Tolerance to mild salinity stress in japonica rice: A genome-wide association mapping study highlights calcium signaling and metabolism genes

Frouin Julien, Languillaume Antoine, Mas Justine, Mieulet Delphine, Boisnard Arnaud, Labeyrie Axel, Bettembourg Mathilde, Bureau Charlotte, Lorenzini Eve, Portefaix Murielle, Turquay Patricia, Vernet Aurore, Périn Christophe, Ahmadi Nourollah, Courtois Brigitte. 2018. Tolerance to mild salinity stress in japonica rice: A genome-wide association mapping study highlights calcium signaling and metabolism genes. PloS One, 13 (1):e0190964, 27 p.

Journal article ; Article de recherche ; Article de revue à facteur d'impact Revue en libre accès total
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Thème(s) HCERES des revues (en SHS) : Psychologie-éthologie-ergonomie; Staps

Abstract : 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. (Résumé d'auteur)

Mots-clés Agrovoc : Oryza sativa, Tolérance au sel, Résistance génétique, Carte génétique, Métabolisme des minéraux, Calcium, Réponse de la plante, Locus des caractères quantitatifs, Identification, Amélioration des plantes, Gène, Marqueur génétique

Mots-clés géographiques Agrovoc : France, Espagne, Italie

Mots-clés complémentaires : Oryza sativa japonica, QTL

Classification Agris : F30 - Plant genetics and breeding
F60 - Plant physiology and biochemistry
H50 - Miscellaneous plant disorders

Champ stratégique Cirad : Axe 1 (2014-2018) - Agriculture écologiquement intensive

Auteurs et affiliations

  • Frouin Julien, CIRAD-BIOS-UMR AGAP (FRA)
  • Languillaume Antoine
  • Mas Justine
  • Mieulet Delphine, CIRAD-BIOS-UMR AGAP (FRA) ORCID: 0000-0001-6220-0372
  • Boisnard Arnaud, CFR (FRA)
  • Labeyrie Axel, CIRAD-BIOS-UMR DIADE (FRA)
  • Bettembourg Mathilde, CIRAD-BIOS-UMR AGAP (FRA)
  • Bureau Charlotte, CIRAD-BIOS-UMR AGAP (FRA)
  • Lorenzini Eve, CIRAD-BIOS-UMR AGAP (FRA)
  • Portefaix Murielle, INRA (FRA)
  • Turquay Patricia, CIRAD-BIOS-UMR AGAP (FRA)
  • Vernet Aurore, CIRAD-BIOS-UMR AGAP (FRA)
  • Périn Christophe, CIRAD-BIOS-UMR AGAP (FRA) ORCID: 0000-0002-2469-310X
  • Ahmadi Nourollah, CIRAD-BIOS-UMR AGAP (FRA) ORCID: 0000-0003-0072-6285
  • Courtois Brigitte, CIRAD-BIOS-UMR AGAP (FRA) ORCID: 0000-0003-2118-7102 - auteur correspondant

Source : Cirad-Agritrop (

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