SNPSelect: A scalable and flexible targeted sequence-based genotyping solution.
In plant breeding the use of molecular markers has resulted in tremendous improvement of the speed with which new crop varieties are introduced into the market. Single Nucleotide Polymorphism (SNP) genotyping is routinely used for association studies, Linkage Disequilibrium (LD) and Quantitative Tra...
| Main Authors: | , , , , , , |
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| Format: | Article |
| Language: | English |
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Public Library of Science (PLoS)
2018-01-01
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| Series: | PLoS ONE |
| Online Access: | http://europepmc.org/articles/PMC6185863?pdf=render |
| _version_ | 1819241215221039104 |
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| author | René C J Hogers Marjo de Ruiter Koen H J Huvenaars Hein van der Poel Antoine Janssen Michiel J T van Eijk Nathalie J van Orsouw |
| author_facet | René C J Hogers Marjo de Ruiter Koen H J Huvenaars Hein van der Poel Antoine Janssen Michiel J T van Eijk Nathalie J van Orsouw |
| author_sort | René C J Hogers |
| collection | DOAJ |
| description | In plant breeding the use of molecular markers has resulted in tremendous improvement of the speed with which new crop varieties are introduced into the market. Single Nucleotide Polymorphism (SNP) genotyping is routinely used for association studies, Linkage Disequilibrium (LD) and Quantitative Trait Locus (QTL) mapping studies, marker-assisted backcrosses and validation of large numbers of novel SNPs. Here we present the KeyGene SNPSelect technology, a scalable and flexible multiplexed, targeted sequence-based, genotyping solution. The multiplex composition of SNPSelect assays can be easily changed between experiments by adding or removing loci, demonstrating their content flexibility. To demonstrate this versatility, we first designed a 1,056-plex maize assay and genotyped a total of 374 samples originating from an F2 and a Recombinant Inbred Line (RIL) population and a maize germplasm collection. Next, subsets of the most informative SNP loci were assembled in 384-plex and 768-plex assays for further genotyping. Indeed, selection of the most informative SNPs allows cost-efficient yet highly informative genotyping in a custom-made fashion, with average call rates between 88.1% (1,056-plex assay) and 99.4% (384-plex assay), and average reproducibility rates between duplicate samples ranging from 98.2% (1056-plex assay) to 99.9% (384-plex assay). The SNPSelect workflow can be completed from a DNA sample to a genotype dataset in less than three days. We propose SNPSelect as an attractive and competitive genotyping solution to meet the targeted genotyping needs in fields such as plant breeding. |
| first_indexed | 2024-12-23T14:20:22Z |
| format | Article |
| id | doaj.art-91ab404ff9fb40d0a8d89a6d4c14806b |
| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2024-12-23T14:20:22Z |
| publishDate | 2018-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj.art-91ab404ff9fb40d0a8d89a6d4c14806b2022-12-21T17:43:49ZengPublic Library of Science (PLoS)PLoS ONE1932-62032018-01-011310e020557710.1371/journal.pone.0205577SNPSelect: A scalable and flexible targeted sequence-based genotyping solution.René C J HogersMarjo de RuiterKoen H J HuvenaarsHein van der PoelAntoine JanssenMichiel J T van EijkNathalie J van OrsouwIn plant breeding the use of molecular markers has resulted in tremendous improvement of the speed with which new crop varieties are introduced into the market. Single Nucleotide Polymorphism (SNP) genotyping is routinely used for association studies, Linkage Disequilibrium (LD) and Quantitative Trait Locus (QTL) mapping studies, marker-assisted backcrosses and validation of large numbers of novel SNPs. Here we present the KeyGene SNPSelect technology, a scalable and flexible multiplexed, targeted sequence-based, genotyping solution. The multiplex composition of SNPSelect assays can be easily changed between experiments by adding or removing loci, demonstrating their content flexibility. To demonstrate this versatility, we first designed a 1,056-plex maize assay and genotyped a total of 374 samples originating from an F2 and a Recombinant Inbred Line (RIL) population and a maize germplasm collection. Next, subsets of the most informative SNP loci were assembled in 384-plex and 768-plex assays for further genotyping. Indeed, selection of the most informative SNPs allows cost-efficient yet highly informative genotyping in a custom-made fashion, with average call rates between 88.1% (1,056-plex assay) and 99.4% (384-plex assay), and average reproducibility rates between duplicate samples ranging from 98.2% (1056-plex assay) to 99.9% (384-plex assay). The SNPSelect workflow can be completed from a DNA sample to a genotype dataset in less than three days. We propose SNPSelect as an attractive and competitive genotyping solution to meet the targeted genotyping needs in fields such as plant breeding.http://europepmc.org/articles/PMC6185863?pdf=render |
| spellingShingle | René C J Hogers Marjo de Ruiter Koen H J Huvenaars Hein van der Poel Antoine Janssen Michiel J T van Eijk Nathalie J van Orsouw SNPSelect: A scalable and flexible targeted sequence-based genotyping solution. PLoS ONE |
| title | SNPSelect: A scalable and flexible targeted sequence-based genotyping solution. |
| title_full | SNPSelect: A scalable and flexible targeted sequence-based genotyping solution. |
| title_fullStr | SNPSelect: A scalable and flexible targeted sequence-based genotyping solution. |
| title_full_unstemmed | SNPSelect: A scalable and flexible targeted sequence-based genotyping solution. |
| title_short | SNPSelect: A scalable and flexible targeted sequence-based genotyping solution. |
| title_sort | snpselect a scalable and flexible targeted sequence based genotyping solution |
| url | http://europepmc.org/articles/PMC6185863?pdf=render |
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