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<em>In vitro vs in silico</em> detected SNPs for the development of a genotyping array : what can we learn from a non-model species?

hal.structure.identifierBiodiversité, Gènes & Communautés [BioGeCo]
hal.structure.identifierInstitut Technologique Forêt Cellulose Bois-construction Ameublement [FCBA]
dc.contributor.authorLEPOITTEVIN, Camille
hal.structure.identifierBiodiversité, Gènes & Communautés [BioGeCo]
dc.contributor.authorFRIGERIO, Jean-Marc
hal.structure.identifierBiodiversité, Gènes & Communautés [BioGeCo]
dc.contributor.authorGARNIER‐GÉRÉ, Pauline
hal.structure.identifierBiodiversité, Gènes & Communautés [BioGeCo]
dc.contributor.authorSALIN, Franck
hal.structure.identifierInstituto Nacional de Investigación y Tecnología Agraria y Alimentaria = National Institute for Agricultural and Food Research and Technology [INIA]
dc.contributor.authorCERVERA, María-Teresa
hal.structure.identifierGeorg-August-University = Georg-August-Universität Göttingen
dc.contributor.authorVORNAM, Barbara
hal.structure.identifierInstitut Technologique Forêt Cellulose Bois-construction Ameublement [FCBA]
dc.contributor.authorHARVENGT, Luc
hal.structure.identifierBiodiversité, Gènes & Communautés [BioGeCo]
dc.contributor.authorPLOMION, Christophe
dc.date.issued2010
dc.identifier.issn1932-6203
dc.description.abstractEnBackground: There is considerable interest in the high-throughput discovery and genotyping of single nucleotide polymorphisms (SNPs) to accelerate genetic mapping and enable association studies. This study provides an assessment of EST-derived and resequencing-derived SNP quality in maritime pine (Pinus pinaster Ait.), a conifer characterized by a huge genome size (~23.8 Gb/C). Methodology/Principal Findings: A 384-SNPs GoldenGate genotyping array was built from i/ 184 SNPs originally detected in a set of 40 re-sequenced candidate genes (in vitro SNPs), chosen on the basis of functionality scores, presence of neighboring polymorphisms, minor allele frequencies and linkage disequilibrium and ii/ 200 SNPs screened from ESTs (in silico SNPs) selected based on the number of ESTs used for SNP detection, the SNP minor allele frequency and the quality of SNP flanking sequences. The global success rate of the assay was 66.9%, and a conversion rate (considering only polymorphic SNPs) of 51% was achieved. In vitro SNPs showed significantly higher genotyping-success and conversion rates than in silico SNPs (+11.5% and +18.5%, respectively). The reproducibility was 100%, and the genotyping error rate very low (0.54%, dropping down to 0.06% when removing four SNPs showing elevated error rates). Conclusions/Significance: This study demonstrates that ESTs provide a resource for SNP identification in non-model species, which do not require any additional bench work and little bio-informatics analysis. However, the time and cost benefits of in silico SNPs are counterbalanced by a lower conversion rate than in vitro SNPs. This drawback is acceptable for population-based experiments, but could be dramatic in experiments involving samples from narrow genetic backgrounds. In addition, we showed that both the visual inspection of genotyping clusters and the estimation of a per SNP error rate should help identify markers that are not suitable to the GoldenGate technology in species characterized by a large and complex genome.
dc.language.isoen
dc.publisherPublic Library of Science
dc.title.en<em>In vitro vs in silico</em> detected SNPs for the development of a genotyping array : what can we learn from a non-model species?
dc.typeArticle de revue
dc.identifier.doi10.1371/journal.pone.0011034
dc.subject.halSciences du Vivant [q-bio]/Biologie cellulaire
bordeaux.journalPLoS ONE
bordeaux.page9 p.
bordeaux.volume5
bordeaux.issue6
bordeaux.peerReviewedoui
hal.identifierhal-02662512
hal.version1
hal.origin.linkhttps://hal.archives-ouvertes.fr//hal-02662512v1
bordeaux.COinSctx_ver=Z39.88-2004&amp;rft_val_fmt=info:ofi/fmt:kev:mtx:journal&amp;rft.jtitle=PLoS%20ONE&amp;rft.date=2010&amp;rft.volume=5&amp;rft.issue=6&amp;rft.spage=9%20p.&amp;rft.epage=9%20p.&amp;rft.eissn=1932-6203&amp;rft.issn=1932-6203&amp;rft.au=LEPOITTEVIN,%20Camille&amp;FRIGERIO,%20Jean-Marc&amp;GARNIER%E2%80%90G%C3%89R%C3%89,%20Pauline&amp;SALIN,%20Franck&amp;CERVERA,%20Mar%C3%ADa-Teresa&amp;rft.genre=article


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