High throughput SNP discovery and genotyping in hexaploid wheat.
Because of their abundance and their amenability to high-throughput genotyping techniques, Single Nucleotide Polymorphisms (SNPs) are powerful tools for efficient genetics and genomics studies, including characterization of genetic resources, genome-wide association studies and genomic selection. In...
| Main Authors: | , , , , , , , , , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
Public Library of Science (PLoS)
2018-01-01
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| Series: | PLoS ONE |
| Online Access: | http://europepmc.org/articles/PMC5749704?pdf=render |
| _version_ | 1819078938487422976 |
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| author | Hélène Rimbert Benoît Darrier Julien Navarro Jonathan Kitt Frédéric Choulet Magalie Leveugle Jorge Duarte Nathalie Rivière Kellye Eversole International Wheat Genome Sequencing Consortium Jacques Le Gouis on behalf The BreedWheat Consortium Alessandro Davassi François Balfourier Marie-Christine Le Paslier Aurélie Berard Dominique Brunel Catherine Feuillet Charles Poncet Pierre Sourdille Etienne Paux |
| author_facet | Hélène Rimbert Benoît Darrier Julien Navarro Jonathan Kitt Frédéric Choulet Magalie Leveugle Jorge Duarte Nathalie Rivière Kellye Eversole International Wheat Genome Sequencing Consortium Jacques Le Gouis on behalf The BreedWheat Consortium Alessandro Davassi François Balfourier Marie-Christine Le Paslier Aurélie Berard Dominique Brunel Catherine Feuillet Charles Poncet Pierre Sourdille Etienne Paux |
| author_sort | Hélène Rimbert |
| collection | DOAJ |
| description | Because of their abundance and their amenability to high-throughput genotyping techniques, Single Nucleotide Polymorphisms (SNPs) are powerful tools for efficient genetics and genomics studies, including characterization of genetic resources, genome-wide association studies and genomic selection. In wheat, most of the previous SNP discovery initiatives targeted the coding fraction, leaving almost 98% of the wheat genome largely unexploited. Here we report on the use of whole-genome resequencing data from eight wheat lines to mine for SNPs in the genic, the repetitive and non-repetitive intergenic fractions of the wheat genome. Eventually, we identified 3.3 million SNPs, 49% being located on the B-genome, 41% on the A-genome and 10% on the D-genome. We also describe the development of the TaBW280K high-throughput genotyping array containing 280,226 SNPs. Performance of this chip was examined by genotyping a set of 96 wheat accessions representing the worldwide diversity. Sixty-nine percent of the SNPs can be efficiently scored, half of them showing a diploid-like clustering. The TaBW280K was proven to be a very efficient tool for diversity analyses, as well as for breeding as it can discriminate between closely related elite varieties. Finally, the TaBW280K array was used to genotype a population derived from a cross between Chinese Spring and Renan, leading to the construction a dense genetic map comprising 83,721 markers. The results described here will provide the wheat community with powerful tools for both basic and applied research. |
| first_indexed | 2024-12-21T19:21:03Z |
| format | Article |
| id | doaj.art-ad7dcfe39d554d579ba9ca2d94ea012b |
| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2024-12-21T19:21:03Z |
| publishDate | 2018-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj.art-ad7dcfe39d554d579ba9ca2d94ea012b2022-12-21T18:52:56ZengPublic Library of Science (PLoS)PLoS ONE1932-62032018-01-01131e018632910.1371/journal.pone.0186329High throughput SNP discovery and genotyping in hexaploid wheat.Hélène RimbertBenoît DarrierJulien NavarroJonathan KittFrédéric ChouletMagalie LeveugleJorge DuarteNathalie RivièreKellye EversoleInternational Wheat Genome Sequencing ConsortiumJacques Le Gouison behalf The BreedWheat ConsortiumAlessandro DavassiFrançois BalfourierMarie-Christine Le PaslierAurélie BerardDominique BrunelCatherine FeuilletCharles PoncetPierre SourdilleEtienne PauxBecause of their abundance and their amenability to high-throughput genotyping techniques, Single Nucleotide Polymorphisms (SNPs) are powerful tools for efficient genetics and genomics studies, including characterization of genetic resources, genome-wide association studies and genomic selection. In wheat, most of the previous SNP discovery initiatives targeted the coding fraction, leaving almost 98% of the wheat genome largely unexploited. Here we report on the use of whole-genome resequencing data from eight wheat lines to mine for SNPs in the genic, the repetitive and non-repetitive intergenic fractions of the wheat genome. Eventually, we identified 3.3 million SNPs, 49% being located on the B-genome, 41% on the A-genome and 10% on the D-genome. We also describe the development of the TaBW280K high-throughput genotyping array containing 280,226 SNPs. Performance of this chip was examined by genotyping a set of 96 wheat accessions representing the worldwide diversity. Sixty-nine percent of the SNPs can be efficiently scored, half of them showing a diploid-like clustering. The TaBW280K was proven to be a very efficient tool for diversity analyses, as well as for breeding as it can discriminate between closely related elite varieties. Finally, the TaBW280K array was used to genotype a population derived from a cross between Chinese Spring and Renan, leading to the construction a dense genetic map comprising 83,721 markers. The results described here will provide the wheat community with powerful tools for both basic and applied research.http://europepmc.org/articles/PMC5749704?pdf=render |
| spellingShingle | Hélène Rimbert Benoît Darrier Julien Navarro Jonathan Kitt Frédéric Choulet Magalie Leveugle Jorge Duarte Nathalie Rivière Kellye Eversole International Wheat Genome Sequencing Consortium Jacques Le Gouis on behalf The BreedWheat Consortium Alessandro Davassi François Balfourier Marie-Christine Le Paslier Aurélie Berard Dominique Brunel Catherine Feuillet Charles Poncet Pierre Sourdille Etienne Paux High throughput SNP discovery and genotyping in hexaploid wheat. PLoS ONE |
| title | High throughput SNP discovery and genotyping in hexaploid wheat. |
| title_full | High throughput SNP discovery and genotyping in hexaploid wheat. |
| title_fullStr | High throughput SNP discovery and genotyping in hexaploid wheat. |
| title_full_unstemmed | High throughput SNP discovery and genotyping in hexaploid wheat. |
| title_short | High throughput SNP discovery and genotyping in hexaploid wheat. |
| title_sort | high throughput snp discovery and genotyping in hexaploid wheat |
| url | http://europepmc.org/articles/PMC5749704?pdf=render |
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