A non-invasive method to genotype cephalopod sex by quantitative PCR

Summary: Coleoid cephalopods (cuttlefish, octopus, and squid) are emerging model organisms in neuroscience, development, and evolutionary biology and are of major economic importance in global fisheries. However, they are notoriously difficult and expensive to culture. The ability to determine sex early in development would enable more efficient and sustainable population management in both laboratory and wild settings. Here, we report a non-invasive method to genotype the sex of dwarf cuttlefish (Ascarosepion bandense) as young as 3 h post-hatching using a skin swab and quantitative PCR assay, which detects a 2-fold dosage difference between ZZ and Z0 sex chromosomes of males and females, respectively. We also report validated primers for four additional cephalopod research species with assembled genomes and for two wild-caught species of economic value using low-coverage whole genome sequencing data. This method enables accurate, non-invasive sex determination from hatchlings to adults across cephalopods, independent of genome quality or availability.