Fig. 2. Flow chart outlining the scheme for targeting subgenomic regions in wheat using bulked segregant analysis. DNA of the two bulks are compared by AFLP or cDNA-AFLP analysis. Positive fragments are cloned and used as RFLP probes to detect fragments on Southern blots containing Chinese Spring (CS), the nullisomic-tetrasomic stocks involving homeologous group 5 chromosomes, and appropriate 5BL chromosome deletion lines to verify the existence of the fragment in the targeted interval. The marker was then placed on the physical map of the corresponding chromosome. The probe was also mapped in segregating populations to generate genetic linkage maps. The genetic maps were compared with the corresponding deletion intervals of the physical map to reveal marker order and estimate physical to genetic distance ratios.