Discovery of SNP markers of red shrimp Aristeus antennatus for population structure in Western Mediterranean Sea

Abstract

Aristeus antennatus is one of the most exploited and economically important resource for fisheries in the Western and Central Mediterranean Sea displaying low population differentiation with mitochondrial and microsatellite markers. The recent development of Genotyping-by-Sequencing (GBS) methods may contribute to the discovery of SNPs and the assessment of genetic differences between populations of this species for fisheries management. Using samples from four geographical sites in Western Mediterranean and Eastern Atlantic, 115,071 putative SNPs were detected. After the stringent quality control measures and the filtering procedure, 232 SNP loci were discovered. Finally, we selected 80 SNP subset panel for Fluidigm Dynamic array application. The results showed significant differentiation among populations from the four sampling sites. Population assignment power and patterns of population differentiation were comparable between the two SNP panels. These markers represent a useful tool for future genetic application of A. antennatus populations.