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

Mehta, Tarang K., Man, Angela, Ciezarek, Adam, Ranson, Keith, Penman, David, Di-Palma, Federica and Haerty, Wilfried ORCID: https://orcid.org/0000-0003-0111-191X (2023) Chromatin accessibility in gill tissue identifies candidate genes and loci associated with aquaculture relevant traits in tilapia. Genomics, 115 (4). ISSN 0888-7543

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Abstract

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.

Item Type: Article
Additional Information: Data availability: All sequencing data generated for this article is available under the ENA study accession PRJEB59919. All other data underlying this article is available in the article, its supplementary material or in the following repository: https://doi.org/10.6084/m9.figshare.22100825. Funding information: This research was funded by the BBSRC Core Strategic Programme Grant BB/CSP1720/1 (TKM, AM, AC, FDP and WH) and its constituent work packages (BBS/E/T/000PR9818 and BBS/E/T/000PR9819). Part of this work was delivered via the BBSRC National Capability in Genomics and Single Cell Analysis (BBS/E/T/000PR9816) at Earlham Institute by members of the Genomics Pipelines Group.
Uncontrolled Keywords: aquaculture,epigenetics,molecular evolution,reguluatory evolution,tilapia,genetics ,/dk/atira/pure/subjectarea/asjc/1300/1311
Faculty \ School: Faculty of Medicine and Health Sciences > Norwich Medical School
University of East Anglia Research Groups/Centres > Theme - ClimateUEA
Faculty of Science > School of Biological Sciences
UEA Research Groups: Faculty of Medicine and Health Sciences > Research Centres > Norwich Institute for Healthy Aging
Related URLs:
Depositing User: LivePure Connector
Date Deposited: 02 May 2023 09:30
Last Modified: 05 Jun 2023 09:30
URI: https://ueaeprints.uea.ac.uk/id/eprint/91920
DOI: 10.1016/j.ygeno.2023.110633

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