Many germplasm resources, often from alien translocations and wild relatives, have been used extensively in common wheat (Triticum aestivum) improvement. In several instances, wheat breeders have recognized unintended consequences (either favorable or unfavorable) after deployment of a particular source that had been utilized for other purposes. DNA marker assisted selection (MAS) simplifies the process of developing appropriate populations that are useful for characterization of the effects of germplasm introgressions in different genetic backgrounds. The objective of this study was to evaluate grain yield and agronomic and end-use quality characteristics of sets of near isogenic lines derived through marker assisted selection (MAS) for high grain protein content (HGPC, from T. dicoccoides) and barley yellow dwarf virus resistance (BYDV, from Thinpyrum intermedium). Five generations of marker-assisted backcross transfer of BYDV resistance (BYAgi marker) and HGPC (Xuhw89 marker) were done in greenhouse environments to produce BC5F2 progenies for several marker/recurrent parent combinations. DNA markers were assayed from field-grown BC5F2 individuals segregating for the presence of BYAgi and Xuhw89. BC5F2 individuals homozygous for either the presence or absence of the respective markers were identified by DNA marker analysis of 11 to 15 BC5F2:3 progenies. Seed of the BC5F2:3 progenies was increased in Yuma, AZ, to allow planting of sets of near-isogenic BC5F2:4 lines at five locations in eastern Colorado in fall 2006. A subset of BC5F2:4 progenies was also planted in a BYDV nursery in Manhattan, KS, in fall 2006. BYDV reaction, grain yield, and agronomic characteristics will be determined during the 2006-2007 field season. End-use quality evaluations will be done in fall 2007 from samples harvested from the field trials in eastern Colorado.