(A) Physical mapping of differentially expressed genes (p < 0.001, FDR < 0.05, ≥ 2-fold difference) between alfalfa genotypes 252 and 1283 in ES internodes (red triangles) and PES internodes (blue circles) onto putative orthologous loci in the Medicago truncatula chromosomes 1 through 8 and (B) Comparison of the frequency distribution on Medicago chromosomes 1 through 8 for the genes differentially expressed between alfalfa genotypes 252 and 1283 in ES (red line) and PES (blue line) internodes. (A) The corresponding physical loci for genes are indicated on the solid line (x-axis) for each chromosome. The y- axis, indicated within the doted lines above and below the solid line, provides a measure of the Log2(252/1283) value for each gene [(Log2(252/1283) = 0 for solid line (x-axis)]. The symbols located above and below the zero center line represent genes up- and down-regulated in 252 compared to 1283 in ES (red triangles) and PES (blue circles) internodes, respectively. The vertical distance of each symbol from the zero center line indicates the degree of differential gene expression [Log2(252/1283)] for the corresponding genes on each chromosome. The orthologous loci of the genes selected on M. truncatula chromosomes are provided in Additional file 3. (B) The y-axis for each panel represents relative gene frequency in a 50 kb sliding window that reads gene frequency over 10 kb intervals.