Elucidating genetic influences on bison growth and body composition is of interest, not only because bison are important for historical, cultural, and agricultural reasons, but also because their unusual population history makes them valuable models for finding influential loci in both domestic cattle and humans. We tested for trait loci associated with body weight, height, and bison mass index (BMI) while controlling for estimated ancestry to reduce potential confounding effects due to population admixture in 1316 bison sampled from four U.S. herds. We used 60 microsatellite markers to model each phenotype as a function of herd, sex, age, marker genotypes, and individual ancestry estimates. Statistical significance for genotype and its interaction with ancestry was evaluated using the adaptive false discovery rate. Of the four herds, two appeared to be admixed and two were nonadmixed. Although none of the main effects of the loci were significant, estimated ancestry and its interaction with marker loci were significantly associated with the phenotypes, illustrating the importance of including ancestry in the models and the dependence of genotype-phenotype associations on background ancestry. Individual loci contributed $2.0% of variation in weight, height, and BMI, which confirms the utility and potential importance of adjusting for population stratification.I NTENSIVE linkage analysis in livestock species over the past two decades has led to the mapping of loci for economically important traits. Numerous regions of the domestic cattle genome, for example, have been linked to quantitative trait loci (QTL) for body weight and carcass characteristics (Casas et al. 1998(Casas et al. , 2000(Casas et al. , 2001Elo et al. 1999;Stone et al. 1999;Grosz and MacNeil 2001;Kim et al. 2003), increasing the potential for using marker-assisted selection to improve traits of economic importance. North American bison (Bison bison) have recently become an important alternative and complementary meat source to beef cattle; .90% of bison are maintained on private ranches (Halbert 2003), where they are raised primarily for meat production. Although bison and domestic cattle are classified into different genera (Bison and Bos) and are estimated to have diverged 1.0-1.5 million years ago (Hartl et al. 1988;Wall et al. 1992;Ritz et al. 2000), they still have the same number of chromosomes (m ¼ 30), the same chromosome banding patterns (Basrur and Moon 1967;Ying and Peden 1977), and a highly similar autosomal gene content and order (Schnabel et al. 2003). Interbreeding between bison and domestic cattle can result in fertile offspring, and modern technologies have been used to detect domestic cattle genetic introgression in many extant bison populations (Polziehn et al. 1995;Ward et al. 1999;Ward 2000;Halbert et al. 2005).Although the recently enriched bovine linkage map (Ihara et al. 2004) has become a critical resource in the dissection of bovine quantitative traits including those of bison, only a few studies have reported mi...