A GWAS approach to find SNPs associated with salt removal in rice leaf sheath
and AimsThe ability for salt removal at the leaf sheath level is considered to be one of the major mechanisms associated with salt tolerance in rice. Thus, understanding the genetic control of the salt removal capacity in leaf sheaths will help improve the molecular breeding of salt-tolerant rice va...
| Main Authors: | , , , , , , , , , , |
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| Format: | Journal Article |
| Language: | Inglés |
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Oxford University Press
2020
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| Subjects: | |
| Online Access: | https://hdl.handle.net/10568/164424 |
| _version_ | 1855537653301116928 |
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| author | Neang, Sarin de Ocampo, Marjorie Egdane, James A. Platten, John Damien Ismail, Abdelbagi M. Seki, Masahide Suzuki, Yutaka Skoulding, Nicola Stephanie Kano-Nakata, Mana Yamauchi, Akira Mitsuya, Shiro |
| author_browse | Egdane, James A. Ismail, Abdelbagi M. Kano-Nakata, Mana Mitsuya, Shiro Neang, Sarin Platten, John Damien Seki, Masahide Skoulding, Nicola Stephanie Suzuki, Yutaka Yamauchi, Akira de Ocampo, Marjorie |
| author_facet | Neang, Sarin de Ocampo, Marjorie Egdane, James A. Platten, John Damien Ismail, Abdelbagi M. Seki, Masahide Suzuki, Yutaka Skoulding, Nicola Stephanie Kano-Nakata, Mana Yamauchi, Akira Mitsuya, Shiro |
| author_sort | Neang, Sarin |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | and AimsThe ability for salt removal at the leaf sheath level is considered to be one of the major mechanisms associated with salt tolerance in rice. Thus, understanding the genetic control of the salt removal capacity in leaf sheaths will help improve the molecular breeding of salt-tolerant rice varieties and speed up future varietal development to increase productivity in salt-affected areas. We report a genome-wide association study (GWAS) conducted to find single nucleotide polymorphisms (SNPs) associated with salt removal in leaf sheaths of rice.MethodsIn this study, 296 accessions of a rice (Oryza sativa) diversity panel were used to identify salt removal-related traits and conduct GWAS using 36 901 SNPs. The sheath:blade ratio of Na+ and Cl– concentrations was used to determine the salt removal ability in leaf sheaths. Candidate genes were further narrowed via Gene Ontology and RNA-seq analysis to those whose putative function was likely to be associated with salt transport and were up-regulated in response to salt stress.Key resultsFor the association signals of the Na+ sheath:blade ratio, significant SNPs were found only in the indica sub-population on chromosome 5. Within candidate genes found in the GWAS study, five genes were upregulated and eight genes were downregulated in the internal leaf sheath tissues in the presence of salt stress.ConclusionsThese GWAS data imply that rice accessions in the indica variety group are the main source of genes and alleles associated with Na+ removal in leaf sheaths of rice under salt stress. |
| format | Journal Article |
| id | CGSpace164424 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2020 |
| publishDateRange | 2020 |
| publishDateSort | 2020 |
| publisher | Oxford University Press |
| publisherStr | Oxford University Press |
| record_format | dspace |
| spelling | CGSpace1644242025-05-14T10:24:25Z A GWAS approach to find SNPs associated with salt removal in rice leaf sheath Neang, Sarin de Ocampo, Marjorie Egdane, James A. Platten, John Damien Ismail, Abdelbagi M. Seki, Masahide Suzuki, Yutaka Skoulding, Nicola Stephanie Kano-Nakata, Mana Yamauchi, Akira Mitsuya, Shiro plant science and AimsThe ability for salt removal at the leaf sheath level is considered to be one of the major mechanisms associated with salt tolerance in rice. Thus, understanding the genetic control of the salt removal capacity in leaf sheaths will help improve the molecular breeding of salt-tolerant rice varieties and speed up future varietal development to increase productivity in salt-affected areas. We report a genome-wide association study (GWAS) conducted to find single nucleotide polymorphisms (SNPs) associated with salt removal in leaf sheaths of rice.MethodsIn this study, 296 accessions of a rice (Oryza sativa) diversity panel were used to identify salt removal-related traits and conduct GWAS using 36 901 SNPs. The sheath:blade ratio of Na+ and Cl– concentrations was used to determine the salt removal ability in leaf sheaths. Candidate genes were further narrowed via Gene Ontology and RNA-seq analysis to those whose putative function was likely to be associated with salt transport and were up-regulated in response to salt stress.Key resultsFor the association signals of the Na+ sheath:blade ratio, significant SNPs were found only in the indica sub-population on chromosome 5. Within candidate genes found in the GWAS study, five genes were upregulated and eight genes were downregulated in the internal leaf sheath tissues in the presence of salt stress.ConclusionsThese GWAS data imply that rice accessions in the indica variety group are the main source of genes and alleles associated with Na+ removal in leaf sheaths of rice under salt stress. 2020-11-24 2024-12-19T12:53:52Z 2024-12-19T12:53:52Z Journal Article https://hdl.handle.net/10568/164424 en Oxford University Press Neang, Sarin; de Ocampo, Marjorie; Egdane, James A; Platten, John Damien; Ismail, Abdelbagi M; Seki, Masahide; Suzuki, Yutaka; Skoulding, Nicola Stephanie; Kano-Nakata, Mana; Yamauchi, Akira and Mitsuya, Shiro. 2020. A GWAS approach to find SNPs associated with salt removal in rice leaf sheath. Annals of botany, (e-first copy); 10 pages |
| spellingShingle | plant science Neang, Sarin de Ocampo, Marjorie Egdane, James A. Platten, John Damien Ismail, Abdelbagi M. Seki, Masahide Suzuki, Yutaka Skoulding, Nicola Stephanie Kano-Nakata, Mana Yamauchi, Akira Mitsuya, Shiro A GWAS approach to find SNPs associated with salt removal in rice leaf sheath |
| title | A GWAS approach to find SNPs associated with salt removal in rice leaf sheath |
| title_full | A GWAS approach to find SNPs associated with salt removal in rice leaf sheath |
| title_fullStr | A GWAS approach to find SNPs associated with salt removal in rice leaf sheath |
| title_full_unstemmed | A GWAS approach to find SNPs associated with salt removal in rice leaf sheath |
| title_short | A GWAS approach to find SNPs associated with salt removal in rice leaf sheath |
| title_sort | gwas approach to find snps associated with salt removal in rice leaf sheath |
| topic | plant science |
| url | https://hdl.handle.net/10568/164424 |
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