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A Useful SNP Panel to Distinguish Two Cockle Species, Cerastoderma edule and C. glaucum, Co-Occurring in Some European Beds, and Their Putative Hybrids

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Department of Zoology, Genetics and Physical Anthropology, ACUIGEN Group, Faculty of Veterinary, Universidade de Santiago de Compostela, Campus of Lugo, 27002 Lugo, Spain
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Centro de Investigacións Mariñas (CIMA), Consellería do Mar, Xunta de Galicia, 36620 Vilanova de Arousa, Spain
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Department of Zoology, Genetics and Physical Anthropology, Mobile Genomes and Disease Group, CIMUS, Universidade de Santiago de Compostela, Campus of Santiago de Compostela, 15706 Santiago de Compostela, Spain
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Department of Life Sciences, University of Alcalá, 28871 Alcalá de Henares, Spain
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Research Centre for Experimental Marine Biology and Biotechnology (PIE), University of the Basque Country (UPV/EHU), 48620 Plentzia, Basque Country, Spain
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Instituto de Acuicultura, Universidade de Santiago de Compostela, 15705 Santiago de Compostela, Spain
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Author to whom correspondence should be addressed.
Present Address: Dipartimento di Scienze della Vita e Biotecnologia (SVeB), Università degli Studi di Ferrara, via Luigi Borsari, 46–44121 Ferrara, Italy.
Genes 2019, 10(10), 760; https://doi.org/10.3390/genes10100760
Received: 29 August 2019 / Revised: 25 September 2019 / Accepted: 26 September 2019 / Published: 27 September 2019
(This article belongs to the Special Issue Genetic Diversity of Marine Populations)
Cockles are highly appreciated mollusks and provide important services in coastal areas. The two European species, edible (Cerastoderma edule) and lagoon (Cerastoderma glaucum) cockles, are not easily distinguishable, especially when young. Interestingly, the species show different resistance to Marteilia cochillia, the parasite responsible for marteiliosis outbreaks, which is devastating cockle production in some areas. C. edule is severely affected by the parasite, while C. glaucum seems to be resistant, although underlying reasons are still unknown. Hybrids between both species might be interesting to introgress allelic variants responsible for tolerance, either naturally or through artificial selection, from lagoon into edible cockle. Here, we used 2b restriction site-associated DNA sequencing (2b–RAD) to identify single nucleotide polymorphisms (SNP) diagnostic for cockle discrimination (fixed for alternative allelic variants). Among the nine diagnostic SNPs selected, seven were validated using a SNaPshot assay in samples covering most of the distribution range of both species. The validated SNPs were used to check cockles that were suggested to be hybrids by a claimed diagnostic tool based on the internal transcribed spacers of the ribosomal RNA. Although these were shown to be false positives, we cannot rule out the fact that hybrids can occur and be viable. The SNP tool here developed will be valuable for their identification and management. View Full-Text
Keywords: 2b–RAD; cockles; diagnostic SNPs; hybrids; New Generation Sequencing (NGS); SNaPshot; wildlife forensic 2b–RAD; cockles; diagnostic SNPs; hybrids; New Generation Sequencing (NGS); SNaPshot; wildlife forensic
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Maroso, F.; Pérez de Gracia, C.; Iglesias, D.; Cao, A.; Díaz, S.; Villalba, A.; Vera, M.; Martínez, P. A Useful SNP Panel to Distinguish Two Cockle Species, Cerastoderma edule and C. glaucum, Co-Occurring in Some European Beds, and Their Putative Hybrids. Genes 2019, 10, 760.

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