Led by Christiaan Henkel at BIOVIT (NMBU), SALMOCODE (the Salmon Map of Organs and Cells for Optimal Development of Embryos) is a three-year collaboration between NMBU, Nofima, UiT, Aqua Kompetanse, and NCE Aquaculture, with industrial partners Benchmark Genetics and MOWI, funded by the Norwegian Seafood Research Fund (FHF). SALMOCODE will use single-cell transcriptomics to investigate the vulnerability of developing Atlantic salmon to environmental conditions.
The Norwegian aquaculture industry produces over 1.6 million tonnes of salmon a year, more than half of the global production. This production level demands fast-growing fish, which has been achieved both by targeting growth rate in selective breeding and by applying high rearing temperatures during early life stages. However, more than 90 million salmon a year are lost before they reach slaughter size, compromising economic, ethical, and environmental sustainability. Losses occur for a variety of reasons, but for a large part can be attributed to deficiencies in organ health, including heart, kidneys, and gills, but also the immune system, skin, and skeleton.
As they develop in eggs exposed to the environment, fishes are especially susceptible to external influences during early development. These include temperature and light, which have been shown to have long-term fitness effects. The new project SALMOCODE will explore the hypothesis that production conditions during embryonic development of Atlantic salmon can have a negative impact on organogenesis, the initial phase of organ development, roughly between gastrulation and hatching. This complex process consists of pluripotent stem cells undergoing successive rounds of differentiation, eventually giving rise to numerous specialized cell types, which combine to form functional organs.
Over the past decade, single-cell transcriptomics (scRNA-seq) has emerged as the leading technology for addressing questions on tissue composition and heterogeneity, developmental biology, and regulation of gene expression. It allows quantification of gene expression for thousands to millions of individual cells, in contrast to regular ‘bulk’ RNA-seq which mixes up the gene expression signals from all cells in a sample. scRNA-seq is still relatively expensive, but increasingly being applied in aquaculture research.
SALMOCODE plan to leverage scRNA-seq to screen developing salmon from a large number of production conditions. First, SALMOCODE will document the entirety of cellular and gene expression changes in the developing salmon embryo. This will yield a comprehensive ‘roadmap’ of organogenesis, detailing the temporal emergence of all cell types, their expression profiles, and cell fate decisions. SALMOCODE will subsequently generate ‘shallow’ (lower-cost) maps for development under diverse production conditions, and by comparing these to the reference precisely identify the first developmental timepoints at which specific organ abnormalities appear. Finally, SALMOCODE will use this knowledge to design protocols that circumvent their emergence and validate these using an array of stress tests.
A project description of SALMOCODE is available in Norwegian on the FHF project base: https://www.fhf.no/prosjekter/prosjektbasen/901864/
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