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Functional Genomics of the Chicken—A Model Organism

L. A. Cogburn^*,1, T. E. Porter, M. J. Duclos, J. Simon, S. C. Burgess, J. J. Zhu^||, H. H. Cheng^#, J. B. Dodgson^** and J. Burnside^*,

^* Department of Animal and Food Sciences, University of Delaware, Newark 19717; Department of Animal and Avian Sciences, University of Maryland, College Park 20742; Station de Recherches Avicoles, Institut National de la Recherche Agronomique, 37380 Nouzilly, France; College of Veterinary Medicine, Mississippi State University, Mississippi State 39762; ^|| Foreign Animal Disease Research Unit, USDA-Agricultural Research Service, Plum Island Animal Disease Center, Greenport, NY 11944; ^# Avian Disease and Oncology Laboratory, USDA-Agricultural Research Service, East Lansing, MI 48823; ^** Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing 48824; and Delaware Biotechnology Institute, University of Delaware, Newark 19717

¹ Corresponding author: cogburn{at}udel.edu

Since the sequencing of the genome and the development of high-throughput tools for the exploration of functional elements of the genome, the chicken has reached model organism status. Functional genomics focuses on understanding the function and regulation of genes and gene products on a global or genome-wide scale. Systems biology attempts to integrate functional information derived from multiple high-content data sets into a holistic view of all biological processes within a cell or organism. Generation of a large collection (600K) of chicken expressed sequence tags, representing most tissues and developmental stages, has enabled the construction of high-density microarrays for transcriptional profiling. Comprehensive analysis of this large expressed sequence tag collection and a set of 20K full-length cDNA sequences indicate that the transcriptome of the chicken represents approximately 20,000 genes. Furthermore, comparative analyses of these sequences have facilitated functional annotation of the genome and the creation of several bioinformatic resources for the chicken. Recently, about 20 papers have been published on transcriptional profiling with DNA microarrays in chicken tissues under various conditions. Proteomics is another powerful high-throughput tool currently used for examining the dynamics of protein expression in chicken tissues and fluids. Computational analyses of the chicken genome are providing new insight into the evolution of gene families in birds and other organisms. Abundant functional genomic resources now support large-scale analyses in the chicken and will facilitate identification of transcriptional mechanisms, gene networks, and metabolic or regulatory pathways that will ultimately determine the phenotype of the bird. New technologies such as marker-assisted selection, transgenics, and RNA interference offer the opportunity to modify the phenotype of the chicken to fit defined production goals. This review focuses on functional genomics in the chicken and provides a road map for large-scale exploration of the chicken genome.

Key Words: transcriptome • proteome • metabolome • systems biology • gene network

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