Jointed goatgrass (Ae. cylindrica) is an allotetraploid (2n=4x=28; CCDD genomes) of the Triticeae tribe that shares the D genome with the cultivated allohexaploid wheat, Triticum aestivum L. (2n=6x=42; AABBDD genomes). Jointed goatgrass is both an important weed of wheat and a source of genetic variation for wheat improvement. Thus, there is considerable interest in understanding Ae. cylindrica's genetic architecture for its better management and use. For this purpose, we have undertaken a project to develop a linkage map of this species. The linkage map will be based on 94 F₂ progeny from a cross between US/OR 13 (FC13), a jointed goatgrass accession from Oregon, and TK16 (PI 486236), an accession from Turkey. So far, the F₂ mapping population has been genotyped with 125 polymorphic markers (40 microsatellites, ESTs, or cloned genes, 84 AFLPs, and one morphological trait). Of 125 loci, 89 coalesced into 18 linkage groups at a LOD of 5.0 while 36 remained unlinked at this threshold. An evaluation of genetic marker co-linearity and synteny between chromosomes of jointed goatgrass and wheat is currently underway.