Novel epigenetic markers of embryo quality to improve fish domestication, PhD in Biosciences Studentship (BBSRC SWBio DTP funded)

The SWBio DTP is one of the 12 Doctoral Training Partnerships funded by the BBSRC to provide PhD training in areas of their strategic relevance. The SWBio DTP is a consortium comprising the Universities of Bristol (lead), Bath, Cardiff, Exeter, and Rothamsted Research. Together, these institutions present a distinctive cadre of bioscience research staff and students with established international, national and regional networks and widely recognised research excellence.

The aim of this DTP is to produce highly motivated and excellently trained postgraduates in the BBSRC priority areas of Agriculture & Food Security (AFS) and World-Class Underpinning Bioscience (WCUB). These are growth areas of the biosciences and for which there will be considerable future demand.

The award:

This project is one of a number that are in competition for funding from the South West Biosciences Doctoral Training Partnership (SWBio DTP).

Project Description:

Sustainable aquaculture relies on domestication, which in fish is very recent compared to birds and mammals. The rearing environment affects both oocyte quality and embryo developmental success and farming conditions are known to cause large phenotypic and epigenetic (methylation) changes, which regulate gene expression without altering the DNA sequence. Reprogramming of DNA methylation during embryogenesis has been studied in very few fish species including zebrafish, medaka, Atlantic salmon and a few other species. Our previous BBSRC and NRN-LCEE funded work suggested that aquaculture rearing conditions affect fish immune respons and induces behavioural and epigenetic changes a proportion of which can be transmitted to the offspring, at least in Atlantic salmon.

The main aim of this project is to assess the generality of epigenetic and transcriptomic alterations related to aquaculture-related conditions (e.g. reading density) at the beginning of spermatogenesis and oogenesis, to identify epigenetic markers related to embryo quality (e.g. stress resistance) which could be used to develop fish strains better adapted to live in captivity. To achieve this, the student will combine genomic, epigenomic and phenotypic/physiological/cellular analyses from two complementary experimental settings that will measure the influence of the rearing environment (density) in the health and performance of two different fish species for which there is abundant genomic information, zebrafish (Danio rerio), where epigenetic memory in the embryo was first described, and Nile tilapia (Oreochormis niloticus), the most 85 / 95 widely cultured fish in aquaculture worldwide.

The particular objectives of the project will be: Objective 1. To assess the role of maternal and paternal epigenetic (methylation) effects in the embryos. For this, the student will compare epigenome (methylome) profiles of sperm from different males raised under the same conditions and embryos those males crossed by the same females or males respectively Objective 2. To compare performance (e.g. growth), transcriptomic (eggs) and epigenomic (eggs, sperm) profiles of individuals reared under two different rearing densities, and their offspring (embryos). Objective 3. To assess the potential for a conserved response to early rearing conditions in fish by comparing genes/regions differentially methylated and expressed in response to temperature in both species. Objective 4. To assess the potential transgenerational effects of early-life rearing conditions by comparing the methylome and transcriptome the F1 and F2 generations (both sperm and embryos).