QTL Analysis Methods

I. Single-Factor Analysis of Variance

The most basic way of determining whether an association exists between a molecular marker and a trait is to conduct single-factor analysis of variance (ANOVA). In this method, a specific marker is the independent variable and a trait of interest is the dependent variable. One essentially asks the question, “Is the mean trait value for all plants with the Parent A marker pattern significantly different than the mean value of plants with the Parent B pattern?” If the answer is “Yes”, the inference is that a QTL is present in the same chromosome region as the marker. A separate ANOVA must be run for each marker in the data set.

Many statistical analysis software packages carry out ANOVA. We will present detailed instructions for conducting QTL analysis via Microsoft Excel, and provide a sample program for doing the same with SAS software (Statistical Analysis System, Cary NC).

  • Microsoft Excel. Click the image for step-by-step instructions for running ANOVA in Excel, using the Oregon Wolfe Barley population as an example.
  • SAS. In SAS software, the appropriate procedure to use is PROC GLM.