title: Phenotypic and genetic dissection of component traits for early vigour in rice using plant growth modelling, sugar content analyses and association mapping.
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.
authors.affiliation: CIAT, Agrobiodiversity, AA 6713, Cali, Colombia m.c.rebolledo@cgiar.org.
authors.forename: M C
authors.initials: MC
authors.lastname: Rebolledo
authors.affiliation: IRRI, CESD Division, DAPO Box 7777, Metro Manila, Philippines CIRAD, UMR AGAP, F-34398 Montpellier, France.
authors.forename: M
authors.initials: M
authors.lastname: Dingkuhn
authors.affiliation: CIRAD, UMR AGAP, F-34398 Montpellier, France.
authors.forename: B
authors.initials: B
authors.lastname: Courtois
authors.affiliation: INRA, Metabolome Platform of UMR 1332, Bordeaux, France.
authors.forename: Y
authors.initials: Y
authors.lastname: Gibon
authors.affiliation: CIRAD, UMR AGAP, F-34398 Montpellier, France.
authors.forename: A
authors.initials: A
authors.lastname: Clément-Vidal
authors.affiliation: CIAT, Agrobiodiversity, AA 6713, Cali, Colombia.
authors.forename: D F
authors.initials: DF
authors.lastname: Cruz
authors.affiliation: CIAT, Agrobiodiversity, AA 6713, Cali, Colombia.
authors.forename: J
authors.initials: J
authors.lastname: Duitama
authors.affiliation: CIAT, Agrobiodiversity, AA 6713, Cali, Colombia IRD, DIADE Research Unit, Institut de Recherche pour le Développement, 34394 Montpellier Cedex 5, France.
authors.forename: M
authors.initials: M
authors.lastname: Lorieux
authors.affiliation: CIRAD, UMR AGAP, F-34398 Montpellier, France.
authors.forename: D
authors.initials: D
authors.lastname: Luquet
mesh_terms: D050260:Carbohydrate Metabolism; D055106:Genome-Wide Association Study; D018519:Meristem / Q000033:anatomy & histology / Q000235:genetics / Q000254:growth & development / Q000378:metabolism; D012275:Oryza / Q000033:anatomy & histology / Q000235:genetics* / Q000254:growth & development / Q000378:metabolism; D010641:Phenotype; D000069600:Plant Breeding; D018515:Plant Leaves / Q000033:anatomy & histology / Q000235:genetics / Q000254:growth & development / Q000378:metabolism; D020641:Polymorphism, Single Nucleotide
keywords: Genome wide association study (GWAS); Oryza sativa L.; genotyping by sequencing; heuristic approach; model-assisted phenotyping; sugar metabolism.