Zebrafish as an Anti-Isogenic Vertebrate Model and What It Reveals About Genetic Background and Reproducibility

Isogenic lines, understood here as lines approaching genome-wide homozygosity while remaining fertile and stable across successive generations, have transformed genetics and toxicology in vertebrate models. In zebrafish (Danio rerio), however, more than four decades of gynogenesis, clonal line production and inbreeding have not yielded stable, broadly usable fully homozygous resources. We argue that, in practice, this reflects biological constraints rather than merely technical limitations. Historical, genomic and developmental evidence points to three major barriers: polygenic and environmentally sensitive sex determination, strong dependence on maternal factors during early development, and a structurally dynamic genome shaped by duplication, copy-number variation and substrain divergence. Together, these features make extreme homozygosity biologically fragile, with recurrent sex-ratio bias, infertility and line collapse, and they support experimental strategies that treat genetic background as a variable to be reported, tested and exploited rather than idealized away.