SALMOCODE will tackle the problems of abnormal organ development by detecting its onset as early as possible, using leading edge technology and concepts from genomics and developmental biology. These diagnostics will be used to formulate evidence-based best practices for preventing the appearance of these abnormalities.

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01. Oct 2023


30. Sep 2026

Funded by

FHF – Norwegian Seafood Research Fund


NMBU, NCE Aquaculture, Aqua Kompetanse, UiT


Currently, 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.

In this project, we will explore the overall hypothesis that production conditions during the embryonic and larval developmental stages can have a negative impact on organ development, and thereby on future heart, kidney, and gill health. In many animals, including salmonids, organs continue to develop and adapt during life.

The initial phase of organ development, roughly between gastrulation and birth or hatching, is known as organogenesis. 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.

Embryo development is tightly governed by conserved genetic programs.

Simultaneously, this period offers some level of flexibility, which allows development to compensate for minor disturbances and environmental priming of the animal for its future. Environmental temperature, for example, can have a major impact on developmental speed, but also induce mortality and organogenesis defects. The trade-offs between the genetic program and phenotypic plasticity are what ultimately determine animal health.

SALMOCODE proposes to document this interplay for Atlantic salmon at the genetic, cellular, organismal, and environmental levels.


The primary objective is the design and validation of best practices for rearing conditions of Atlantic salmon from fertilization to first feeding. 

What we do

We will collate information from the industry through a survey and workshop (lead by NCE Aquaculture), and the scientific literature to develop an overview of current knowledge on the early environmental production conditions and later performance and robustness.

Together with UiT, NMBU and Aqua Kompetanse, we will rear Atlantic salmon under a number of conditions from fertilization to yolk sac depletion (start feeding), each corresponding to a specific hypothesis about the influence of the environment on the embryo.

The developing embryos and larvae will be analyzed.

In addition to early life trials, we will conduct longer term trials to document the robustness of fish raised using optimized protocols. We hypothesised that differences in organ development are caused by asynchronous development of cell lineages. At NMBU this will be tested by constructing a full map of early development in salmon using scRNA-seq. This method generates a moderate-depth gene expression profile for thousands of individual cells in the embryo.

Computational grouping of these transcriptomic states result in clusters of distinct cell types. Some cells will be on a ‘trajectory’ between such clusters, implying active development from a stem or progenitor cell to a more differentiated state. scRNA-seq profiling of cells from the embryo and larvae allows the full mapping of fate commitment from blastula to specialized organs and tissues.

Together with NMBU, we will evaluate the consequences of the different production conditions on the robustness of fish, we will expose salmon to several husbandry relevant stressors. Stress tests will be carried out at 2 periods: alevins (before first feeding) and smolts (after seawater transfer). These periods were selected to identify how early we can detect differences in the robustness of fish reared under different production conditions, and whether early rearing environment can shape the responses of fish to stressors later in life.

Finally, we will collectively analyze existing knowledge and project results (developmental and functional) to understand the emergence and effects of suboptimal organ development. We will use this new knowledge to design production conditions that give Atlantic salmon a good start in life, and communicate these with the industry.