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Development of whole-genome multiplex assays and construction of an integrated genetic map using SSR markers in Senegalese sole

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dc.contributor.author Guerrero-Cózar, Israel
dc.contributor.author Perez-Garcia, Cathaysa
dc.contributor.author Benzekri, Hicham
dc.contributor.author Sánchez, J. J.
dc.contributor.author Seoane, Pedro
dc.contributor.author Cruz, Fernando
dc.contributor.author Gut, Marta
dc.contributor.author Zamorano, Maria Jesus
dc.contributor.author Gonzalo, Claros M.
dc.contributor.author Manchado, Manuel
dc.date.accessioned 2022-06-14T09:05:19Z
dc.date.available 2022-06-14T09:05:19Z
dc.date.issued 2020
dc.identifier.citation Guerrero-Cózar I, Perez-Garcia C, Benzekri H, Sánchez JJ, Seoane P, Cruz F et al. Development of whole-genome multiplex assays and construction of an integrated genetic map using SSR markers in Senegalese sole. Sci Rep. 2020 Dec 14;10(1):21905. DOI:10.1038/s41598-020-78397-w
dc.identifier.issn 2045-2322
dc.identifier.uri http://hdl.handle.net/10230/53486
dc.description.abstract The Senegalese sole (Solea senegalensis) is an economically important flatfish species. In this study, a genome draft was analyzed to identify microsatellite (SSR) markers for whole-genome genotyping. A subset of 224 contigs containing SSRs were preselected and validated by using a de novo female hybrid assembly. Overall, the SSR density in the genome was 886.7 markers per megabase of genomic sequences and the dinucleotide motif was the most abundant (52.4%). In silico comparison identified a set of 108 SSRs (with di-, tetra- or pentanucleotide motifs) widely distributed in the genome and suitable for primer design. A total of 106 markers were structured in thirteen multiplex PCR assays (with up to 10-plex) and the amplification conditions were optimized with a high-quality score. Main genetic diversity statistics and genotyping reliability were assessed. A subset of 40 high polymorphic markers were selected to optimize four supermultiplex PCRs (with up to 11-plex) for pedigree analysis. Theoretical exclusion probabilities and real parentage allocation tests using parent-offspring information confirmed their robustness and effectiveness for parental assignment. These new SSR markers were combined with previously published SSRs (in total 229 makers) to construct a new and improved integrated genetic map containing 21 linkage groups that matched with the expected number of chromosomes. Synteny analysis with respect to C. semilaevis provided new clues on chromosome evolution in flatfish and the formation of metacentric and submetacentric chromosomes in Senegalese sole.
dc.description.sponsorship This study was funded by project RTA2017-00054-C03-01, RTA2017-00054-C03-02 and RTA2017-00054-C03-03 funded from MCIU/AEI/FEDER, UE. IGC is funded by a predoctoral fellowship from INIA
dc.format.mimetype application/pdf
dc.language.iso eng
dc.publisher Nature Research
dc.rights © Israel Guerrero-Cózar et al 2020. This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made
dc.rights.uri https://creativecommons.org/licenses/by/4.0/
dc.subject.other Genòmica
dc.subject.other Genètica
dc.subject.other Llenguados
dc.title Development of whole-genome multiplex assays and construction of an integrated genetic map using SSR markers in Senegalese sole
dc.type info:eu-repo/semantics/article
dc.identifier.doi http://dx.doi.org/10.1038/s41598-020-78397-w
dc.rights.accessRights info:eu-repo/semantics/openAccess
dc.type.version info:eu-repo/semantics/publishedVersion


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