Non-coding RNAs in the adaptation of root growth to phosphate starvation – RNAdapt

Methods for plant growth and seedlings transfert on different P conditions were developed by Partner 2. Culture conditions were validated. Root apex harvest protocols was improved and RNA samples preparation for sequecing was developed. Partner 1 has optimised the most suitable conditions for the harvest of root tip sample after a transfert in +/- P deficiency. The first tasks aimed to homogenize culture conditions between partners and to perform a first test for the transcriptome analysis.

Development and validation by Partners 1 and 2 of methods for root apex sample obtention and RNA extraction. A first experment performed by partner 2 and analysed by partner 1 yielded 52 new non-coding RNAs in the -P transcriptome and allowed a first test of a pipeline for ncRNA detection.

The RNA samples will be produced for sequencing and bioinformatic analysis.

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Non-coding RNAs are emerging actors in the adaptation of plants to environmental constraints. Indeed, alteration in gene regulation, linked to the non-coding portion of the genome, rather than changes in protein coding genes, may be major forces acting in evolution and adaptation. Phosphorus is an essential mineral for plants and very often a limiting factor for crop yield. World phosphorus resources are expected to be exhausted before the end of the XXI century. Molecular and genetic approaches have revealed several regulatory elements controlling many responses triggered in plants to cope with phosphate starvation, notably root architecture, and significant differences were found among Arabidopsis ecotypes on root growth in phosphate depleted soils. We performed QTL studies that revealed the root tip as a central organ for Pi-sensing and the control of root growth. Furthermore, a consequent genetic approach identified many mutants affected in this root growth response. In parallel, the importance of transcriptomic control and of specific non coding RNAs in plant responses to phosphate starvation was established.
In the present project we propose to analyze the root apex response to an environmental constraint using global genomic analysis on different Arabidopsis ecotypes showing contrasting adaptation of their root growth to phosphate starvation. We will analyze complete transcriptomes of mRNAs, non-coding RNAs and small RNAs in root apexes submitted to low and high phosphate and establish regulatory correlations between them. The advantages of the well-studied accessions of Arabidopsis together with advanced genomics approaches (RNAseq) will serve to address the impact of non-coding RNAs in adaptation to environmental constraints and in the evolution of gene regulation. We will assess the degree of evolution of expressed non-coding RNAs among ecotypes to link root adaptive traits to phosphate starvation and specific non-coding RNAs. Using the mutant collection in the Columbia ecotype affected in the responses of roots to phosphate starvation, the proposed regulatory interactions between non-coding RNAs and root growth will be further confirmed. Functional analysis of the identified key non-coding RNAs based on their inactivation and cell-specific modification will be used to define their role in the control of root architecture adaptation to low phosphate. This innovative project uses genome-wide comparisons of differently adapted genotypes to identify regulatory cascades linking root growth and phosphate nutrition. The fundamental and applied data that we expect to obtain would hopefully shed light on global regulatory mechanisms controlling root growth in phosphate-depleted soils and may have a direct impact on crop productivity through novel original patents in this field. More generally, this project will give novel insights on the role of regulatory non-coding RNAs in the evolution of gene regulation in response to the environment.