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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.</jats:p>","journal":"G3 Genes|Genomes|Genetics","year":2015,"id":637802,"datarank":0.42498200160843247,"base_score":2.833213344056216,"endowment":2.833213344056216,"self_citation_contribution":0.42498200160843247,"citation_network_contribution":0.0,"self_endowment_contribution":0.42498200160843247,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":16,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":null,"is_data_producer":false,"deposit_databanks":null,"is_oa":false,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":null,"fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":288934,"name":"Simon Boitard","orcid":"0000-0002-2499-5052","position":1,"is_corresponding":false},{"id":1656239,"name":"Yuna Blum","orcid":null,"position":2,"is_corresponding":false},{"id":1656241,"name":"Brian Parks","orcid":null,"position":3,"is_corresponding":false},{"id":1656244,"name":"Alexandra Montagner","orcid":null,"position":4,"is_corresponding":false},{"id":1656247,"name":"Etienne Mouisel","orcid":null,"position":5,"is_corresponding":false},{"id":1656249,"name":"Anis Djari","orcid":null,"position":6,"is_corresponding":false},{"id":1656251,"name":"Diane Esquerré","orcid":null,"position":7,"is_corresponding":false},{"id":1576368,"name":"Colette Désert","orcid":null,"position":8,"is_corresponding":false},{"id":1656254,"name":"Morgane Boutin","orcid":null,"position":9,"is_corresponding":false},{"id":1656255,"name":"Sophie Leroux","orcid":null,"position":10,"is_corresponding":false},{"id":123004,"name":"Frédéric Lecerf","orcid":"0000-0002-6471-1771","position":11,"is_corresponding":false},{"id":1651259,"name":"Elisabeth Le Bihan-Duval","orcid":null,"position":12,"is_corresponding":false},{"id":122144,"name":"Christophe Klopp","orcid":"0000-0001-7126-5477","position":13,"is_corresponding":false},{"id":1656256,"name":"Bertrand Servin","orcid":null,"position":14,"is_corresponding":false},{"id":123007,"name":"Frédérique Pitel","orcid":"0000-0002-1477-7633","position":15,"is_corresponding":false},{"id":1656257,"name":"Michel Jean Duclos","orcid":null,"position":16,"is_corresponding":false},{"id":934834,"name":"Hervé Guillou","orcid":"0000-0002-5363-9081","position":17,"is_corresponding":false},{"id":1535957,"name":"Aldons J Lusis","orcid":null,"position":18,"is_corresponding":false},{"id":1656258,"name":"Olivier Demeure","orcid":null,"position":19,"is_corresponding":false},{"id":122143,"name":"Sandrine Lagarrigue","orcid":"0000-0002-4887-7245","position":20,"is_corresponding":false},{"id":1656237,"name":"Pierre-François Roux","orcid":null,"position":0,"is_corresponding":false}],"reference_count":0,"raw_metadata":{"has_enrichment":true,"resolved":true,"title":"Combined QTL and Selective Sweep Mappings with Coding SNP Annotation and<i>cis</i>-eQTL Analysis Revealed<i>PARK2</i>and<i>JAG2</i>as New Candidate Genes for Adiposity Regulation","abstract":"<jats:title>Abstract</jats:title><jats:p>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. 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