Differential gene expression in femoral bone from red junglefowl and domestic chicken, differing for bone phenotypic traits

Carl-Johan Rubin¹ , Johan Lindberg² , Carolyn Fitzsimmons³ , Peter Savolainen² , Per Jensen⁴ , Joakim Lundeberg² , Leif Andersson³^,5 and Andreas Kindmark¹

¹Department of Medical Sciences, Uppsala University, Sweden

²Department of Gene Technology, School of Biotechnology, Royal Institute of Technology, Stockholm, Sweden

³Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden

⁴IFM Biology, Linköping University, SE-585 83, Linköping, Sweden

⁵Department of Medical Biochemistry and Microbiology, Uppsala University, Box 597, SE-75124 Uppsala, Sweden

author email corresponding author email

BMC Genomics 2007, 8:208doi:10.1186/1471-2164-8-208


Published:	2 July 2007

Abstract

Background

Osteoporosis is frequently observed among aging hens from egg-producing strains (layers) of domestic chicken. White Leghorn (WL) has been intensively selected for egg production and it manifests striking phenotypic differences for a number of traits including several bone phenotypes in comparison with the wild ancestor of chicken, the red junglefowl (RJ). Previously, we have identified four Quantitative Trait Loci (QTL) affecting bone mineral density and bone strength in an intercross between RJ and WL. With the aim of further elucidating the genetic basis of bone traits in chicken, we have now utilized cDNA-microarray technology in order to compare global RNA-expression in femoral bone from adult RJ and WL (five of each sex and population).

Results

When contrasting microarray data for all WL-individuals to that of all RJ-individuals we observed differential expression (False discovery rate adjusted p-values < 0.015) for 604 microarray probes. In corresponding male and female contrasts, differential expression was observed for 410 and 270 probes, respectively. Altogether, the three contrasts between WL and RJ revealed differential expression of 779 unique transcripts, 57 of which are located to previously identified QTL-regions for bone traits. Some differentially expressed genes have previously been attributed roles in bone metabolism and these were: WNT inhibitory factor 1 (WIF1), WD repeat-containing protein 5 (WDR5) and Syndecan 3 (SDC3). Among differentially expressed transcripts, those encoding structural ribosomal proteins were highly enriched and all 15 had lower expression in WL.

Conclusion

We report the identification of 779 differentially expressed transcripts, several residing within QTL-regions for bone traits. Among differentially expressed transcripts, those encoding structural ribosomal proteins were highly enriched and all had lower expression levels in WL. In addition, transcripts encoding four translation initiation and translation elongation factor proteins also had lower expression levels in WL, possibly indicating perturbation of protein biosynthesis pathways between the two populations. Information derived from this study could be relevant to the bone research field and may also aid in further inference of genetic changes accompanying animal domestication.