Duration: October 2021 – September 2026
Responsible: Christiaan Henkel
Funding source: FHF
Project number: 901864
Awarded: 19 155 000 NOK
Summary:
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. 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.
In SALMOCODE, we plan to leverage scRNA-seq to screen developing salmon from a large number of production conditions. First, we 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. We 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, we will use this knowledge to design protocols that circumvent their emergence and validate these using an array of stress tests.
Information about the project (in Norwegian) is available on the Veterinary College pages of the NMBU website, as well as on the project pages of the FHF website.
CIGENE researchers involved: Christiaan Henkel, Øyvind Andersen, Junsoung Kwak, Simen Rød Sandve