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.