mQTL analysis
Log10 transformed data together with the tomato linkage map containing
865 SNP markers were used for performing QTL analysis using Rqtl v3.3.1
(Arends et al. 2010; Broman et al. 2003). We performed QTL
analysis using the approach as previously described by Joosen et al.,
(2013) for Arabidopsis and Kazmi et al., (2017) for tomato, with small
modifications. A model (Y = G + E + G×E + Ɛ) was used for the whole RIL
population to identify the effect of genotype (G), maternal environment
(E) and their interaction (G×E). Furthermore, in order to identify the
metabolic variation explained by the genetic component we carried out
the QTL analysis for known metabolites in each sub-population with
simple interval mapping (SIM) using MapQTL® 6.0 (Van
Ooijen 2004). In both QTL analysis (Rqtl and MapQTL) 1000 permutation
tests were applied to our data to estimate the LOD threshold at a
significance level of 0.05.