Two distinct structural variants involvingEDN3cause hyperpigmentation in chicken

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Abstract

Phenotypic diversity and its genetic basis are central questions in biology, with domesticated animals offering valuable insights due to their rapid evolution the last 10,000 years. In chickens, fibromelanosis (FM) is a striking pigmentation phenotype characterized by hyperpigmentation. A previous study identified a complex structural variant causing upregulated expression of the Endothelin 3 ( EDN3 ) gene. However, the detailed structural arrangement and functional consequences of the variant remained unclear. In this study, we conducted a comprehensive genomic survey of 692 FM chickens representing 55 breeds and uncovered two distinct structural variants causing the FM phenotype: FM*A, the previously reported complex rearrangement involving the EDN3 locus 1 , and FM*B , a tandem duplication of a 16 kb region upstream of EDN3 . We demonstrate that both structural variants (SVs) significantly upregulate EDN3 expression, with FM*B associated with even higher expression than FM*A . A luciferase reporter assays showed that the 16 kb region in FM*B contains powerful enhancers and the copy number expansion of this element is a likely explanation for EDN3 upregulation and hyperpigmentation. Furthermore, our analysis of linkage disequilibrium patterns allowed us to resolve the complex arrangement of duplications and inversion on the FM*A haplotype.
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Skip to main content Home About Submit ALERTS / RSS Search for this keyword Advanced Search Withdrawn WITHDRAWN: Two distinct structural variants involving EDN3 cause hyperpigmentation in chicken Cheng Ma , Xun-He Huang , Feng-Juan Wang , Shu-Run Zhang , Xian Shi , Zhuo-Xian Weng , Bingwang Du , Ya-Ping Zhang , View ORCID Profile Leif Andersson , Min-Sheng Peng doi: https://doi.org/10.1101/2024.12.04.626589 Cheng Ma 1 Key Laboratory of Genetic Evolution & Animal Models and Yunnan Key Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences , Kunming, China 2 Department of Medical Biochemistry and Microbiology, Uppsala University , Uppsala, Sweden Find this author on Google Scholar Find this author on PubMed Search for this author on this site Xun-He Huang 3 Guangdong Provincial Key Laboratory of Conservation and Precision Utilization of Characteristic Agricultural Resources in Mountainous Areas, Guangdong Innovation Centre for Science and Technology of Wuhua Yellow Chicken, School of Life Science, Jiaying University , Meizhou, China Find this author on Google Scholar Find this author on PubMed Search for this author on this site Feng-Juan Wang 1 Key Laboratory of Genetic Evolution & Animal Models and Yunnan Key Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences , Kunming, China 4 Kunming College of Life Science, University of Chinese Academy of Sciences , Kunming, China Find this author on Google Scholar Find this author on PubMed Search for this author on this site Shu-Run Zhang 1 Key Laboratory of Genetic Evolution & Animal Models and Yunnan Key Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences , Kunming, China Find this author on Google Scholar Find this author on PubMed Search for this author on this site Xian Shi 1 Key Laboratory of Genetic Evolution & Animal Models and Yunnan Key Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences , Kunming, China 4 Kunming College of Life Science, University of Chinese Academy of Sciences , Kunming, China Find this author on Google Scholar Find this author on PubMed Search for this author on this site Zhuo-Xian Weng 3 Guangdong Provincial Key Laboratory of Conservation and Precision Utilization of Characteristic Agricultural Resources in Mountainous Areas, Guangdong Innovation Centre for Science and Technology of Wuhua Yellow Chicken, School of Life Science, Jiaying University , Meizhou, China Find this author on Google Scholar Find this author on PubMed Search for this author on this site Bingwang Du 3 Guangdong Provincial Key Laboratory of Conservation and Precision Utilization of Characteristic Agricultural Resources in Mountainous Areas, Guangdong Innovation Centre for Science and Technology of Wuhua Yellow Chicken, School of Life Science, Jiaying University , Meizhou, China Find this author on Google Scholar Find this author on PubMed Search for this author on this site Ya-Ping Zhang 1 Key Laboratory of Genetic Evolution & Animal Models and Yunnan Key Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences , Kunming, China 4 Kunming College of Life Science, University of Chinese Academy of Sciences , Kunming, China Find this author on Google Scholar Find this author on PubMed Search for this author on this site Leif Andersson 2 Department of Medical Biochemistry and Microbiology, Uppsala University , Uppsala, Sweden 5 Department of Veterinary Integrative Biosciences, Texas A&M University , College Station, USA Find this author on Google Scholar Find this author on PubMed Search for this author on this site ORCID record for Leif Andersson Min-Sheng Peng 1 Key Laboratory of Genetic Evolution & Animal Models and Yunnan Key Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences , Kunming, China 4 Kunming College of Life Science, University of Chinese Academy of Sciences , Kunming, China Find this author on Google Scholar Find this author on PubMed Search for this author on this site For correspondence: pengminsheng{at}mail.kiz.ac.cn Abstract Info/History Metrics Preview PDF Withdrawal statement The authors have withdrawn this manuscript because [We decided to split this preprint into two parts in order to make different topics as clear as possible, the first topic is the correct structural rearrangement of the previously studied structural variation, and the other topic is the genetic mechanism of another copy number variation]. Therefore, the authors do not wish this work to be cited as reference for the project. If you have any questions, please contact the corresponding author. Competing Interest Statement The authors have declared no competing interest. Copyright The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission. View the discussion thread. Back to top Previous Next Posted December 23, 2024. Download PDF Email Thank you for your interest in spreading the word about bioRxiv. NOTE: Your email address is requested solely to identify you as the sender of this article. Your Email * Your Name * Send To * Enter multiple addresses on separate lines or separate them with commas. 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