Selection on the promoter regions plays an important role in complex traits during duck domestication

Zhong-Tao Yin, Xiao-Qin Li, Yun-Xiao Sun, Jacqueline Smith, Maxwell Hincke, Ning Yang, Zhuo-Cheng Hou

Research output: Contribution to journalArticlepeer-review

Abstract / Description of output

Background
Identifying the key factors that underlie complex traits during domestication is a great challenge for evolutionary and biological studies. In addition to the protein-coding region differences caused by variants, a large number of variants are located in the non-coding regions containing multiple types of regulatory elements. However, the roles of accumulated variants in gene regulatory elements during duck domestication and economic trait improvement are poorly understood.

Results
We constructed a genomics, transcriptomics, and epigenomics map of the duck genome, and assessed the evolutionary forces that have been in play across the whole genome during domestication. In total, 304 (42.94%) gene promoters have been specifically selected in Pekin duck among all selected genes. Joint multi-omics analysis reveals that 218 genes (72.01%) with selected promoters are located in open and active chromatin, and 267 genes (87.83%) 35 with selected promoters were highly and differentially expressed in domestic trait-related tissues. One important candidate gene ELOVL3, with a strong signature of differentiation on the core promoter region, is known to regulate fatty acid elongation. Functional experiments showed that the nearly fixed variants in the top selected ELOVL3 promoter in Pekin duck decreased binding ability with HLF and increased gene expression, with the over-expression of ELOVL3 able to increase lipid deposition and unsaturated fatty acid enrichment.

Conclusions
This study presents genome resequencing, RNA-Seq, Hi-C, and ATAC-Seq data of mallard and Pekin duck, showing that selection of the gene promoter region plays an important role in gene expression and phenotypic changes during domestication, and highlights that the variants of the ELOVL3 promoter may have multiple effects on fat and long-chain fatty acid content in ducks.
Original languageEnglish
Article number303
Pages (from-to)1-19
Number of pages19
JournalBMC Biology
Early online date21 Dec 2023
DOIs
Publication statusE-pub ahead of print - 21 Dec 2023

Keywords / Materials (for Non-textual outputs)

  • Promoter
  • Accumulated variants
  • Gene expression
  • Domestication
  • Duck

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