Enriched-GWAS and transcriptome analysis to refine and characterize a major QTL for anaerobic germination tolerance in rice
Tolerance of anaerobic germination (AG) is a key trait in the development of direct seeded rice. Through rapid and sustained coleoptile elongation, AG tolerance enables robust seedling establishment under flooded conditions. Previous attempts to fine map and characterize AG2 (qAG7.1), a major centro...
| Main Authors: | , , , , , , , , |
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| Format: | Journal Article |
| Language: | Inglés |
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MDPI
2021
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| Subjects: | |
| Online Access: | https://hdl.handle.net/10568/164291 |
| _version_ | 1855528611226845184 |
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| author | Tnani, Hedia Chebotarov, Dmytro Thapa, Ranjita Ignacio, John Carlos I. Israel, Walter K. Quilloy, Fergie A. Dixit, Shalabh Septiningsih, Endang M. Kretzschmar, Tobias |
| author_browse | Chebotarov, Dmytro Dixit, Shalabh Ignacio, John Carlos I. Israel, Walter K. Kretzschmar, Tobias Quilloy, Fergie A. Septiningsih, Endang M. Thapa, Ranjita Tnani, Hedia |
| author_facet | Tnani, Hedia Chebotarov, Dmytro Thapa, Ranjita Ignacio, John Carlos I. Israel, Walter K. Quilloy, Fergie A. Dixit, Shalabh Septiningsih, Endang M. Kretzschmar, Tobias |
| author_sort | Tnani, Hedia |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | Tolerance of anaerobic germination (AG) is a key trait in the development of direct seeded rice. Through rapid and sustained coleoptile elongation, AG tolerance enables robust seedling establishment under flooded conditions. Previous attempts to fine map and characterize AG2 (qAG7.1), a major centromere-spanning AG tolerance QTL, derived from the indica variety Ma-Zhan Red, have failed. Here, a novel approach of “enriched haplotype” genome-wide association study based on the Ma-Zhan Red haplotype in the AG2 region was successfully used to narrow down AG2 from more than 7 Mb to less than 0.7 Mb. The AG2 peak region contained 27 genes, including the Rc gene, responsible for red pericarp development in pigmented rice. Through comparative variant and transcriptome analysis between AG tolerant donors and susceptible accessions several candidate genes potentially controlling AG2 were identified, among them several regulatory genes. Genome-wide comparative transcriptome analysis suggested differential regulation of sugar metabolism, particularly trehalose metabolism, as well as differential regulation of cell wall modification and chloroplast development to be implicated in AG tolerance mechanisms. |
| format | Journal Article |
| id | CGSpace164291 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2021 |
| publishDateRange | 2021 |
| publishDateSort | 2021 |
| publisher | MDPI |
| publisherStr | MDPI |
| record_format | dspace |
| spelling | CGSpace1642912024-12-22T05:44:55Z Enriched-GWAS and transcriptome analysis to refine and characterize a major QTL for anaerobic germination tolerance in rice Tnani, Hedia Chebotarov, Dmytro Thapa, Ranjita Ignacio, John Carlos I. Israel, Walter K. Quilloy, Fergie A. Dixit, Shalabh Septiningsih, Endang M. Kretzschmar, Tobias physical and theoretical chemistry inorganic chemistry organic chemistry spectroscopy molecular biology catalysis general medicine computer science applications Tolerance of anaerobic germination (AG) is a key trait in the development of direct seeded rice. Through rapid and sustained coleoptile elongation, AG tolerance enables robust seedling establishment under flooded conditions. Previous attempts to fine map and characterize AG2 (qAG7.1), a major centromere-spanning AG tolerance QTL, derived from the indica variety Ma-Zhan Red, have failed. Here, a novel approach of “enriched haplotype” genome-wide association study based on the Ma-Zhan Red haplotype in the AG2 region was successfully used to narrow down AG2 from more than 7 Mb to less than 0.7 Mb. The AG2 peak region contained 27 genes, including the Rc gene, responsible for red pericarp development in pigmented rice. Through comparative variant and transcriptome analysis between AG tolerant donors and susceptible accessions several candidate genes potentially controlling AG2 were identified, among them several regulatory genes. Genome-wide comparative transcriptome analysis suggested differential regulation of sugar metabolism, particularly trehalose metabolism, as well as differential regulation of cell wall modification and chloroplast development to be implicated in AG tolerance mechanisms. 2021-04-24 2024-12-19T12:53:43Z 2024-12-19T12:53:43Z Journal Article https://hdl.handle.net/10568/164291 en Open Access MDPI Tnani, Hedia; Chebotarov, Dmytro; Thapa, Ranjita; Ignacio, John Carlos I.; Israel, Walter K.; Quilloy, Fergie A.; Dixit, Shalabh; Septiningsih, Endang M. and Kretzschmar, Tobias. 2021. Enriched-GWAS and transcriptome analysis to refine and characterize a major QTL for anaerobic germination tolerance in rice. IJMS, Volume 22 no. 9 p. 4445 |
| spellingShingle | physical and theoretical chemistry inorganic chemistry organic chemistry spectroscopy molecular biology catalysis general medicine computer science applications Tnani, Hedia Chebotarov, Dmytro Thapa, Ranjita Ignacio, John Carlos I. Israel, Walter K. Quilloy, Fergie A. Dixit, Shalabh Septiningsih, Endang M. Kretzschmar, Tobias Enriched-GWAS and transcriptome analysis to refine and characterize a major QTL for anaerobic germination tolerance in rice |
| title | Enriched-GWAS and transcriptome analysis to refine and characterize a major QTL for anaerobic germination tolerance in rice |
| title_full | Enriched-GWAS and transcriptome analysis to refine and characterize a major QTL for anaerobic germination tolerance in rice |
| title_fullStr | Enriched-GWAS and transcriptome analysis to refine and characterize a major QTL for anaerobic germination tolerance in rice |
| title_full_unstemmed | Enriched-GWAS and transcriptome analysis to refine and characterize a major QTL for anaerobic germination tolerance in rice |
| title_short | Enriched-GWAS and transcriptome analysis to refine and characterize a major QTL for anaerobic germination tolerance in rice |
| title_sort | enriched gwas and transcriptome analysis to refine and characterize a major qtl for anaerobic germination tolerance in rice |
| topic | physical and theoretical chemistry inorganic chemistry organic chemistry spectroscopy molecular biology catalysis general medicine computer science applications |
| url | https://hdl.handle.net/10568/164291 |
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