Chromatin accessibility in gill tissue identifies candidate genes and loci associated with aquaculture relevant traits in tilapia

Tarang K. Mehta, Angela Man, Adam Ciezarek, Keith Ranson, David Penman, Federica Di-Palma, Wilfried Haerty

Research output: Contribution to journalArticlepeer-review


The Nile tilapia (Oreochromis niloticus) accounts for ~9% of global freshwater finfish production however, extreme cold weather and decreasing freshwater resources has created the need to develop resilient strains. By determining the genetic bases of aquaculture relevant traits, we can genotype and breed desirable traits into farmed strains. We generated ATAC-seq and gene expression data from O. niloticus gill tissues, and through the integration of SNPs from 27 tilapia species, identified 1168 highly expressed genes (4% of all Nile tilapia genes) with highly accessible promoter regions with functional variation at transcription factor binding sites (TFBSs). Regulatory variation at these TFBSs is likely driving gene expression differences associated with tilapia gill adaptations, and differentially segregate in freshwater and euryhaline tilapia species. The generation of novel integrative data revealed candidate genes e.g., prolactin receptor 1 and claudin-h, genetic relationships, and loci associated with aquaculture relevant traits like salinity and osmotic stress acclimation.
Original languageEnglish
Article number110633
Issue number4
Early online date28 Apr 2023
Publication statusPublished - Jul 2023


  • Aquaculture
  • Epigenetics
  • Molecular evolution
  • Reguluatory evolution
  • Tilapia

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