Lignin pathway genes differentially expressed in stem tissues of two alfalfa genotypes. Pair-wise comparisons were made between stem tissues (ES, PES) of genotypes 708 and 773. Columns in each heatmap from left to right: Log2(708ES/773ES), Log2(708PES/773PES), Log2(708PES/708ES), and Log2(773PES/773ES). The rows in each heatmap represent lignin gene sequences identified in MSGI 1.0. The Log2 expression ratio values were false color-coded using a scale of -3 to 3. The intensity of blue and red indicates the degree of up- and down-regulation of the corresponding lignin gene in the denominator in each column mentioned above. The red and blue color saturates at -3 and 3, respectively. See Methods for details. The heatmaps generated were inserted next to the corresponding lignin gene in the lignin biosynthetic pathway diagram downloaded from the KEGG pathway database http://www.genome.jp/kegg/pathway/map/map00940.html. PAL, phenylalanine ammonia-lyase; C4H, cinnamate-4-hydroxylase; 4CL, 4-coumarate-CoA ligase; HCT, hydroxycinnamoyltransferase; C3H, p-coumarate 3-hydroxylase; CCoAOMT, caffeoyl-CoA 3-O-methyltransferase; CCR1, cinnamoyl-CoA reductase 1; F5H, ferulate 5-hydroxylase; COMT, caffeic acid O-methyltransferase; CAD, cinnamyl-alcohol dehydrogenase.