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Comparative and Functional Genomics
Volume 5 (2004), Issue 3, Pages 253-261
http://dx.doi.org/10.1002/cfg.402
Conference review

Functional Genomics in Chickens: Development of Integrated-Systems Microarrays for Transcriptional Profiling and Discovery of Regulatory Pathways

1Department of Animal and Food Sciences, University of Delaware, Newark, DE 19717, USA
2Statistics Program, Department of Food and Resource Economics, University of Delaware, Newark, DE 19717, USA
3Department of Poultry Science, University of Georgia, Athens, GA 30602, USA
4Station de Recherches Avicoles, Institut National de la Recherche Agronomique, Nouzilly 37 380, France
5Department of Animal and Avian Sciences, University of Maryland, College Park, MD 20742, USA

Received 16 February 2004; Accepted 16 February 2004

Copyright © 2004 Hindawi Publishing Corporation. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Abstract

The genetic networks that govern the differentiation and growth of major tissues of economic importance in the chicken are largely unknown. Under a functional genomics project, our consortium has generated 30 609 expressed sequence tags (ESTs) and developed several chicken DNA microarrays, which represent the Chicken Metabolic/Somatic (10 K) and Neuroendocrine/Reproductive (8 K) Systems (http://udgenome.ags.udel.edu/cogburn/). One of the major challenges facing functional genomics is the development of mathematical models to reconstruct functional gene networks and regulatory pathways from vast volumes of microarray data. In initial studies with liver-specific microarrays (3.1 K), we have examined gene expression profiles in liver during the peri-hatch transition and during a strong metabolic perturbation—fasting and re-feeding—in divergently selected broiler chickens (fast vs. slow-growth lines). The expression of many genes controlling metabolic pathways is dramatically altered by these perturbations. Our analysis has revealed a large number of clusters of functionally related genes (mainly metabolic enzymes and transcription factors) that control major metabolic pathways. Currently, we are conducting transcriptional profiling studies of multiple tissues during development of two sets of divergently selected broiler chickens (fast vs. slow growing and fat vs. lean lines). Transcriptional profiling across multiple tissues should permit construction of a detailed genetic blueprint that illustrates the developmental events and hierarchy of genes that govern growth and development of chickens. This review will briefly describe the recent acquisition of chicken genomic resources (ESTs and microarrays) and our consortium's efforts to help launch the new era of functional genomics in the chicken.