QTL analyses in the AI-RIL population
All obtained phenotypical data were used in QTL mapping that was performed using R software (R Core Team, 2012, https://www.R-project.org/) with R/qtl package (Arends, Prins, Jansen, & Broma, 2010; Broman, Wu, Sen, & Churchill, 2003; http://www.rqtl.org/). Stepwise qtl function was used to detect multiple-QTL models (Broman, 2008, http://www.rqtl.org/tutorials/new_multiqtl.pdf). This function requires single-QTL genome scan to locate QTLs with the highest LOD scores, then the initial model is tested using arguments for additional QTLs and interactions between QTLs search, model refinement and backward elimination of each QTL detected back to the null model. Obtained QTL models were refined with the refineqtl function; any possible interactions between QTLs were verified by the addint function. See Table S2 for detailed description of the procedure of selection of candidate genes from chosen QTL intervals.