DS05 - Sécurité alimentaire et défi démographique

Determination of MASTER regulatory genes controlling crown ROOT development for cereals water deficit tolerance engineering. – MASTEROOT

Submission summary

There is an increasing demand for cereal varieties capable to maintain their yield under limited soil resources (e.g. water, nitrate) both in developed and developing countries. In 2012 breeding companies have released maize lines marketed for drought resistance which occupied in 2014 more than 10% of the maize planted surface in the USA. Most of these varieties are improved for global water use efficiency and osmoprotection mechanisms. However, many traits contribute to drought tolerance but none is effective in all contexts and some can reduce yield under well-watered conditions. Thus there is an increasing interest to breed for root architectures allowing plants to better exploit the water and mineral resources of the soil. This has been largely underexploited up to now most likely because the root system is not easily observable. The root system of cereals is mainly composed of shoot borne crown roots. Their number is an important component of the root ideotypes that have been proposed to adapt plants to water and/or mineral nutrient deficiencies. Mutations in the rice transcription factor CROWNROOTLESS 1 (CRL1) and in its ortholog ROOTLESS CONCERNING CROWN AND SEMINAL ROOTS (RTCS) in maize lead to the impossibility to initiate crown roots. To identify new master regulatory genes involved in crown root development, we are developing a systems biology approach to determine the gene regulatory network (GRN) involved in crown root formation in rice. The GRN modelling is based on spatial and kinetic transcriptome data obtained using an original crown root inducible system byCRL1 transcription factor that we engineered in rice, and TDCor, an algorithm using time delay analysis of gene expression kinetics to infer the regulatory relationship between genes, without a priori on the function of the genes. This approach will allow us to identify new master regulator genes of crown root formation that escaped the classical genetic investigations due to the high functional redundancy observed in the genome of cultivated cereals. Five master rice regulatory genes corresponding to major hubs of the GRN will be selected prior to the start of the project, their orthologs identified and expressed in maize under the control of a constitutive or drought inducible promoters. Maize T0 plants are thus expected at the early beginning of the project. In addition, we propose to identify the direct targets of CRL1 by chromatin immunoprecipitation sequencing experiments, to validate in vivo the regulatory interaction of major hubs of the network, to refine GRN inference and to select 2 new candidate genes. The function of the selected genes (5+2) will be then studied by inactivating them via CRISPR-Cas9 in rice, or expressing them constitutively or in a drought inducible manner in rice and maize. Those lines will be phenotyped using dedicated platforms available in our consortium or onto specialized platforms. The most promising genes modifying the root system architecture and plant drought tolerance will be patented. The corresponding maize lines will be used to generate hybrids that will be challenged in field for their capacity to maintain yield under drought conditions. To reach this objective our public-private-partnership joins together two academic teams with a private company. The “cereal root system” team from UMR DIADE (IRD-UM) has expertise in cereal root development, system biology and applied mathematics. The “Adaptive Development of Rice” team from UMR AGAP (CIRAD) has a strong background in rice functional genomics including rice transformation. The private company Biogemma has expertise in maize transformation, phenotyping and field experimentation. We expect that this three years project will lead to the identification of new genes allowing suitable modification of rice and/or maize root architecture, drought tolerance and yield under water deficit condition.

Project coordinator

Monsieur Pascal Gantet (Diversité, adaptation et développement des plantes)

The author of this summary is the project coordinator, who is responsible for the content of this summary. The ANR declines any responsibility as for its contents.


AGAP Amélioration Génétique et Adaptation des Plantes méditerranéennes et Tropicales
UMR DIADE Diversité, adaptation et développement des plantes

Help of the ANR 410,429 euros
Beginning and duration of the scientific project: - 36 Months

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