Genes controlling root development in rice

Abstract

In this review, we report on the recent developments made using both genetics and functional genomics approaches in the discovery of genes controlling root development in rice. QTL detection in classical biparental mapping populations initially enabled the identification of a very large number of large chromosomal segments carrying root genes. Two segments with large effects have been positionally cloned, allowing the identification of two major genes. One of these genes conferred a tolerance to low phosphate content in soil, while the other conferred a tolerance to drought by controlling root gravitropism, resulting in root system expansion deep in the soil. Findings based on the higher-resolution QTL detection offered by the development of association mapping are discussed. In parallel with genetics approaches, efforts have been made to screen mutant libraries for lines presenting alterations in root development, allowing for the identification of several genes that control different steps of root development, such as crown root and lateral root initiation and emergence, meristem patterning, and the control of root growth. Some of these genes are closely phylogenetically related to Arabidopsis genes involved in the control of lateral root initiation. This close relationship stresses the conservation among plant species of an auxin responsive core gene regulatory network involved in the control of post-embryonic root initiation. In addition, we report on several genetic regulatory pathways that have been described only in rice. The complementarities and the expected convergence of the direct and reverse genetic approaches used to decipher the genetic determinants of root development in rice are discussed in regards to the high diversity characterizing this species and to the adaptations of rice root system architecture to different edaphic environments.

Figure 1

Number of root related QTLs detected in rice per chromosome interval. QTL for root to shoot ratio (R/S, violet), root number (RN, green) maximum root length (MRL, red), and root thickness (THK, blue). The figure was built from data reported in Courtois et al. ([2009]).

Figure 2

Gene networks controlling root development in rice . Arrows represent the positive regulatory action of one element of the network on another one. A line ending with a trait represents the negative regulatory action of one element of the network on another one. Dotted line represent hypothetical link between two elements. Text color code: genes, black; hormones, blue; signals, red; biological processes, green.