Complex trait subtypes identification using transcriptome profiling reveals an interaction between two QTL affecting adiposity in chicken - Institut Agro Rennes-Angers Accéder directement au contenu
Article Dans Une Revue BMC Genomics Année : 2011

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

Yuna Blum
Olivier Filangi
Pascale Le Roy

Résumé

Background: 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. Results: 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. Conclusion: 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.
Fichier principal
Vignette du fichier
1471-2164-12-567.pdf (1.14 Mo) Télécharger le fichier
Origine : Fichiers éditeurs autorisés sur une archive ouverte
Loading...

Dates et versions

hal-00730144 , version 1 (16-11-2012)

Identifiants

Citer

Yuna Blum, Guillaume Le Mignon, David Causeur, Olivier Filangi, Colette Désert, et al.. Complex trait subtypes identification using transcriptome profiling reveals an interaction between two QTL affecting adiposity in chicken. BMC Genomics, 2011, 12 (november), pp.8. ⟨10.1186/1471-2164-12-567⟩. ⟨hal-00730144⟩
356 Consultations
183 Téléchargements

Altmetric

Partager

Gmail Facebook X LinkedIn More