SNPs for thornback ray Raja clavata, validated from genotyped individuals

Date 2019-11-29
Author(s) Le Cam SabrinaORCID1, Bidault Adeline2, Charrier GregoryORCID2, Cornette Florence1, Lamy Jean-BaptisteORCID1, Lapegue SylvieORCID1, Lorance PascalORCID1, Marandel FlorianneORCID1, Trenkel VerenaORCID1
Affiliation(s) 1 : Ifremer, France
2 : Université de Brest, France
DOI 10.17882/70546
Publisher SEANOE
Keyword(s) thornback ray, Raja clavata, SNP, DNA sequences, population genetics, close-kin mark-recapture, DNA chip, Bay of Biscay
Abstract

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

Licence CC-BY-SA
Acknowledgements 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
Data
File Size Format Processing Access
DNA sequences for developping 9120 SNP markers 2 MB CSV Processed data Open access
Call frequency and minor allel frequency by SNP, based on genotyping of 7746 samples 273 KB CSV Processed data Open access
Data description 1 KB TEXTE Open access
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How to cite 

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