Combined QTL and selective sweep mappings with coding SNP annotation and cis-eQTL analysis revealed PARK2 and JAG2 as new candidate genes for adiposity regulation.

TitleCombined QTL and selective sweep mappings with coding SNP annotation and cis-eQTL analysis revealed PARK2 and JAG2 as new candidate genes for adiposity regulation.
Publication TypeJournal Article
Year of Publication2015
AuthorsRoux, P-F, Boitard, S, Blum, Y, Parks, B, Montagner, A, Mouisel, E, Djari, A, Esquerré, D, Désert, C, Boutin, M, Leroux, S, Lecerf, F, Le Bihan-Duval, E, Klopp, C, Servin, B, Pitel, F, Duclos, MJean, Guillou, H, Lusis, AJ, Demeure, O, Lagarrigue, S
JournalG3 (Bethesda)
Volume5
Issue4
Pagination517-29
Date Published2015 Apr
ISSN2160-1836
Abstract

Very few causal genes have been identified by quantitative trait loci (QTL) mapping because of the large size of QTL, and most of them were identified thanks to functional links already known with the targeted phenotype. Here, we propose to combine selection signature detection, coding SNP annotation, and cis-expression QTL analyses to identify potential causal genes underlying QTL identified in divergent line designs. As a model, we chose experimental chicken lines divergently selected for only one trait, the abdominal fat weight, in which several QTL were previously mapped. Using new haplotype-based statistics exploiting the very high SNP density generated through whole-genome resequencing, we found 129 significant selective sweeps. Most of the QTL colocalized with at least one sweep, which markedly narrowed candidate region size. Some of those sweeps contained only one gene, therefore making them strong positional causal candidates with no presupposed function. We then focused on two of these QTL/sweeps. The absence of nonsynonymous SNPs in their coding regions strongly suggests the existence of causal mutations acting in cis on their expression, confirmed by cis-eQTL identification using either allele-specific expression or genetic mapping analyses. Additional expression analyses of those two genes in the chicken and mice contrasted for adiposity reinforces their link with this phenotype. This study shows for the first time the interest of combining selective sweeps mapping, coding SNP annotation and cis-eQTL analyses for identifying causative genes for a complex trait, in the context of divergent lines selected for this specific trait. Moreover, it highlights two genes, JAG2 and PARK2, as new potential negative and positive key regulators of adiposity in chicken and mice.

DOI10.1534/g3.115.016865
Alternate JournalG3 (Bethesda)
PubMed ID25653314
PubMed Central IDPMC4390568
Grant ListHL28481 / HL / NHLBI NIH HHS / United States
HL30568 / HL / NHLBI NIH HHS / United States
T32 HD007228 / HD / NICHD NIH HHS / United States