Sequence-based genotyping for marker discovery and co-dominant scoring in germplasm and populations.

Conventional marker-based genotyping platforms are widely available, but not without their limitations. In this context, we developed Sequence-Based Genotyping (SBG), a technology for simultaneous marker discovery and co-dominant scoring, using next-generation sequencing. SBG offers users several ad...

Descripción completa

Guardado en:
Detalles Bibliográficos
Autores principales: Hoa T Truong, A Marcos Ramos, Feyruz Yalcin, Marjo de Ruiter, Hein J A van der Poel, Koen H J Huvenaars, René C J Hogers, Leonora J G van Enckevort, Antoine Janssen, Nathalie J van Orsouw, Michiel J T van Eijk
Formato: article
Lenguaje:EN
Publicado: Public Library of Science (PLoS) 2012
Materias:
R
Q
Acceso en línea:https://doaj.org/article/82ba998d5b8d41808173c5600968d3fa
Etiquetas: Agregar Etiqueta
Sin Etiquetas, Sea el primero en etiquetar este registro!
id oai:doaj.org-article:82ba998d5b8d41808173c5600968d3fa
record_format dspace
spelling oai:doaj.org-article:82ba998d5b8d41808173c5600968d3fa2021-11-18T07:17:23ZSequence-based genotyping for marker discovery and co-dominant scoring in germplasm and populations.1932-620310.1371/journal.pone.0037565https://doaj.org/article/82ba998d5b8d41808173c5600968d3fa2012-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/22662172/?tool=EBIhttps://doaj.org/toc/1932-6203Conventional marker-based genotyping platforms are widely available, but not without their limitations. In this context, we developed Sequence-Based Genotyping (SBG), a technology for simultaneous marker discovery and co-dominant scoring, using next-generation sequencing. SBG offers users several advantages including a generic sample preparation method, a highly robust genome complexity reduction strategy to facilitate de novo marker discovery across entire genomes, and a uniform bioinformatics workflow strategy to achieve genotyping goals tailored to individual species, regardless of the availability of a reference sequence. The most distinguishing features of this technology are the ability to genotype any population structure, regardless whether parental data is included, and the ability to co-dominantly score SNP markers segregating in populations. To demonstrate the capabilities of SBG, we performed marker discovery and genotyping in Arabidopsis thaliana and lettuce, two plant species of diverse genetic complexity and backgrounds. Initially we obtained 1,409 SNPs for arabidopsis, and 5,583 SNPs for lettuce. Further filtering of the SNP dataset produced over 1,000 high quality SNP markers for each species. We obtained a genotyping rate of 201.2 genotypes/SNP and 58.3 genotypes/SNP for arabidopsis (n = 222 samples) and lettuce (n = 87 samples), respectively. Linkage mapping using these SNPs resulted in stable map configurations. We have therefore shown that the SBG approach presented provides users with the utmost flexibility in garnering high quality markers that can be directly used for genotyping and downstream applications. Until advances and costs will allow for routine whole-genome sequencing of populations, we expect that sequence-based genotyping technologies such as SBG will be essential for genotyping of model and non-model genomes alike.Hoa T TruongA Marcos RamosFeyruz YalcinMarjo de RuiterHein J A van der PoelKoen H J HuvenaarsRené C J HogersLeonora J G van EnckevortAntoine JanssenNathalie J van OrsouwMichiel J T van EijkPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 7, Iss 5, p e37565 (2012)
institution DOAJ
collection DOAJ
language EN
topic Medicine
R
Science
Q
spellingShingle Medicine
R
Science
Q
Hoa T Truong
A Marcos Ramos
Feyruz Yalcin
Marjo de Ruiter
Hein J A van der Poel
Koen H J Huvenaars
René C J Hogers
Leonora J G van Enckevort
Antoine Janssen
Nathalie J van Orsouw
Michiel J T van Eijk
Sequence-based genotyping for marker discovery and co-dominant scoring in germplasm and populations.
description Conventional marker-based genotyping platforms are widely available, but not without their limitations. In this context, we developed Sequence-Based Genotyping (SBG), a technology for simultaneous marker discovery and co-dominant scoring, using next-generation sequencing. SBG offers users several advantages including a generic sample preparation method, a highly robust genome complexity reduction strategy to facilitate de novo marker discovery across entire genomes, and a uniform bioinformatics workflow strategy to achieve genotyping goals tailored to individual species, regardless of the availability of a reference sequence. The most distinguishing features of this technology are the ability to genotype any population structure, regardless whether parental data is included, and the ability to co-dominantly score SNP markers segregating in populations. To demonstrate the capabilities of SBG, we performed marker discovery and genotyping in Arabidopsis thaliana and lettuce, two plant species of diverse genetic complexity and backgrounds. Initially we obtained 1,409 SNPs for arabidopsis, and 5,583 SNPs for lettuce. Further filtering of the SNP dataset produced over 1,000 high quality SNP markers for each species. We obtained a genotyping rate of 201.2 genotypes/SNP and 58.3 genotypes/SNP for arabidopsis (n = 222 samples) and lettuce (n = 87 samples), respectively. Linkage mapping using these SNPs resulted in stable map configurations. We have therefore shown that the SBG approach presented provides users with the utmost flexibility in garnering high quality markers that can be directly used for genotyping and downstream applications. Until advances and costs will allow for routine whole-genome sequencing of populations, we expect that sequence-based genotyping technologies such as SBG will be essential for genotyping of model and non-model genomes alike.
format article
author Hoa T Truong
A Marcos Ramos
Feyruz Yalcin
Marjo de Ruiter
Hein J A van der Poel
Koen H J Huvenaars
René C J Hogers
Leonora J G van Enckevort
Antoine Janssen
Nathalie J van Orsouw
Michiel J T van Eijk
author_facet Hoa T Truong
A Marcos Ramos
Feyruz Yalcin
Marjo de Ruiter
Hein J A van der Poel
Koen H J Huvenaars
René C J Hogers
Leonora J G van Enckevort
Antoine Janssen
Nathalie J van Orsouw
Michiel J T van Eijk
author_sort Hoa T Truong
title Sequence-based genotyping for marker discovery and co-dominant scoring in germplasm and populations.
title_short Sequence-based genotyping for marker discovery and co-dominant scoring in germplasm and populations.
title_full Sequence-based genotyping for marker discovery and co-dominant scoring in germplasm and populations.
title_fullStr Sequence-based genotyping for marker discovery and co-dominant scoring in germplasm and populations.
title_full_unstemmed Sequence-based genotyping for marker discovery and co-dominant scoring in germplasm and populations.
title_sort sequence-based genotyping for marker discovery and co-dominant scoring in germplasm and populations.
publisher Public Library of Science (PLoS)
publishDate 2012
url https://doaj.org/article/82ba998d5b8d41808173c5600968d3fa
work_keys_str_mv AT hoattruong sequencebasedgenotypingformarkerdiscoveryandcodominantscoringingermplasmandpopulations
AT amarcosramos sequencebasedgenotypingformarkerdiscoveryandcodominantscoringingermplasmandpopulations
AT feyruzyalcin sequencebasedgenotypingformarkerdiscoveryandcodominantscoringingermplasmandpopulations
AT marjoderuiter sequencebasedgenotypingformarkerdiscoveryandcodominantscoringingermplasmandpopulations
AT heinjavanderpoel sequencebasedgenotypingformarkerdiscoveryandcodominantscoringingermplasmandpopulations
AT koenhjhuvenaars sequencebasedgenotypingformarkerdiscoveryandcodominantscoringingermplasmandpopulations
AT renecjhogers sequencebasedgenotypingformarkerdiscoveryandcodominantscoringingermplasmandpopulations
AT leonorajgvanenckevort sequencebasedgenotypingformarkerdiscoveryandcodominantscoringingermplasmandpopulations
AT antoinejanssen sequencebasedgenotypingformarkerdiscoveryandcodominantscoringingermplasmandpopulations
AT nathaliejvanorsouw sequencebasedgenotypingformarkerdiscoveryandcodominantscoringingermplasmandpopulations
AT michieljtvaneijk sequencebasedgenotypingformarkerdiscoveryandcodominantscoringingermplasmandpopulations
_version_ 1718423675765522432