Tilapia skin mucus swabs for ddRAD and the major sex determining locus in GIFT tilapia

Skin mucus swabs have been used as a source for fish DNA in many targeted locus PCR-based studies, but their suitability for assaying genome wide variability through RADseq and related next generation sequencing methodologies has not been examined. We extracted genomic DNA from mucus (collected from skin swabs using filter paper), muscle and fin samples of two Nile tilapia and performed double-digest restriction-site associated DNA (ddRAD) sequencing. The results indicate that DNA derived from skin mucus swabs can be reliably used for genotyping by sequencing projects for tilapia and is likely to be much more widely applicable. Different major sex-determining loci have been detected in tilapia. The ‘genetically improved farmed tilapia’ (GIFT) stock, founded from multiple Nile tilapia (Oreochromis niloticus) populations, is a key resource for tilapia aquaculture. The main sex-determining loci present in GIFT fish are unknown. A bulk segregant analysis (BSA) version of double-digest restriction-site associated DNA sequencing (BSA-ddRADseq) was used to detect and position sex-linked single nucleotide polymorphism (SNP) markers in 19 GIFT stock pedigrees and two Stirling stock pedigrees. Phenotypic sex in Stirling families showed strong association with LG1 (previously known), whereas SNPs located in LG23 showed clear association with sex in all 19 GIFT families. No other genomic regions linked to sex-determination were apparent.