Functional genomics of the chicken - A model organism

L. A. Cogburn, T. E. Porter, M. J. Duclos, J. Simon, Shane C Burgess, J. J. Zhu, H. H. Cheng, J. B. Dodgson, J. Burnside

Research output: Contribution to journalArticle

76 Citations (Scopus)

Abstract

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.

Original languageEnglish (US)
Pages (from-to)2059-2094
Number of pages36
JournalPoultry Science
Volume86
Issue number10
StatePublished - Oct 1 2007
Externally publishedYes

Fingerprint

chickens
genomics
organisms
genome
expressed sequence tags
genes
phenotype
birds
RNA interference
bioinformatics
marker-assisted selection
transcriptome
proteomics
protein synthesis
developmental stages
genetically modified organisms
Biological Sciences
tissues

Keywords

  • Gene network
  • Metabolome
  • Proteome
  • Systems biology
  • Transcriptome

ASJC Scopus subject areas

  • Animal Science and Zoology

Cite this

Cogburn, L. A., Porter, T. E., Duclos, M. J., Simon, J., Burgess, S. C., Zhu, J. J., ... Burnside, J. (2007). Functional genomics of the chicken - A model organism. Poultry Science, 86(10), 2059-2094.

Functional genomics of the chicken - A model organism. / Cogburn, L. A.; Porter, T. E.; Duclos, M. J.; Simon, J.; Burgess, Shane C; Zhu, J. J.; Cheng, H. H.; Dodgson, J. B.; Burnside, J.

In: Poultry Science, Vol. 86, No. 10, 01.10.2007, p. 2059-2094.

Research output: Contribution to journalArticle

Cogburn, LA, Porter, TE, Duclos, MJ, Simon, J, Burgess, SC, Zhu, JJ, Cheng, HH, Dodgson, JB & Burnside, J 2007, 'Functional genomics of the chicken - A model organism', Poultry Science, vol. 86, no. 10, pp. 2059-2094.
Cogburn LA, Porter TE, Duclos MJ, Simon J, Burgess SC, Zhu JJ et al. Functional genomics of the chicken - A model organism. Poultry Science. 2007 Oct 1;86(10):2059-2094.
Cogburn, L. A. ; Porter, T. E. ; Duclos, M. J. ; Simon, J. ; Burgess, Shane C ; Zhu, J. J. ; Cheng, H. H. ; Dodgson, J. B. ; Burnside, J. / Functional genomics of the chicken - A model organism. In: Poultry Science. 2007 ; Vol. 86, No. 10. pp. 2059-2094.
@article{799ccf89a87642848cf63f4ce1f58701,
title = "Functional genomics of the chicken - A model organism",
abstract = "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.",
keywords = "Gene network, Metabolome, Proteome, Systems biology, Transcriptome",
author = "Cogburn, {L. A.} and Porter, {T. E.} and Duclos, {M. J.} and J. Simon and Burgess, {Shane C} and Zhu, {J. J.} and Cheng, {H. H.} and Dodgson, {J. B.} and J. Burnside",
year = "2007",
month = "10",
day = "1",
language = "English (US)",
volume = "86",
pages = "2059--2094",
journal = "Poultry Science",
issn = "0032-5791",
publisher = "Poultry Science Association",
number = "10",

}

TY - JOUR

T1 - Functional genomics of the chicken - A model organism

AU - Cogburn, L. A.

AU - Porter, T. E.

AU - Duclos, M. J.

AU - Simon, J.

AU - Burgess, Shane C

AU - Zhu, J. J.

AU - Cheng, H. H.

AU - Dodgson, J. B.

AU - Burnside, J.

PY - 2007/10/1

Y1 - 2007/10/1

N2 - 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.

AB - 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.

KW - Gene network

KW - Metabolome

KW - Proteome

KW - Systems biology

KW - Transcriptome

UR - http://www.scopus.com/inward/record.url?scp=35348826030&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=35348826030&partnerID=8YFLogxK

M3 - Article

C2 - 17878436

AN - SCOPUS:35348826030

VL - 86

SP - 2059

EP - 2094

JO - Poultry Science

JF - Poultry Science

SN - 0032-5791

IS - 10

ER -