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The objective of this study was to characterize the <jats:italic>CEL<\/jats:italic> gene, investigate the association between the <jats:italic>CEL<\/jats:italic> promoter variants and chicken phenotypic traits, and explore the <jats:italic>CEL<\/jats:italic> gene regulatory mechanism. An insertion\/deletion (indel) caused by a 99-bp insertion fragment was shown for the first time in the chicken <jats:italic>CEL<\/jats:italic> promoter, and large differences in allelic frequency were found among commercial breeds, indigenous and feral birds. Association analysis demonstrated that this indel site had significant effects on shank length, shank girth, chest breadth at 8 weeks (<jats:italic>p<\/jats:italic>\u2009&lt;\u20090.01), evisceration weight, sebum weight, breast muscle weight, and leg weight (<jats:italic>p<\/jats:italic>\u2009&lt;\u20090.05). Tissue expression profiles showed extremely high levels of the <jats:italic>CEL<\/jats:italic> gene in pancreatic tissue. Moreover, the expression levels of the genes <jats:italic>APOB<\/jats:italic>, <jats:italic>MTTP<\/jats:italic>, <jats:italic>APOV1<\/jats:italic> and <jats:italic>SREBF1<\/jats:italic>, which are involved in lipid transport, were significantly reduced by adding a 4% oxidized soybean oil diet treatment at the individual level and transfecting the embryonic primary hepatocytes with a <jats:italic>CEL<\/jats:italic>-overexpression vector. Interestingly, the results showed that the expression level of the II homozygous genotype was significantly higher than that of the ID and DD genotypes, while individuals with DD genotypes had higher phenotypic values. Therefore, these data suggested that the <jats:italic>CEL<\/jats:italic> gene might affect body growth by participating in hepatic lipoprotein metabolism and that the 99-bp indel polymorphism could be a potentially useful genetic marker for improving the economically important traits of chickens.<\/jats:p>","DOI":"10.1038\/s41598-020-60168-2","type":"journal-article","created":{"date-parts":[[2020,2,21]],"date-time":"2020-02-21T11:03:29Z","timestamp":1582283009000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":4,"title":["Association of a new 99-bp indel of the CEL gene promoter region with phenotypic traits in chickens"],"prefix":"10.1038","volume":"10","author":[{"given":"Xiangnan","family":"Wang","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xinlei","family":"Wang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Bingjie","family":"Chen","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yaping","family":"Guo","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hehe","family":"Tang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Donghua","family":"Li","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Danli","family":"Liu","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yanbin","family":"Wang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Guoxi","family":"Li","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xiangtao","family":"Kang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7595-0604","authenticated-orcid":false,"given":"Zhuanjian","family":"Li","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ruili","family":"Han","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2020,2,21]]},"reference":[{"key":"60168_CR1","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1016\/0005-2760(96)00085-9","volume":"1303","author":"DY Hui","year":"1996","unstructured":"Hui, D. 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