Very few causal genes have been identified by quantitative trait loci (QTLs) mapping because of the large size of QTLs, 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 QTLs 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 QTLs were previously mapped. Using a new haplotype-based statistics exploiting the very high SNP density generated through whole genome re-sequencing, we found 129 significant selective sweeps. Most of the QTLs co-localized 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 QTLs/sweeps. The absence of non-synonymous 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 on 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.
- Received November 24, 2014.
- Accepted January 28, 2015.
- Copyright © 2015 Author et al.
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