Figure 3

Correlations between the expression levels of genes and metabolite contents in peel. The different groups of genes have different colors. Grey: structural genes of the phenylpropanoid pathway. Blue: the putative transcription factor genes that were detected in the mQTL hotspot; Yellow: the putative transcription factor genes that were outside the mQTL hotspot but on LG16; Pink: putative transcription factor genes of the phenylpropanoid pathway that are not located on LG16 but are at other regions of the genome. The metabolites are highlighted in purple and their correlations with the expression levels of all the genes are given in bold text. The metabolites contents (ions count per second) and expression data (expression relatively to the reference gene MdGAPDH) were ¹⁰log transformed before calculation of the correlation coefficients. Scatter plots (data not shown) were made to evaluate the distributions and to exclude outliers that might strongly affect the correlations. The correlations between the expression level of MdLAR1 and metabolite content are given in bold italics text. Green color shows other correlations (r > 0.7). Red color highlights negative correlations between − 0.5 and − 1.0. For each metabolite group that had an mQTL at the LG16 hotspot, a representative metabolite is included in this correlation matrix. Similar results were also found in flesh (Additional file 3).