Phenotypic and genetic dissection of component traits for early vigour in rice using plant growth modelling, sugar content analyses and association mapping

Rebolledo Maria Camila, Dingkuhn Michaël, Courtois Brigitte, Gibon Yves, Clément-Vidal Anne, Cruz Daniel F., Duitama Jorge, Lorieux Mathias, Luquet Delphine. 2015. Phenotypic and genetic dissection of component traits for early vigour in rice using plant growth modelling, sugar content analyses and association mapping. Journal of Experimental Botany, 66 (18), n.spéc. Phenotyping in Plants : pp. 5555-5566.

Journal article ; Article de recherche ; Article de revue à facteur d'impact
Published version - Anglais
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Quartile : Outlier, Sujet : PLANT SCIENCES

Abstract : Early vigour of rice, defined as seedling capacity to accumulate shoot dry weight (SDW) rapidly, is a complex trait. It depends on a genotype propensity to assimilate, store, and/or use non-structural carbohydrates (NSC) for producing large and/or numerous leaves, involving physiological trade-offs in the expression of component traits and, possibly, physiological and genetic linkages. This study explores a plant-model-assisted phenotyping approach to dissect the genetic architecture of rice early vigour, applying the Genome Wide Association Study (GWAS) to morphological and NSC measurements, as well as fitted parameters for the functional–structural plant model, Ecomeristem. Leaf size, number, SDW, and source-leaf NSC concentration were measured on a panel of 123 japonica accessions. The data were used to estimate Ecomeristem genotypic parameters driving organ appearance rate, size, and carbon dynamics. GWAS was performed based on 12 221 single-nucleotide polymorphisms (SNP). Twenty-three associations were detected at P <1×10–4 and 64 at P <5×10–4. Associations for NSC and model parameters revealed new regions related to early vigour that had greater significance than morphological traits, providing additional information on the genetic control of early vigour. Plant model parameters were used to characterize physiological and genetic trade-offs among component traits. Twelve associations were related to loci for cloned genes, with nine related to organogenesis, plant height, cell size or cell number. The potential use of these associations as markers for breeding is discussed. (Résumé d'auteur)

Mots-clés Agrovoc : Oryza sativa, Vigueur, Précocité, Modèle de simulation, Modélisation des cultures, Modèle mathématique, Génotype, Séquence nucléotidique, Métabolisme des glucides, saccharose, Croissance, Carte génétique, Morphologie végétale, Phénotype, Génie génétique

Mots-clés géographiques Agrovoc : France

Mots-clés complémentaires : Séquencage

Classification Agris : F62 - Plant physiology - Growth and development
F30 - Plant genetics and breeding
U10 - Computer science, mathematics and statistics

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

Auteurs et affiliations

  • Rebolledo Maria Camila, CIAT (COL)
  • Dingkuhn Michaël, CIRAD-BIOS-UMR AGAP (PHL)
  • Courtois Brigitte, CIRAD-BIOS-UMR AGAP (FRA) ORCID: 0000-0003-2118-7102
  • Gibon Yves, INRA (FRA)
  • Clément-Vidal Anne, CIRAD-BIOS-UMR AGAP (FRA)
  • Cruz Daniel F., CIAT (COL)
  • Duitama Jorge, CIAT (COL)
  • Lorieux Mathias, IRD (FRA)
  • Luquet Delphine, CIRAD-BIOS-UMR AGAP (FRA) ORCID: 0000-0002-2543-7140

Source : Cirad-Agritrop (

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