Comparison of Broiler Chicken Retina and Pineal Gland Transcriptome

Light scheduling, intensity, and technology are of interest to the poultry industry because of their impact on bird behavior and growth. There are a variety of programs used among broiler chicken producers to optimize growth, and subsequently profit; however, little is known about how the visual systems in the chicken interact to cause a physiological response. Greater understanding of these processes would give insight into the most beneficial lighting composition for broiler growth and health. This project examined the transcript profile of retinal and pineal gland tissues isolated from male Ross 708 broiler chickens at 35 days post-hatch through a variety of computational methods. RNA-seq was utilized to compare genes between the retina and pineal gland to better know how these photoreceptive organs communicate with the central nervous system, and each other, to interpret the chickens’ environment. The Tuxedo Suite was used to determine the transcription levels in Fragments Per Kilobase of transcript per Million (FPKM) of sample libraries. JMP Pro 11, Cytoscape, and Biolayout were utilized to identify differentially expressed genes, significant pathways, and functional clustering in each tissue. Relative tissue expression (RTE) analysis was carried out on the retina and pineal gland samples to observe genes in each that were significantly expressed in relation to all Gallus tissue libraries uploaded to the University of Delaware BigBird Database. Through this method, 836 genes were significantly differentially regulated in the pineal gland, and 914 were differentially regulated in the retina. These genes were further queried via JMP Pro 11 and Biolayout to isolate genes specifically up-regulated in each tissue, yielding 34 genes in the retina and 28 genes in the pineal gland. The hypothesis of this study is that utilization of a variety of computational methods, in addition to experimental bird performance data, will allow for improved identification of genes that are integral to broiler chickens’ physiological response to light.