Recipient name: the governors of the university of albertacooperative agreement number: G25AC00208PROJECT title: the role of DNA methylation in morphological deformities in artificially reared…

Recipient name: the governors of the university of albertacooperative agreement number: G25AC00208PROJECT title: the role of DNA methylation in morphological deformities in artificially reared ciscooverall project period: 04 16 2025 through 04 15 2030OVERALL budget period: 04 16 2025 through 04 15 2026AWARD purpose: the purpose of this award is to investigate the effects of different captive rearing protocols during supplementation and conservation efforts on cisco (coregonus artedi). We will assess how different temperature rearing protocols affect DNA methylation, a molecular mechanism that affects gene expression and is often implicated as a mechanism for the reduced fitness and survival of captive-reared fish. We will determine if specific rearing protocols minimize the unintended molecular effects of captive rearing, leading to the production of captive cisco that resemble wild cisco and survive better in the wild.activities to be performed:cisco will be sampled from different captive rearing facilities focused on supplementation of wild populations, including the jordan river hatchery and USGS hammond BAY biological station. Specifically, we will sample captive-reared cisco reared in different thermal environments, including (1) an outdoor artificial stream, (2) a hatchery environment under standard rearing temperature for fish production, and (3) a hatchery environment with a natural thermal regime. Wild cisco will be sampled from several nearby regions in lake huron through collaboration with US fish and wildlife, the BAY mills indian community, and the ontario ministry of natural resources. DNA will be extracted from 80 samples (ideally 40 wild and 40 captive-reared cisco) for whole-genome enzymatic methyl-SEQ to characterize whole-genome differences in methylation among (1) captive and wild cisco, and (2) cisco from different captive rearing protocols. We will assess how differences in captive rearing protocols affect DNA methylation, and which genes are affected by different protocols. We will also determine whether specific rearing protocols lead to cisco DNA methylation patterns that more closely resemble wild fish, which could improve cisco survival after release into the wild. We will determine whether there are shared methylation differences among all captive reared cisco, which could support the future development of epigenetic biomarkers to differentiate captive-reared and wild cisco based on FIN clips.deliverables and expected outcomes:we will generate whole genome DNA methylation data for captive and wild cisco. We will determine whether the use of different captive rearing protocols can reduce the unintended effects of captive rearing on cisco DNA methylation, which likely serves as the mechanism for the reduced fitness of captive-reared fish when released into the wild. We will test for consistent effects of captive rearing across different captive rearing protocols, which will serve as a pilot study towards the development of epigenetic biomarkers to differentiate captive-reared and wild fish. We expect that these results will provide further insight into the effects of different rearing environments on captive-reared cisco, with the ultimate goal of producing more natural fish ready to face nature.intended beneficiary(IES): this work will benefit USGS research goals and objectives in coregonine restoration, including understanding the effects of different rearing environments on cisco, and the potential for epigenetic biomarkers to nonlethally identify artificially reared cisco. The results will also be shared with interested stakeholders, including the jordan river hatchery and others involved in coregonine restoration in the great lakes.