Discovery of SNP markers of red shrimp Aristeus antennatus for population structure in Western Mediterranean Sea
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TECHNICAL NOTE
Discovery of SNP markers of red shrimp Aristeus antennatus for population structure in Western Mediterranean Sea Gaetano Catanese1,2 · Jean Remi Trotta3 · Mikel Iriondo4 · Antoni Maria Grau5 · Andone Estonba4 Received: 31 March 2020 / Accepted: 29 October 2020 © Springer Nature B.V. 2020
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. Keywords Conservation genetics · Aristeus antennatus · Genotyping-by-sequencing · Single nucleotide polymorphism · SNP selection
Introduction
Electronic supplementary material The online version of this article (https://doi.org/10.1007/s12686-020-01178-0) contains supplementary material, which is available to authorized users. * Gaetano Catanese [email protected] 1
Laboratori d’Investigacions Marines i Aqüicultura (LIMIA), Govern de les Illes Balears, Av. Gabriel Roca 69, 07158 Port d’Andratx, Balearic Islands, Spain
2
INAGEA (INIA-CAIB-UIB), Carr. de Valldemossa, km 7.5, 07122 Palma, Balearic Islands, Spain
3
CNAG‑CRG, Centre for Genomic Regulation (CRG), Barcelona, Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain
4
Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), 48940 Leioa‑Bilbao, Spain
5
Direcció General de Pesca i Medi Marí, Govern de les Illes Balears, Balearic Government, C/ Foners 10, 07006 Palma de Mallorca, Spain
The red shrimp Aristeus antennatus is a demersal crustacean species in temperate waters. The distribution of the species is wider including the entire Mediterranean region, the Atlantic Ocean south to Senegal, and up to North of Portugal (Arrobas and Ribeiro-Cascalho 1987). It inhabits the sandy and muddy bottoms of the continental slope at depths between 500 and 3000 m (Sardá et al. 2003). The red shrimp is one of the most exploited and economically important resource for fisheries in Central Mediterranean Sea and Western Mediterranean (Carbonell et al. 1999). However, all the genetic studies performed
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