Edinburgh Research Explorer

Complex trait subtypes identification using transcriptome profiling reveals an interaction between two QTL affecting adiposity in chicken

Research output: Contribution to journalArticle

  • Yuna Blum
  • Guillaume Le Mignon
  • David Causeur
  • Olivier Filangi
  • Colette Désert
  • Olivier Demeure
  • Pascale Le Roy
  • Sandrine Lagarrigue

Related Edinburgh Organisations

Open Access permissions



  • Download as Adobe PDF

    Rights statement: This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

    Final published version, 1.14 MB, PDF document

Original languageEnglish
Article number567
JournalBMC Genomics
Publication statusPublished - Nov 2011


Integrative genomics approaches that combine genotyping and transcriptome profiling in segregating populations have been developed to dissect complex traits. The most common approach is to identify genes whose eQTL colocalize with QTL of interest, providing new functional hypothesis about the causative mutation. Another approach includes defining subtypes for a complex trait using transcriptome profiles and then performing QTL mapping using some of these subtypes. This approach can refine some QTL and reveal new ones.

In this paper we introduce Factor Analysis for Multiple Testing (FAMT) to define subtypes more accurately and reveal interaction between QTL affecting the same trait. The data used concern hepatic transcriptome profiles for 45 half sib male chicken of a sire known to be heterozygous for a QTL affecting abdominal fatness (AF) on chromosome 5 distal region around 168 cM.

Using this methodology which accounts for hidden dependence structure among phenotypes, we identified 688 genes that are significantly correlated to the AF trait and we distinguished 5 subtypes for AF trait, which are not observed with gene lists obtained by classical approaches. After exclusion of one of the two lean bird subtypes, linkage analysis revealed a previously undetected QTL on chromosome 5 around 100 cM. Interestingly, the animals of this subtype presented the same q paternal haplotype at the 168 cM QTL. This result strongly suggests that the two QTL are in interaction. In other words, the "q configuration" at the 168 cM QTL could hide the QTL existence in the proximal region at 100 cM. We further show that the proximal QTL interacts with the previous one detected on the chromosome 5 distal region.

Our results demonstrate that stratifying genetic population by molecular phenotypes followed by QTL analysis on various subtypes can lead to identification of novel and interacting QTL.

    Research areas

  • Adiposity, Animals, Chickens, Gene Expression Profiling, Male, Quantitative Trait Loci, Transcriptome

Download statistics

No data available

ID: 13079817