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Title: Functional genomics of the chicken - a model organism

Author
item COGBURN, LARRY - UNIV OF DELAWARE
item PORTER, TOM - UNIV OF MARYLAND
item DUCLOS, MICHEL - INRA FRANCE
item SIMON, JEAN - INRA FRANCE
item BURGESS, SHANE - MISSISSIPPI STATE UNIV
item ZHU, JAMES - TEXAS A & M
item Cheng, Hans
item DODGSON, JERRY - MICHIGAN STATE UNIV
item BURNSIDE, JOAN - UNIV OF DELAWARE

Submitted to: Poultry Science
Publication Type: Review Article
Publication Acceptance Date: 7/5/2007
Publication Date: 10/1/2007
Citation: Cogburn, L.A., Porter, T.E., Duclos, M.J., Simon, J., Burgess, S.C., Zhu, J., Cheng, H.H., Dodgson, J.B., Burnside, J. 2007. Functional genomics of the chicken - a model organism. Poultry Science. 86:2059-2094.

Interpretive Summary:

Technical Abstract: The chicken has reached model organism status after genome sequencing and development of high-throughput tools for the exploration of functional elements of the genome. 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 datasets into a holistic view of all biological processes within a cell or organism. Generation of a large collection of chicken expressed sequence tags (~600K ESTs), representing most tissues and developmental stages, has enabled the construction of high-density microarrays for transcriptional profiling. Comprehensive analysis of this large EST collection and a set of ~20K full-length cDNA sequences indicate that the chicken’s transcriptome represents about 20,000 genes. Furthermore, comparative analyses of these sequences facilitated functional annotation of the genome and creation of several bioinformatic resources for the chicken. Recently, nearly two dozen 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 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/regulatory pathways that ultimately determine the bird’s phenotype. New technologies such as marker-assisted selection, transgenics and RNA interference give us the opportunity to modify the chicken’s phenotype to fit defined production goals. This review focuses on functional genomics in the chicken and provides a roadmap for large-scale exploration of the chicken’s genome.