All animals develop from a single fertilized egg into juveniles and adults consisting of a multitude of specialized cells. In recent years, single-cell transcriptomics (scRNA -seq) has emerged as the leading technology for studying thi s developmental process. By measuring the expression of all genes in individual cells dissociated from a tissue, it creates thousands to millions of gene expression profiles. These can be clustered into profiles specific for cell types and states , as well as into trajectories that reflect developmental change. This has enabled the mapping in exquisite detail of all cell types emerging during embryo development in zebrafish, frogs, and mice.
Single-cell transcriptomics is relevant for aquaculture, as it also allows the precise identification of the onset of developmental defects. These can have both external and internal causes. As they develop in eggs exposed to the environment, fishes are especially susceptible to external influences during embryogenesis. In addition, egg quality has a strong influence on embryogenesis. Finally, a single-cell atlas identifies when, and in which cell types, genes exert their function, and could therefore inform marker selection for breeding programs.
In Norway, we have recently started to generate a single-cell atlas of organogenesis (early embryogenesis) in Atlantic salmon. This reference will be used to diagnose the quality of embryos reared under a wide range of environmental conditions, with the aim of optimizing production conditions towards better organ health in adults.
A similar effort would highly valuable for understanding the early development of the European eel. Eel embryogenesis often aborts before hatching, and scRNA -seq could be used to identify the mechanisms involved, as well as their vulnerable time-windows. Such diagnostics could also help to decipher the influence of broodstock quality, which is a strong predictor of successful embryogenesis. As a first step towards a single-cell atlas of eel development , we have optimized the isolation of viable nuclei from individual embryos, which can be used for the affordable and large-scale scRNA -seq protocols.
This abstract is based upon work from COST Action EEL SUPPORT, CA22163, supported by COST (European Cooperation in Science and Technology) , and the SALMOCODE project, supported by the Norwegian Seafood Research Fund (FHF grant 901864).