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.
Highlights
Rice (O. sativa L.) is the most important staple food crop worldwide
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 non-structural carbohydrates (NSC) measurements, as well as fitted parameters for the functional–structural plant model, Ecomeristem
shoot dry weight (SDW) was significantly correlated with morphological traits (LLL, NBT, NBL, DR), model parameters (MGR, PLASTO, ICT, DEV_PLASTO_MGR), and metabolic traits (SUC)
Summary
Rice (O. sativa L.) is the most important staple food crop worldwide. In 2011, rice crops occupied 164.1 M ha [http:// faostat.fao.org (accessed 28/01/2013)]. Rice is grown in a variety of environments, covering a wide range of latitudes, altitudes, and hydrologies This broad adaptation as a species is associated with large genetic and phenotypic diversity (McNally et al, 2009). By providing rapid access to aboveand below-ground resources and the ability to compete with Vigour is commonly estimated by the capacity of seedlings to accumulate shoot biomass rapidly It is a complex trait, the genetic improvement of which may benefit from its dissection into component traits of lesser genetic complexity. Specific Leaf Area (SLA, cm g–1), tillering, leaf size, leaf appearance, and leaf expansion rates were studied for rice and wheat (Rebetzke et al, 2007; Maydup et al, 2012). Ter Steege et al (2005) reported negative genetic linkages among traits constituting early vigour in wheat, such as leaf size and leaf number. Tisné et al (2008) reported, for A. thaliana, a genetic negative linkage between leaf area determination at meristem level and whole-plant leaf production
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