Tolerance to mild salinity stress in japonica rice: A genome-wide association mapping study highlights calcium signaling and metabolism genes.
Salinity tolerance is an important quality for European rice grown in river deltas. We evaluated the salinity tolerance of a panel of 235 temperate japonica rice accessions genotyped with 30,000 SNP markers. The panel was exposed to mild salt stress (50 mM NaCl; conductivity of 6 dS m-1) at the seed...
| Main Authors: | , , , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Public Library of Science (PLoS)
2018-01-01
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| Series: | PLoS ONE |
| Online Access: | http://europepmc.org/articles/PMC5771603?pdf=render |
| _version_ | 1818034574150598656 |
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| author | Julien Frouin Antoine Languillaume Justine Mas Delphine Mieulet Arnaud Boisnard Axel Labeyrie Mathilde Bettembourg Charlotte Bureau Eve Lorenzini Muriel Portefaix Patricia Turquay Aurore Vernet Christophe Périn Nourollah Ahmadi Brigitte Courtois |
| author_facet | Julien Frouin Antoine Languillaume Justine Mas Delphine Mieulet Arnaud Boisnard Axel Labeyrie Mathilde Bettembourg Charlotte Bureau Eve Lorenzini Muriel Portefaix Patricia Turquay Aurore Vernet Christophe Périn Nourollah Ahmadi Brigitte Courtois |
| author_sort | Julien Frouin |
| collection | DOAJ |
| description | Salinity tolerance is an important quality for European rice grown in river deltas. We evaluated the salinity tolerance of a panel of 235 temperate japonica rice accessions genotyped with 30,000 SNP markers. The panel was exposed to mild salt stress (50 mM NaCl; conductivity of 6 dS m-1) at the seedling stage. Eight different root and shoot growth parameters were measured for both the control and stressed treatments. The Na+ and K+ mass fractions of the stressed plants were measured using atomic absorption spectroscopy. The salt treatment affected plant growth, particularly the shoot parameters. The panel showed a wide range of Na+/K+ ratio and the temperate accessions were distributed over an increasing axis, from the most resistant to the most susceptible checks. We conducted a genome-wide association study on indices of stress response and ion mass fractions in the leaves using a classical mixed model controlling structure and kinship. A total of 27 QTLs validated by sub-sampling were identified. For indices of stress responses, we also used another model that focused on marker × treatment interactions and detected 50 QTLs, three of which were also identified using the classical method. We compared the positions of the significant QTLs to those of approximately 300 genes that play a role in rice salt tolerance. The positions of several QTLs were close to those of genes involved in calcium signaling and metabolism, while other QTLs were close to those of kinases. These results reveal the salinity tolerance of accessions with a temperate japonica background. Although the detected QTLs must be confirmed by other approaches, the number of associations linked to candidate genes involved in calcium-mediated ion homeostasis highlights pathways to explore in priority to understand the salinity tolerance of temperate rice. |
| first_indexed | 2024-12-10T06:41:19Z |
| format | Article |
| id | doaj.art-66c8175afccd43c99704c02eb7ec5d5d |
| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2024-12-10T06:41:19Z |
| publishDate | 2018-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj.art-66c8175afccd43c99704c02eb7ec5d5d2022-12-22T01:58:46ZengPublic Library of Science (PLoS)PLoS ONE1932-62032018-01-01131e019096410.1371/journal.pone.0190964Tolerance to mild salinity stress in japonica rice: A genome-wide association mapping study highlights calcium signaling and metabolism genes.Julien FrouinAntoine LanguillaumeJustine MasDelphine MieuletArnaud BoisnardAxel LabeyrieMathilde BettembourgCharlotte BureauEve LorenziniMuriel PortefaixPatricia TurquayAurore VernetChristophe PérinNourollah AhmadiBrigitte CourtoisSalinity tolerance is an important quality for European rice grown in river deltas. We evaluated the salinity tolerance of a panel of 235 temperate japonica rice accessions genotyped with 30,000 SNP markers. The panel was exposed to mild salt stress (50 mM NaCl; conductivity of 6 dS m-1) at the seedling stage. Eight different root and shoot growth parameters were measured for both the control and stressed treatments. The Na+ and K+ mass fractions of the stressed plants were measured using atomic absorption spectroscopy. The salt treatment affected plant growth, particularly the shoot parameters. The panel showed a wide range of Na+/K+ ratio and the temperate accessions were distributed over an increasing axis, from the most resistant to the most susceptible checks. We conducted a genome-wide association study on indices of stress response and ion mass fractions in the leaves using a classical mixed model controlling structure and kinship. A total of 27 QTLs validated by sub-sampling were identified. For indices of stress responses, we also used another model that focused on marker × treatment interactions and detected 50 QTLs, three of which were also identified using the classical method. We compared the positions of the significant QTLs to those of approximately 300 genes that play a role in rice salt tolerance. The positions of several QTLs were close to those of genes involved in calcium signaling and metabolism, while other QTLs were close to those of kinases. These results reveal the salinity tolerance of accessions with a temperate japonica background. Although the detected QTLs must be confirmed by other approaches, the number of associations linked to candidate genes involved in calcium-mediated ion homeostasis highlights pathways to explore in priority to understand the salinity tolerance of temperate rice.http://europepmc.org/articles/PMC5771603?pdf=render |
| spellingShingle | Julien Frouin Antoine Languillaume Justine Mas Delphine Mieulet Arnaud Boisnard Axel Labeyrie Mathilde Bettembourg Charlotte Bureau Eve Lorenzini Muriel Portefaix Patricia Turquay Aurore Vernet Christophe Périn Nourollah Ahmadi Brigitte Courtois Tolerance to mild salinity stress in japonica rice: A genome-wide association mapping study highlights calcium signaling and metabolism genes. PLoS ONE |
| title | Tolerance to mild salinity stress in japonica rice: A genome-wide association mapping study highlights calcium signaling and metabolism genes. |
| title_full | Tolerance to mild salinity stress in japonica rice: A genome-wide association mapping study highlights calcium signaling and metabolism genes. |
| title_fullStr | Tolerance to mild salinity stress in japonica rice: A genome-wide association mapping study highlights calcium signaling and metabolism genes. |
| title_full_unstemmed | Tolerance to mild salinity stress in japonica rice: A genome-wide association mapping study highlights calcium signaling and metabolism genes. |
| title_short | Tolerance to mild salinity stress in japonica rice: A genome-wide association mapping study highlights calcium signaling and metabolism genes. |
| title_sort | tolerance to mild salinity stress in japonica rice a genome wide association mapping study highlights calcium signaling and metabolism genes |
| url | http://europepmc.org/articles/PMC5771603?pdf=render |
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