Mapping causal mutations by exome sequencing in a wheat TILLING population: a tall mutant case study
Forward genetic screens of induced mutant plant populations are powerful tools to identify genes underlying phenotypes of interest. Using traditional techniques, mapping causative mutations from forward screens is a lengthy, multi-step process, requiring the identification of a broad genetic region...
| Autores principales: | , , , , , |
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| Formato: | info:ar-repo/semantics/artículo |
| Lenguaje: | Inglés |
| Publicado: |
Springer
2019
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| Materias: | |
| Acceso en línea: | http://hdl.handle.net/20.500.12123/4462 https://doi.org/10.1007/s00438-017-1401-6 |
| _version_ | 1855035327775768576 |
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| author | Mo, Youngjun Howell, Tyson Vasquez Gross, Hans De Haro, Luis Alejandro Dubcovsky, Jorge Pearce, Stephen |
| author_browse | De Haro, Luis Alejandro Dubcovsky, Jorge Howell, Tyson Mo, Youngjun Pearce, Stephen Vasquez Gross, Hans |
| author_facet | Mo, Youngjun Howell, Tyson Vasquez Gross, Hans De Haro, Luis Alejandro Dubcovsky, Jorge Pearce, Stephen |
| author_sort | Mo, Youngjun |
| collection | INTA Digital |
| description | Forward genetic screens of induced mutant plant populations are powerful tools to identify genes underlying phenotypes of interest. Using traditional techniques, mapping causative mutations from forward screens is a lengthy, multi-step process, requiring the identification of a broad genetic region followed by candidate gene sequencing to characterize the causal variant. Mapping by whole genome sequencing accelerates the identification of causal mutations by simultaneously defining a mapping region and providing information on the induced genetic variants. In wheat, although the availability of a high-quality draft genome assembly facilitates mapping and mutation calling, whole genome resequencing remains prohibitively expensive due to its large genome. In the current study, we used exome sequencing as a complexity reduction strategy to detect mutations associated with a target phenotype. In a segregating wheat EMS population, we identified a clear peak region on chromosome arm 4BS associated with increased plant height. Although none of the significant SNPs seemed causative for the mutant phenotype, they were sufficient to identify a linked ~ 1.9 Mb deletion encompassing nine genes. These genes included Rht-B1, which is known to have a strong effect on plant height and is a strong candidate for the observed phenotype. We performed simulation experiments to determine the impacts of sequencing depth and bulk size and discuss the importance of considering each factor when designing mapping-by-sequencing experiments in wheat. This approach can accelerate the identification of candidate causal point mutations or linked deletions underlying important phenotypes. |
| format | info:ar-repo/semantics/artículo |
| id | INTA4462 |
| institution | Instituto Nacional de Tecnología Agropecuaria (INTA -Argentina) |
| language | Inglés |
| publishDate | 2019 |
| publishDateRange | 2019 |
| publishDateSort | 2019 |
| publisher | Springer |
| publisherStr | Springer |
| record_format | dspace |
| spelling | INTA44622019-02-18T18:27:37Z Mapping causal mutations by exome sequencing in a wheat TILLING population: a tall mutant case study Mo, Youngjun Howell, Tyson Vasquez Gross, Hans De Haro, Luis Alejandro Dubcovsky, Jorge Pearce, Stephen Wheat Mutation Trigo Triticum Aestivum Mutación Rht1 Mutation Mapping Exome Capture Forward genetic screens of induced mutant plant populations are powerful tools to identify genes underlying phenotypes of interest. Using traditional techniques, mapping causative mutations from forward screens is a lengthy, multi-step process, requiring the identification of a broad genetic region followed by candidate gene sequencing to characterize the causal variant. Mapping by whole genome sequencing accelerates the identification of causal mutations by simultaneously defining a mapping region and providing information on the induced genetic variants. In wheat, although the availability of a high-quality draft genome assembly facilitates mapping and mutation calling, whole genome resequencing remains prohibitively expensive due to its large genome. In the current study, we used exome sequencing as a complexity reduction strategy to detect mutations associated with a target phenotype. In a segregating wheat EMS population, we identified a clear peak region on chromosome arm 4BS associated with increased plant height. Although none of the significant SNPs seemed causative for the mutant phenotype, they were sufficient to identify a linked ~ 1.9 Mb deletion encompassing nine genes. These genes included Rht-B1, which is known to have a strong effect on plant height and is a strong candidate for the observed phenotype. We performed simulation experiments to determine the impacts of sequencing depth and bulk size and discuss the importance of considering each factor when designing mapping-by-sequencing experiments in wheat. This approach can accelerate the identification of candidate causal point mutations or linked deletions underlying important phenotypes. Instituto de Biotecnología Fil: Mo, Youngjun. University of California. Department of Plant Sciences; Estados Unidos Fil: Howell, Tyson. University of California. Department of Plant Sciences; Estados Unidos Fil: Vasquez Gross, Hans. University of California. Department of Plant Sciences; Estados Unidos Fil: De Haro, Luis Alejandro. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; Argentina Fil: Dubcovsky, Jorge. University of California. Department of Plant Sciences; Estados Unidos. Howard Hughes Medical Institute; Estados Unidos Fil: Pearce, Stephen. Colorado State University. Department of Soil and Crop Sciences; Estados Unidos 2019-02-18T18:21:21Z 2019-02-18T18:21:21Z 2018-04 info:ar-repo/semantics/artículo info:eu-repo/semantics/article info:eu-repo/semantics/publishedVersion http://hdl.handle.net/20.500.12123/4462 1617-4615 1617-4623 (Online) https://doi.org/10.1007/s00438-017-1401-6 eng info:eu-repo/semantics/openAccess http://creativecommons.org/licenses/by-nc-sa/4.0/ Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0) application/pdf Springer Molecular genetics and genomics 293 (2) : 463–477. (April 2018) |
| spellingShingle | Wheat Mutation Trigo Triticum Aestivum Mutación Rht1 Mutation Mapping Exome Capture Mo, Youngjun Howell, Tyson Vasquez Gross, Hans De Haro, Luis Alejandro Dubcovsky, Jorge Pearce, Stephen Mapping causal mutations by exome sequencing in a wheat TILLING population: a tall mutant case study |
| title | Mapping causal mutations by exome sequencing in a wheat TILLING population: a tall mutant case study |
| title_full | Mapping causal mutations by exome sequencing in a wheat TILLING population: a tall mutant case study |
| title_fullStr | Mapping causal mutations by exome sequencing in a wheat TILLING population: a tall mutant case study |
| title_full_unstemmed | Mapping causal mutations by exome sequencing in a wheat TILLING population: a tall mutant case study |
| title_short | Mapping causal mutations by exome sequencing in a wheat TILLING population: a tall mutant case study |
| title_sort | mapping causal mutations by exome sequencing in a wheat tilling population a tall mutant case study |
| topic | Wheat Mutation Trigo Triticum Aestivum Mutación Rht1 Mutation Mapping Exome Capture |
| url | http://hdl.handle.net/20.500.12123/4462 https://doi.org/10.1007/s00438-017-1401-6 |
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