The mapping population was a set of 154 doubled-haploid lines derived from a cross between IR62266-42-6-2 x CT9993-5-10-1-M. CT9993 was originally developed at CIAT from a complex cross involving primarily African upland varieties (some japonica background in pedigree), whereas IR62266, a lowland indica, was developed at IRRI. A total of 315 markers (145 RFLP, 158 AFLP, and 12 SSR) were mapped at a LOD threshold of 3.0. The total map length was 1788 cM; the average distance between two markers 6 cM.