Chickens exhibit considerable variation in morphological traits, with some populations having undergone intensive selection for uniqueness and uniformity. These populations are a source of experimental material to study the genetics of morphological traits. An important first step in such studies is to map the genes and the causal mutations that influence these traits. This research focused on gene mapping of 12 morphological traits including 4 intra-feather color patterns (Pattern, Columbian, Melanotic, and mottling), 2 inter-feather color patterns (Blue and chocolate), 2 forms of feathered-legs, polydactyly, dark brown eggshell color, vulture hock, and creeper. Ten backcross and/or F2 populations were designed to produce 1,880 individuals. An additional 339 DNA samples from other populations were included. The procedures for gene mapping were: 1. Pooling of DNA samples of backcross or F2 individuals based on their shared phenotypes, followed by microarray assays for genotyping, a cost-effective initial screen for the candidate genomic regions, 2. Linkage mapping to narrow the range of candidate genes, 3. Sequencing to identify the candidate mutations, 4. Diagnostic tests to confirm the association between the candidate mutation and the phenotype. Of the 12 traits studied, 3 (mottling, Blue, and chocolate) made progress into step 4. Complexities due to genomic context, modifiers, and environmental factors precluded step 4 for the first form of the feathered-leg gene, step 3 for the mapping of Melanotic, and earlier stages for the mapping of Pattern, Columbian, dark brown egg, vulture hock, and the second form of feathered-leg. These findings provide insights of the complexity of how background genome can influence the phenotypic expression of single genes (gene genetic background interactions) and an understanding of cellular and molecular mechanisms involved in morphogenesis. / Ph. D. / Chickens, one of the major protein sources in diets for humans, have a long cultural, sport and religious history since their initial domestication during the neolithic period. Darwin wrote of the importance of variation, which today we see for example in size of body, length of shank, number of toes, distribution of feathers, comb types, and plumage color patterns resulting in a plethora of breeds of chickens that differ in appearance. Some of these traits are "simply" inherited, which in the molecular era facilitates the study of relationships between DNA sequences and phenotypes. This dissertation focuses on identification of differences in DNA sequences among chickens responsible for these "simply" inherited phenotypes. The 12 phenotypes that were studied included 6 plumage color patterns (Pattern, Columbian, Melanotic, mottling, Blue, and chocolate), 2 forms of feathered-legs, polydactyly, dark brown eggshell color, vulture hock, and creeper. Designed were ten 3-generation populations to produce 1,880 chickens. An additional 339 DNA samples from other populations were included. Of the 12 phenotypes, 8 involved genotyping of pooled DNA samples, a cost-effective initial screen to target DNA sequences. This was followed by genotyping individual samples in 5 of the more promising studies. Candidate genes identified as associated with these 5 phenotypes underwent further studies which identified differences in DNA sequences associated with 4 of them (mottling, feathered-leg, Blue, and chocolate). These findings provide insights of how DNA sequences contribute to the phenotypic appearance of animals.