PgmNr P337: Systems genetics for industry: combining QTL mapping, GWAS and RNA sequencing to improve bone strength in laying hens.

Authors:
D. J. de Koning 1,2 ; H. A. McCormack 2 ; B. Raymond 1 ; A. M. Johansson 1 ; R. Preisinger 3 ; M. Schmutz 3 ; I. C. Dunn 2


Institutes
1) Swedish University of Agricultural Sciences, Uppsala, Sweden; 2) The Roslin Institute and R(D)SVS, University of Edinburgh, UK; 3) Lohmann Tierzucht GmbH, Cuxhaven, Germany.


Abstract:

Bone fractures are a major welfare problem in laying hens. In order to determine the potential to selectively breed for bone strength, divergent selection lines were established in the nineties from a commercial breeding line of White Leghorns. Bishop et al (2000) showed a heritability of 0.40 for a bone index that combined breaking strength from different bones. Subsequently an F2 was created from G9 of the selection lines  and a quantitative trait locus (QTL)  with a large effect was mapped  on Chromosome 1 (Dunn et al., 2007).

In this study, we refined the QTL in the F2 by adding SNP markers. We then tested the SNPs from the refined region on the 2006 generation of the White Leghorn line from which the F2 was derived after 9 generations of divergent selection.  Subsequently, birds from the 2011 generation were genotyped for the QTL haplotype and birds with alternative QTL haplotypes were selected for qPCR of candidate genes and RNA sequencing. 

For the SNPs with the most consistent effects, the tibial breaking strength for the alternative haplotypes in the 2006 population was 200.4 vs 218.1 Newtons (p<0.002). 

The RNA sequencing showed strong differential expression for a single candidate gene in the QTL region with clear allelic imbalance suggesting a cis-acting effect within the candidate gene.

Subsequently, a full GWAS was carried out on ~750 birds from the 2006 generation using the Affymetrix high-density SNP chip. After quality control around 225K SNP remained for a mixed model GWAS using GenAbel. Additional QTL were identified on chromosomes 3, 8 and 16. The most significant QTL on chromosome 8 had an additive effect of 20 Newton.  At present we are validating these SNP effects in commercial crossbred layers from different companies, with different feeding regimes and in different housing systems. This will be the ultimate test for the utility of these genetic markers to improve bone strength under practical farming conditions.