Single nuclei transcriptomics reveals programming of metabolic functions by embryonic temperature in the developing Atlantic salmon liver

Environmental temperature pervasively affects the physiology of poikilothermic fishes. Embryogenesis is a sensitive period of development, where altering temperature can promote plasticity in phenotypes that persist deeper into the life cycle, with potential implications for aquaculture. However, the mechanisms by which embryonic temperature shapes phenotypic plasticity remain poorly understood. Here, we investigate the impact of embryonic temperature regime on the transcriptome of 15,688 liver cells from farmed Atlantic salmon fry. Three fish groups were grown at 4, 6 or 8°C solely from fertilization to the eyed-stage of embryogenesis, then reared at the same temperature until sampling, one-month post start-feeding (three months post treatment). Single nuclei transcriptomics revealed hepatocyte, cholangiocyte, mesenchymal, endothelial and immune cell populations. Seven hepatocyte subpopulations were identified with distinct expression and functional characteristics. We identified strong impacts of embryonic temperature on the transcriptome of hepatocytes, implicating diverse metabolic functions, pathways and regulatory genes. This included changes in mevalonate and steroid biosynthesis pathways, as well as the growth hormone-insulin-like growth factor axis, consistent with alterations in cholesterol/lipid metabolism and the endocrine regulation of growth. We provide evidence for increased antiviral gene expression in the 4oC group, alongside significant changes in the expression of epigenetic and stress regulation genes across temperature groups. Collectively, our results indicate that altering temperature for a short window of Atlantic salmon embryogenesis programs the development of hepatic, metabolic and immune functions deeper into the aquaculture production cycle.