Genome-wide confirmation of isogenicity of clone founders (G1) in European seabass (Dicentrarchus labrax)

Isogenic clonal lines of fish are a valuable tool for aquaculture-related research, as inbred animals have been in biomedical research, yet to date they are available in only a few species. Although the production of such lines can be achieved in two generations through induced parthenogenesis (either mitotic gynogenesis or androgenesis), challenges such as reduced survival of doubled haploid clone founders and spontaneous, partially heterozygous meiotic gynogenetics (due to non-targeted retention of second polar body in the mitotic gynogenesis process) hamper the successful establishment of such lines. Until recently only small numbers of genetic markers were available for the verification of such lines. Reliable marker technologies are needed for genome-wide screening during development of isogenic lines, and next generation sequencing offers this potential. In the present study, we analysed DNA from 17 putative mitotic gynogenetics (clone founders) of European seabass, using double-digestion restriction-associated DNA sequencing (ddRAD-seq). A total of over 31 million raw sequence reads were produced and assembled into an average of 6,830 unique ddRAD loci. Based on an average of 1,950 polymorphic single nucleotide polymorphism (SNP) loci, 17 out of 18 fish were identified as isogenic (mitotic gynogenetics), while one fish represented a clear case of spontaneous meiotic gynogenesis, with no sire contribution but heterozygous for 49% of informative maternal loci. Although these fish were genotyped first using 12 microsatellite loci which suggested isogenicity of all samples, the single meiotic gynogenetic was only detected with the higher power of genome-wide screening in one fish, proving the efficacy of NGS for this purpose. Provided that the clonal founders are fertile, they will be used for producing isogenic clonal lines in European seabass in the successive generation. Successful establishment of such lines in species of prime commercial interest in Europe is one of the objectives of the AQUAEXCEL2020 as a resource for aquaculture-related research. [Münevver Oral, PhD These: https://hdl.handle.net/1893/24909]