Comparisons of marker orders between the BnaWAIT_01_2010a integrated map and each population-specific consolidated map, BnaSNDH_05_2010a, BnaSGDH_03_2010a and BnaDYDH_05_2010a. The vertical axis indicates the BnaWAIT_01_2010a integrated map, and the horizontal axis indicates the three population-specific maps with solid vertical lines separating them. LG (a) A01, (b) A02, (c) A07, (d) A08, (e) C05 and (f) C07 are shown. A01, A02 and C07 display a good marker order consistency between the BnaWAIT_01_2010a map and component maps, and A07, A08 and C05 show relatively low level of agreement. Remainder of dot-plots are shown in Additional File 4.