MapMan overview of metabolism showing genes that are differentially expressed between alfalfa genotypes 252 and 1283 in ES (A) and PES (B) internodes. The Log2(252/1283) values for the differentially expressed genes (p < 0.001, FDR < 0.05, ≥ 2-fold difference) were false color coded using a scale of -3 to +3. The intensity of blue and red colors indicates the degree of preferential expression of the corresponding genes in 252 and 1283, respectively. Color saturates at ±3 (8-fold difference or higher). See Methods for details. A complete list of the differentially expressed genes, corresponding MapMan functional categories, signal intensities and log ratios are provided in Additional file 1.