Genomic selection for salinity tolerance in japonica rice

Bartholome Jérôme, Frouin Julien, Brottier Laurent, Cao Tuong-Vi, Boisnard Arnaud, Ahmadi Nourollah, Courtois Brigitte. 2023. Genomic selection for salinity tolerance in japonica rice. PloS One, 18 (9):e0291833, 22 p.

Url - jeu de données - Dataverse Cirad : https://doi.org/10.18167/DVN1/O1AYGP

Liste HCERES des revues (en SHS) : oui

Thème(s) HCERES des revues (en SHS) : Psychologie-éthologie-ergonomie; Staps

Résumé : Improving plant performance in salinity-prone conditions is a significant challenge in breeding programs. Genomic selection is currently integrated into many plant breeding programs as a tool for increasing selection intensity and precision for complex traits and for reducing breeding cycle length. A rice reference panel (RP) of 241 Oryza sativa L. japonica accessions genotyped with 20,255 SNPs grown in control and mild salinity stress conditions was evaluated at the vegetative stage for eight morphological traits and ion mass fractions (Na and K). Weak to strong genotype-by-condition interactions were found for the traits considered. Cross-validation showed that the predictive ability of genomic prediction methods ranged from 0.25 to 0.64 for multi-environment models with morphological traits and from 0.05 to 0.40 for indices of stress response and ion mass fractions. The performances of a breeding population (BP) comprising 393 japonica accessions were predicted with models trained on the RP. For validation of the predictive performances of the models, a subset of 41 accessions was selected from the BP and phenotyped under the same experimental conditions as the RP. The predictive abilities estimated on this subset ranged from 0.00 to 0.66 for the multi-environment models, depending on the traits, and were strongly correlated with the predictive abilities on cross-validation in the RP in salt condition (r = 0.69). We show here that genomic selection is efficient for predicting the salt stress tolerance of breeding lines. Genomic selection could improve the efficiency of rice breeding strategies for salinity-prone environments.

Mots-clés Agrovoc : Oryza sativa, tolérance au sel, amélioration des plantes, génotype, génome, sélection, phénotype, amélioration génétique, stress osmotique, génomique, Oryza, variation génétique, polymorphisme génétique, riz, marqueur génétique

Classification Agris : F30 - Génétique et amélioration des plantes
F60 - Physiologie et biochimie végétale
H50 - Troubles divers des plantes

Champ stratégique Cirad : CTS 2 (2019-) - Transitions agroécologiques

Agences de financement hors UE : Agence Nationale de la Recherche

Projets sur financement : (FRA) Sustainable and environmental friendly rice cultivation systems in Europe

Auteurs et affiliations

• Bartholome Jérôme, CIRAD-BIOS-UMR AGAP (FRA) ORCID: 0000-0002-0855-3828 - auteur correspondant
• Frouin Julien, CIRAD-BIOS-UMR AGAP (FRA) ORCID: 0000-0003-1591-0755
• Brottier Laurent, IRD (FRA)
• Cao Tuong-Vi, CIRAD-BIOS-UMR AGAP (FRA) ORCID: 0000-0002-7011-2003
• Boisnard Arnaud, CFR (FRA)
• Ahmadi Nourollah, CIRAD-BIOS-UMR AGAP (FRA) ORCID: 0000-0003-0072-6285
• Courtois Brigitte, CIRAD-BIOS-UMR AGAP (FRA) ORCID: 0000-0003-2118-7102

Source : Cirad-Agritrop (https://agritrop.cirad.fr/606858/)

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