross), where there are more than two possible genotypes, one uses a more general form of ANOVA, which provides a so-called [[F-statistics|F-statistic]]. The ANOVA approach for QTL mapping has three important weaknesses. First, we do not receive separate estimates of QTL location and QTL effect. QTL location is indicated only by looking at which markers give the greatest differences between genotype group averages, and the apparent QTL effect at a marker will be smaller than the true QTL effect as a result of [[Genetic recombination|recombination]] between the marker and the QTL. Second, we must discard individuals whose genotypes are missing at the marker. Third, when the markers are widely spaced, the QTL may be quite far from all markers, and so the power for QTL detection will decrease.{{cn|date=July 2024}}