mQTL analysis
The substantial variation caused by G, E and G×E may be an indication of a sophisticated regulation of metabolites in developing tomato seeds. Thus, metabolite content of the seeds must be considered as a complex trait which is likely regulated by multiple quantitative trait loci (QTLs) (Keurentjes & Sulpice 2009; Lisec et al. 2008).
To detect these mQTLs, we analysed metabolite profiles in the dry mature seeds of all the RILs. PCA analysis of this data revealed a clear separation between the known metabolites of the seeds grown in the two nutritional maternal environments (Figure 2A ). Twenty-three and 15% of the total variation was explained by PC1 and PC2 respectively. Similar results were obtained after analysis of all 118 detected metabolites (Figure S1A ). Both PCA plots show that predominantly PC2 explained the variation related to the maternal environment. The loading plot of the PCA showed that the main components contributing to PC2 were organic acids including glycolate, glycerate, malonate and succinate and amino acids such as glutamate, serine, threonine and asparagine (Figure 2B, Table S4 ).