Exploring the Realm of Gene Expression Differences Between White Leghorn and Red Junglefowl Chickens

In this thesis we attempted to elicit patterns of gene expression that influence phenotype, and that may also have been altered by thousands of years of domestication and selection, between red junglefowl and White Leghorn chickens. Red junglefowl are the wild ancestor to all domesticated chickens, and poultry in general are highly valued as a research animal and food resource. The project was also begun in order to complement an earlier study of an intercross between White Leghorn and red junglefowl, which identified several regions that were linked with phenotypic differences between the two birds. We began by creating our own cDNA microarray via generating four cDNA libraries from red junglefowl/White Leghorn brain and testis. We generated 12,549 unique transcripts. This included 400 new putative transcripts specific to chickens, and 180 transcripts that were not found in any other database. When investigating polymorphisms between White Leghorn and red junglefowl we found a SNP rate of 1.9/kb coding region, and a synonymous and non-synonymous percentage for these SNPs of 80 and 20% respectively. In the last two studies we used the cDNA microarray to measure gene expression differences between White Leghorn and red junglefowl in both hypothalamus/thalamus and liver. We found that there appears to be a significant number of genes down-regulated in White Leghorn hypothalamus/thalamus, plus an over-representation of up-regulated genes from well-known pathways, as compared with red junglefowl. We hypothesize that domestication/selection may be connected with this characteristic. We also found that the p-arm of chicken chromosome 4, which is an ancestral microchromosome, was over represented with differentially expressed genes in hypothalamus/thalamus. A number of differentially expressed genes are shared between the two tissues, and these genes are expressed in same manner between red junglefowl and White Leghorn