*2.6. QTL Analysis*

Inclusive composite interval mapping (ICIM) (http://www.isbreeding.net/) software was used to analyze the LOD profiles with informative markers, as detected by Joinmap. The LOD thresholds for QTL significance were determined by a permutation test (1000 replications) with a genome-wide significance level α = 0.1. ICIM tests both additive and epistasis e ffects and it avoids the possible increase in sampling variance and the complicated background marker selection process, which are common problems in composite interval mapping.
