Differential Gene Expression from Genome-Wide Microarray Analyses Distinguishes Lohmann Selected Leghorn and Lohmann Brown Layers

Christin Habig,Robert Geffers,Ottmar Distl,Ioannis P. Androulakis

doi:10.1371/journal.pone.0046787

Christin Habig, Robert Geffers + Show 2 more

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https://doi.org/10.1371/journal.pone.0046787

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Abstract

The Lohmann Selected Leghorn (LSL) and Lohmann Brown (LB) layer lines have been selected for high egg production since more than 50 years and belong to the worldwide leading commercial layer lines. The objectives of the present study were to characterize the molecular processes that are different among these two layer lines using whole genome RNA expression profiles. The hens were kept in the newly developed small group housing system Eurovent German with two different group sizes. Differential expression was observed for 6,276 microarray probes (FDR adjusted P-value <0.05) among the two layer lines LSL and LB. A 2-fold or greater change in gene expression was identified on 151 probe sets. In LSL, 72 of the 151 probe sets were up- and 79 of them were down-regulated. Gene ontology (GO) enrichment analysis accounting for biological processes evinced 18 GO-terms for the 72 probe sets with higher expression in LSL, especially those taking part in immune system processes and membrane organization. A total of 32 enriched GO-terms were determined among the 79 down-regulated probe sets of LSL. Particularly, these terms included phosphorus metabolic processes and signaling pathways. In conclusion, the phenotypic differences among the two layer lines LSL and LB are clearly reflected in their gene expression profiles of the cerebrum. These novel findings provide clues for genes involved in economically important line characteristics of commercial laying hens.

Highlights

Microarray expression profiling became a universal tool, with a range of applications that benefit from the accurate determination of differential gene expression [1,2]
Lohmann Selected Leghorn (LSL) layers showed a significantly worse plumage score of the different body regions and a worse total plumage score compared to hens of the Lohmann Brown (LB) layer line
In LSL hens, probe sets belonging to the gene ontology (GO)-cluster of phosphorus metabolism were down-regulated, which may be related to an enhanced calcium requirement of LSL

Summary

Introduction

Microarray expression profiling became a universal tool, with a range of applications that benefit from the accurate determination of differential gene expression [1,2]. Buitenhuis et al [5] explored differentially expressed genes for aggressive pecking behaviour in laying hens from a high feather pecking selection line produced from a foundation stock of a White Leghorn layer strain. They compared genome-wide profiles of chicken brain samples from aggressive and receiver hens using a 20 K chicken microarray that contained 20,678 oligonucleotides and corresponded to 20,640 chicken transcripts. Among the differently expressed genes they found genes involved in disorders, such as intestinal inflammation and insulin resistance

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