An epigenetic pathway in rice connects genetic variation to anaerobic germination and seedling establishment
Rice production is shifting from transplanting seedlings to direct sowing of seeds. Following heavy rains, directly sown seeds may need to germinate under anaerobic environments, but most rice (Oryza sativa) genotypes cannot survive these conditions. To identify the genetic architecture of complex t...
| Main Authors: | , , , , |
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| Format: | Journal Article |
| Language: | Inglés |
| Published: |
Oxford University Press
2021
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| Subjects: | |
| Online Access: | https://hdl.handle.net/10568/164329 |
| _version_ | 1855535946619944960 |
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| author | Castano-Duque, Lina Ghosal, Sharmistha Quilloy, Fergie A. Mitchell-Olds, Thomas Dixit, Shalabh |
| author_browse | Castano-Duque, Lina Dixit, Shalabh Ghosal, Sharmistha Mitchell-Olds, Thomas Quilloy, Fergie A. |
| author_facet | Castano-Duque, Lina Ghosal, Sharmistha Quilloy, Fergie A. Mitchell-Olds, Thomas Dixit, Shalabh |
| author_sort | Castano-Duque, Lina |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | Rice production is shifting from transplanting seedlings to direct sowing of seeds. Following heavy rains, directly sown seeds may need to germinate under anaerobic environments, but most rice (Oryza sativa) genotypes cannot survive these conditions. To identify the genetic architecture of complex traits, we quantified percentage anaerobic germination (AG) in 2,700 (wet-season) and 1,500 (dry-season) sequenced rice genotypes and performed genome-wide association studies (GWAS) using 693,502 single nucleotide polymorphisms. This was followed by post-GWAS analysis with a generalized SNP-to-gene set analysis, meta-analysis, and network analysis. We determined that percentage AG is intermediate-to-high among indica subpopulations, and AG is a polygenic trait associated with transcription factors linked to ethylene responses or genes involved in metabolic processes that are known to be associated with AG. Our post-GWAS analysis identified several genes involved in a wide variety of metabolic processes. We subsequently performed functional analysis focused on the small RNA and methylation pathways. We selected CLASSY 1 (CLSY1), a gene involved in the RNA-directed DNA methylation (RdDm) pathway, for further analyses under AG and found several lines of evidence that CLSY1 influences AG. We propose that the RdDm pathway plays a role in rice responses to water status during germination and seedling establishment developmental stages. |
| format | Journal Article |
| id | CGSpace164329 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2021 |
| publishDateRange | 2021 |
| publishDateSort | 2021 |
| publisher | Oxford University Press |
| publisherStr | Oxford University Press |
| record_format | dspace |
| spelling | CGSpace1643292025-05-14T10:24:23Z An epigenetic pathway in rice connects genetic variation to anaerobic germination and seedling establishment Castano-Duque, Lina Ghosal, Sharmistha Quilloy, Fergie A. Mitchell-Olds, Thomas Dixit, Shalabh plant science genetics physiology Rice production is shifting from transplanting seedlings to direct sowing of seeds. Following heavy rains, directly sown seeds may need to germinate under anaerobic environments, but most rice (Oryza sativa) genotypes cannot survive these conditions. To identify the genetic architecture of complex traits, we quantified percentage anaerobic germination (AG) in 2,700 (wet-season) and 1,500 (dry-season) sequenced rice genotypes and performed genome-wide association studies (GWAS) using 693,502 single nucleotide polymorphisms. This was followed by post-GWAS analysis with a generalized SNP-to-gene set analysis, meta-analysis, and network analysis. We determined that percentage AG is intermediate-to-high among indica subpopulations, and AG is a polygenic trait associated with transcription factors linked to ethylene responses or genes involved in metabolic processes that are known to be associated with AG. Our post-GWAS analysis identified several genes involved in a wide variety of metabolic processes. We subsequently performed functional analysis focused on the small RNA and methylation pathways. We selected CLASSY 1 (CLSY1), a gene involved in the RNA-directed DNA methylation (RdDm) pathway, for further analyses under AG and found several lines of evidence that CLSY1 influences AG. We propose that the RdDm pathway plays a role in rice responses to water status during germination and seedling establishment developmental stages. 2021-06-11 2024-12-19T12:53:44Z 2024-12-19T12:53:44Z Journal Article https://hdl.handle.net/10568/164329 en Open Access Oxford University Press Castano-Duque, Lina; Ghosal, Sharmistha; Quilloy, Fergie A; Mitchell-Olds, Thomas and Dixit, Shalabh. 2021. An epigenetic pathway in rice connects genetic variation to anaerobic germination and seedling establishment. , Volume 186 no. 2 p. 1042-1059 |
| spellingShingle | plant science genetics physiology Castano-Duque, Lina Ghosal, Sharmistha Quilloy, Fergie A. Mitchell-Olds, Thomas Dixit, Shalabh An epigenetic pathway in rice connects genetic variation to anaerobic germination and seedling establishment |
| title | An epigenetic pathway in rice connects genetic variation to anaerobic germination and seedling establishment |
| title_full | An epigenetic pathway in rice connects genetic variation to anaerobic germination and seedling establishment |
| title_fullStr | An epigenetic pathway in rice connects genetic variation to anaerobic germination and seedling establishment |
| title_full_unstemmed | An epigenetic pathway in rice connects genetic variation to anaerobic germination and seedling establishment |
| title_short | An epigenetic pathway in rice connects genetic variation to anaerobic germination and seedling establishment |
| title_sort | epigenetic pathway in rice connects genetic variation to anaerobic germination and seedling establishment |
| topic | plant science genetics physiology |
| url | https://hdl.handle.net/10568/164329 |
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