Molecular Genetics of Rice Root Development

Abstract

Plant roots have a large range of functions, including acquisition of water and nutrients, as well as structural support. Dissecting the genetic and molecular mechanisms controlling rice root development is critical for the development of new rice ideotypes that are better adapted to adverse conditions and for the production of sustainably achieved rice yield potential. Most knowledge regarding the gene networks involved in root development has been accumulated in the model dicotyledon plant species Arabidopsis thaliana. Rice, the model monocotyledon species, presents several singularities compared to A. thaliana, including a root architecture characterized by a fibrous root system comprising five types of embryonic and postembryonic roots. The anatomy and morphology of the rice root system, which is typical for a cereal, differs from that of A. thaliana, for instance, by the presence of a lysigenous cortex and additional cell layers compared to the dicotyledon model. Moreover, the structure and functions of the root apical meristem (RAM) of rice are distinct from those of A. thaliana. Recently, several rice root mutants have been identified via forward or reverse genetics, and these will aid in forming hypothesis to characterize either the divergence or conservation of genetic pathways relative to A. thaliana. Furthermore, these mutants will help to identify key genes in rice roots that may be missing in A. thaliana. This review summarizes both classical and recent data concerning the molecular genetics of rice root development, including root anatomy and morphology, RAM structure, RAM patterning, and root mutants.

Three-Dimensional Root Phenotyping with a Novel Imaging and Software Platform

“…In monocots, the rapid elongation and lateral root establishment of the primary and embryonic crown roots is critical for early seedling vigor, whereas postembryonic crown roots become increasingly important during further plant growth (Hochholdinger and Tuberosa, 2009). Additionally, through mutant analysis studies in rice, it has been found that these root types are controlled by distinctly different genetic and developmental networks (Hochholdinger et al, 2004;Rebouillat et al, 2009). The ability of this root imaging and analysis platform to separate and track the growth features of these five root types individually can help detect and further characterize the genetic and developmental changes that occur as the root system develops and the plant matures.…”

“…Taking advantage of the phenotyping platform's ability to capture and measure both dynamic and local traits, five specific rice root types can be identified and separated from whole root system reconstructions based on emergence time and visual characteristics, as described by Rebouillat et al (2009;Fig. 3A).…”

Root system architecture: insights fromArabidopsisand cereal crops

“…Crown roots start to emerge from below-ground stem nodes by 5 -10 days post-germination. By contrast, brace roots emerge from above-ground stem nodes much later, approximately 6 weeks after germination [36,37]. Lateral root initiation also differs somewhat in cereals: both pericycle and endodermal cells can progress to become lateral root cells, and lateral roots form at the phloem poles rather than the xylem poles [38].…”

Rice Root Genetic Architecture: Meta-analysis from a Drought QTL Database

“…However, all genes within the confidence interval could be candidates for further work, and those with no known function could not be eliminated either. Links between the gene function and the QTL can be reinforced by the involvement of the gene in a relevant pathway such as those described by Malamy (2005), Nibau et al (2008), or Rebouillat et al (2008 for root development or by the expression of the gene in root tissues, a method explored by Norton et al (2008). Mutants with t-DNA insertion in the candidate genes can also be searched in OrygenesDB, their expression in root tissues checked by using Oryza-Tag Line GUS and GFP data (Larmande et al 2008) and the mutants analyzed to check for the mutation effect on root morphology or development.…”

“…Allometric ratios such as rootto-shoot weight ratio (R/S), root dry weight per tiller, (R/T), deep root to shoot weight (DR/S), or deep root weight per tiller (DR/T) are used to describe the coordination between growth and development of the roots and shoots. A more precise description of the morphology and anatomy of the rice root system at tissue level has recently been provided (Rebouillat et al 2008).…”