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Volume 5


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In Silico Biology 5, 0053 (2005); ©2005, Bioinformation Systems e.V.  



Identification of candidate genes at quantitative trait loci on chicken chromosome Z using orthologous comparison of chicken, mouse, and human genomes

Georgina A. Ankra-Badu and Samuel E. Aggrey*

Poultry Genetics and Biotechnology Laboratory, Department of Poultry Science and Institute of Bioinformatics, University of Georgia, Athens, GA 30602-2772, USA

* Corresponding author
   Department of Poultry Science, University of Georgia, Athens, GA 30602-2772; Email: saggrey@uga.edu


Edited by E. Wingender; received June 28, 2005; revised August 25/October 27, 2005; accepted October 27, 2005; published January 04, 2006


Abstract

This study was undertaken to identify novel candidate genes at quantitative trait loci (QTL) on chicken chromosome Z (GGAZ) by comparing orthologous regions of chicken, human and mouse genomes. Primer sequences from marker flanking QTL positions (https://acedb.asg.wur.nl/) were obtained from www.iastate.edu/chickmap and blasted against the chicken genome (www.ensembl.org) using BLASTN. The best matches were those with the highest score, lowest E-values and highest percent identity. Orthologous regions in mice and humans, together with genes located on or around those loci were identified using the Ensembl website. Forty-six chicken genes, 91 mouse genes and 60 human genes associated with QTL on GGAZ were identified in the current study. Among the most promising candidate genes for egg production and egg shell quality are annexin A1 (ANXA1), osteoclast stimulating factor (OSF), thrombospondin-4 (THBS4), programmed cell death proteins (PDCD), follistatin (FST), growth hormone receptor (GHR), interferon (IFN) α and β. The chicken IFN α and β were located on GGAZ around position 13,000,000 bp on the draft chicken sequence map. The neuronal nicotinic acetylcholine receptor (nAChR) is located at a QTL region for abdominal fat (GGAZ 25483091 bp). Nicotine is an agonist at the nAChRs and has been shown to decrease lipolysis and triglyceride uptake, thereby reducing net storage in adipose tissue. Therefore, the nAchRs could be used as therapeutic targets for regulating feed intake and obesity. This study has identified 197 putative candidate genes in probable QTL regions of chicken chromosome Z.


Keywords: candidate genes, quantitative trait loci, chicken chromosome Z, comparative mapping