TABLE 3.

Alignment of chromosome 1D contigs to the RH map

Contig name	Markers used for alignment	Coretention frequency (%)
ctg605	cdo57-0.90–cdo92-0.30	97.7
ctg3467	BE500570-0.35–BE443071-0.80	86.2
ctg5162	BF293779-0.39–bcd808-0.50	89.7
ctg8420	BE423482-0.15–BE403717-0.80	83.9
ctg8420	BE494877-0.39
ctg8420	BE403553-0.03
ctg8420	BE406901-0.20–BE423482-0.15	83.9
ctg8420	BE406901-0.20–BE494877-0.39	86.2
ctg8420	BE403553-0.03–BE403717-0.80	82.8
ctg8420	BE403717-0.80–BE403553-1.00	82.8
ctg9212	BF475048-0.07–BE443931-0.62	97.7
ctg4625	BE489565-1.60–BE490041-0.50	93.1

Markers used in the wheat RH mapping work in this study were used to identify wheat D-genome BAC contigs derived from the wheat D-genome physical mapping project (http://wheat.pw.usda.gov/PhysicalMapping/index.html). In most cases, the left and right markers of a contig are given, as well as single markers that mapped to a particular contig. The ordering of these markers by using the comprehensive RH map (Figure 1) provides a method for the physical ordering of the contigs. The percentage of coretention frequency between two markers is calculated by subtracting the total number of breaks between those two markers from the total number of possible breaks (87) divided by the total number of possible breaks multiplied by 100.