Crop-model assisted phenomics and genome-wide association study for climate adaptation of indica rice. 2. Thermal stress and spikelet sterility

Dingkuhn Michael, Pasco Richard, Pasuquin Julie, Damo Jean, Soulie Jean-Christophe, Raboin Louis-Marie, Dusserre Julie, Sow Abdoulaye, Manneh Baboucarr, Shrestha Suchit, Kretzschmar Tobias. 2017. Crop-model assisted phenomics and genome-wide association study for climate adaptation of indica rice. 2. Thermal stress and spikelet sterility. Journal of Experimental Botany, 68 (15) : 4389-4406.

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Note générale : Corrigendum paru dans Journal of Experimental Botany, (2018)69 p.713

Résumé : Low night and high day temperatures during sensitive reproductive stages cause spikelet sterility in rice. Phenotyping of tolerance traits in the field is difficult because of temporal interactions with phenology and organ temperature differing from ambient. Physiological models can be used to separate these effects. A 203-accession indica rice diversity panel was phenotyped for sterility in ten environments in Senegal and Madagascar and climate data were recorded. Here we report on sterility responses while a companion study reported on phenology. The objectives were to improve the RIDEV model of rice thermal sterility, to estimate response traits by fitting model parameters, and to link the response traits to genomic regions through genome-wide association studies (GWAS). RIDEV captured 64% of variation of sterility when cold acclimation during vegetative stage was simulated, but only 38% when it was not. The RIDEV parameters gave more and stronger quantitative trait loci (QTLs) than index variables derived more directly from observation. The 15 QTLs identified at P<1 × 10−5 (33 at P<1 × 10−4) were related to sterility effects of heat, cold, cold acclimation, or unexplained causes (baseline sterility). Nine annotated genes were found on average within the 50% linkage disequilibrium (LD) region. Among them, one to five plausible candidate genes per QTL were identified based on known expression profiles (organ, stage, stress factors) and function. Meiosis-, development- and flowering-related genes were frequent, as well a stress signaling kinases and transcription factors. Putative epigenetic factors such as DNA methylases or histone-related genes were frequent in cold-acclimation QTLs, and positive-effect alleles were frequent in cold-tolerant highland rice from Madagascar. The results indicate that epigenetic control of acclimation may be important in indica rice genotypes adapted to cool environments. (Résumé d'auteur)

Mots-clés Agrovoc : Oryza sativa, adaptation aux changements climatiques, Changement climatique, Infertilité mâle, Tolérance au froid, Tolérance à la chaleur, Modèle de simulation, Modèle mathématique, Stress thermique, Génotype, Identification, Gène, Phénologie, Locus des caractères quantitatifs

Mots-clés géographiques Agrovoc : Sénégal, Madagascar

Mots-clés complémentaires : Épigénétique, QTL

Mots-clés libres : Candidate genes, Cold and heat tolerance, Epigenetics, Heuristics, Male sterility, Oryza sativa L., RIDEV crop model

Classification Agris : F30 - Génétique et amélioration des plantes
P40 - Météorologie et climatologie
U10 - Méthodes mathématiques et statistiques
U40 - Méthodes de relevé
F63 - Physiologie végétale : reproduction
H50 - Troubles divers des plantes

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

Auteurs et affiliations

  • Dingkuhn Michael, CIRAD-BIOS-UMR AGAP (FRA)
  • Pasco Richard, IRRI (PHL)
  • Pasuquin Julie, IRRI (PHL)
  • Damo Jean, IRRI (PHL)
  • Soulie Jean-Christophe, CIRAD-BIOS-UMR AGAP (FRA) ORCID: 0000-0003-2904-9548
  • Raboin Louis-Marie, CIRAD-PERSYST-UPR AIDA (FRA)
  • Dusserre Julie, CIRAD-PERSYST-UPR AIDA (FRA) ORCID: 0000-0002-4971-8799
  • Sow Abdoulaye, Centre du riz pour l'Afrique (SEN)
  • Manneh Baboucarr, Centre du riz pour l'Afrique (SEN)
  • Shrestha Suchit, IRRI (PHL)
  • Kretzschmar Tobias, IRRI (PHL)

Source : Cirad-Agritrop (

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