seanoe:70546 LORANCE Pascal Ifremer, France 2022-01-28 ISO 19115:2003/19139 1.0 SNPs for thornback ray Raja clavata, validated from genotyped individuals 2019-11-29 2022-01-28 Le Cam Sabrina, Bidault Adeline, Charrier Gregory, Cornette Florence, Lamy Jean-Baptiste, Lapegue Sylvie, Lorance Pascal, Marandel Florianne, Trenkel Verena (2019). SNPs for thornback ray Raja clavata, validated from genotyped individuals. SEANOE. https://doi.org/10.17882/70546 We developed a panel of single nucleotide polymorphism (SNP) markers for thornback ray Raja clavata using a RADSeq protocole. Demultiplexed sequences were aligned to the genome of Leucoraja erinacea which was used as reference genome. From an initial set of 389 483 putative SNPs, 7741 SNPs with the largest minor allele frequency were selected for implementation on an Infinium® XT iSelect-96 SNP-array implemented by LABOGENA DNA. For the array, SNPs [T/C] and [T/G] were replaced by those from the complementary strand [A/G] and [A/C] respectively. For some SNPs, a second SNP was found in the 50 nucleotide bases flanking sequence. In these cases, two SNP probes were developed with each of the two alleles of the second SNP. A SNP probe naming convention was adopted to identify these pairs of probes corresponding to the same SNP locus: “MAJ” or “MIN” followed by the corresponding base was included in the probe name. For some of these pairs, only one of the two markers could be developed, resulting in a total set of 9120 SNP probes, including 6360 single SNP probes, 10 MAJ or MIN probes for which a single probe was successfully developed, and 1375 pairs of probes with MAJ and MIN versions. The 9120 SNP genotypes were then scored using the clustering algorithm implemented in the Illumina® GenomeStudio Genotyping Analysis Module v2.0.3 for 7726 individual samples, including duplicates, mostly from the Bay of Biscay but also from the Mediterranean Sea and West Iberia. Overall, 1643 SNPs failed to be genotyped in all individuals, for 319 markers the minor allele was not found and 7158 markers (including 1974 for 987 MIN-MAJ pairs) produced bi-allelic genotypes. The majority of these SNPs had a minor allele frequency between 0.1 and 0.5. The MIN-MAJ probes can be used for quality checking the genotyping results The creation of this set of SNP probes was funded by French “Agence Nationale de la Recherche” (ANR) under the GenoPopTaille project (ANR-14-CE02-0006-01) and from the European Union's Horizon 2020 research and innovation programme under the grant agreement No. 773713 LE CAM Sabrina Ifremer, France BIDAULT Adeline Université de Brest, France CHARRIER Gregory Université de Brest, France CORNETTE Florence Ifremer, France LAMY Jean-Baptiste Ifremer, France LAPEGUE Sylvie Ifremer, France LORANCE Pascal Ifremer, France MARANDEL Florianne Ifremer, France TRENKEL Verena Ifremer, France SEANOE https://www.seanoe.org/data/00593/70546/illustration.gif thornback ray Raja clavata SNP DNA sequences population genetics close-kin mark-recapture DNA chip Bay of Biscay Fisheries and aquaculture H2020 PANDORA (Agreement: 773713) Bioinformatics ODATIS aggregation parameters and Essential Variable names 2024-09-16 geonetwork.thesaurus.external.theme.NVS.OD1 Fisheries and aquaculture SeaDataNet Parameter Disciplines 2021-04-07 geonetwork.thesaurus.external.parameter.NVS.P08 /Observational data/in-situ Type de jeux de donnée ODATIS 2024-10-15 geonetwork.thesaurus.local.theme.type_jeux_donnee CC-BY-SA (Creative Commons - Attribution, Sharing under the same conditions) Close-kin mark–recapture abundance estimation: practical insights and lessons learned 2022 Oxford University Press (OUP) TRENKEL VERENA CHARRIER GREGORY LORANCE PASCAL BRAVINGTON MARK V 10.1093/icesjms/fsac002 Data for CKMR abundance estimation for thornback ray (Raja clavata) in the central Bay of Biscay 2021 SEANOE Trenkel Verena Charrier Gregory Lorance Pascal 10.17882/84524 SNPs for thornback ray Raja clavata used for identifying sex-linked SNPs and carrying out sex assignment 2020 SEANOE Trenkel Verena Lorance Pascal 10.17882/74390 10.18142/11 10.18142/8 10.18142/17 oceans 26.0 -29.0 35.0 52.0 CSV TEXTE https://www.seanoe.org/data/00593/70546/data/68714.csv WWW:DOWNLOAD-1.0-link--download Processed data DNA sequences for developping 9120 SNP markers - 2 MB https://www.seanoe.org/data/00593/70546/data/68715.csv WWW:DOWNLOAD-1.0-link--download Processed data Call frequency and minor allel frequency by SNP, based on genotyping of 7746 samples - 273 KB https://www.seanoe.org/data/00593/70546/data/68857.txt WWW:DOWNLOAD-1.0-link--download Data description - 1 KB https://doi.org/10.17882/70546 WWW:LINK-1.0-http--metadata-URL DOI of the product https://www.seanoe.org/data/00593/70546/ rel-canonical Seanoe