Gene Mapping of Morphological Traits in Chickens

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.