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

<h4>Background</h4>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...

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Autores principales:	Camille Lepoittevin, Jean-Marc Frigerio, Pauline Garnier-Géré, Franck Salin, María-Teresa Cervera, Barbara Vornam, Luc Harvengt, Christophe Plomion
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2010
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/3911a40f6fdf4e8cbb449258b6969cd0
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spelling	oai:doaj.org-article:3911a40f6fdf4e8cbb449258b6969cd02021-12-02T20:21:05ZIn vitro vs in silico detected SNPs for the development of a genotyping array: what can we learn from a non-model species?1932-620310.1371/journal.pone.0011034https://doaj.org/article/3911a40f6fdf4e8cbb449258b6969cd02010-06-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/20543950/pdf/?tool=EBIhttps://doaj.org/toc/1932-6203<h4>Background</h4>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 ( approximately 23.8 Gb/C).<h4>Methodology/principal findings</h4>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).<h4>Conclusions/significance</h4>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.Camille LepoittevinJean-Marc FrigerioPauline Garnier-GéréFranck SalinMaría-Teresa CerveraBarbara VornamLuc HarvengtChristophe PlomionPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 5, Iss 6, p e11034 (2010)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Camille Lepoittevin Jean-Marc Frigerio Pauline Garnier-Géré Franck Salin María-Teresa Cervera Barbara Vornam Luc Harvengt Christophe Plomion In vitro vs in silico detected SNPs for the development of a genotyping array: what can we learn from a non-model species?
description	<h4>Background</h4>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 ( approximately 23.8 Gb/C).<h4>Methodology/principal findings</h4>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).<h4>Conclusions/significance</h4>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.
format	article
author	Camille Lepoittevin Jean-Marc Frigerio Pauline Garnier-Géré Franck Salin María-Teresa Cervera Barbara Vornam Luc Harvengt Christophe Plomion
author_facet	Camille Lepoittevin Jean-Marc Frigerio Pauline Garnier-Géré Franck Salin María-Teresa Cervera Barbara Vornam Luc Harvengt Christophe Plomion
author_sort	Camille Lepoittevin
title	In vitro vs in silico detected SNPs for the development of a genotyping array: what can we learn from a non-model species?
title_short	In vitro vs in silico detected SNPs for the development of a genotyping array: what can we learn from a non-model species?
title_full	In vitro vs in silico detected SNPs for the development of a genotyping array: what can we learn from a non-model species?
title_fullStr	In vitro vs in silico detected SNPs for the development of a genotyping array: what can we learn from a non-model species?
title_full_unstemmed	In vitro vs in silico detected SNPs for the development of a genotyping array: what can we learn from a non-model species?
title_sort	in vitro vs in silico detected snps for the development of a genotyping array: what can we learn from a non-model species?
publisher	Public Library of Science (PLoS)
publishDate	2010
url	https://doaj.org/article/3911a40f6fdf4e8cbb449258b6969cd0
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In vitro vs in silico detected SNPs for the development of a genotyping array: what can we learn from a non-model species?

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