Hydropatterning

Food security represents a major global issue. Significant improvements in crop yields are urgently required to meet the 50% increase in world population by 2050. The degree of root branching determines the efficiency of water uptake and acquisition of nutrients in crops. Understanding the regulation of lateral root (LR) development is therefore of vital agronomic importance. We have recently observed using a new form of X-ray imaging that root branching is profoundly influenced by the distribution of water in soil. Lateral roots (LR) form on the side of the main root in contact with water, but rarely on the dry side, using a mechanism termed 'hydropatterning' that is highly conserved in all plant species studied to date.
This project will investigate how hydropatterning actually works to cause new branches to form on the wet, but not dry, side of a root. To help our studies, we have already identified several genes and processes that are important for this process. This includes a special protein called ARF7 that regulates where root branches are formed. We will test whether the ARF7 protein on the dry side of a root is modified by another protein called SUMO, causing ARF7 to become inactivated. We will perform a series of experiments to test this idea at the start of the project. Next, we will find out where and how ARF7 and SUMO regulate lateral root hydropatterning. Finally, we will explore whether this is a highly conserved mechanism that all plants have inherited from the very first land plants that colonised dry land. The knowledge gained from this study will provide information about the key genes and processes controlling root branching, helping scientists design strategies to manipulate root branching and enhance crop yield.

Understanding the regulation of root branching is of vital agronomic importance since it determines the efficiency of water uptake and acquisition of nutrients in crops. Using microCT imaging, we recently observed that the distribution of water in soil profoundly influences root branching (Bao et al, PNAS, under review). Plants achieve this via a novel mechanism termed 'hydropatterning', where lateral roots (LR) form on the side of the main root in contact with water, but rarely on the dry side. LR hydropatterning occurs in both dicot and monocot species and therefore appears to be a highly conserved adaptive root trait. Mutant studies in Arabidopsis revealed that LR hydropatterning is dependent on the auxin response (transcription) factor ARF7 and components of the Small Ubiquitin-like Modifier (SUMO) machinery. This proposal investigates whether LR hydropatterning is dependent on ARF7 (and its target genes) being differentially regulated on wet and dry root sides through SUMOylation and whether this is a highly conserved mechanism in land plants. This multidisciplinary project aims to exploit these new insights and uncover the mechanistic basis of LR hydropatterning.

Objective 1 will address whether ARF7 (like its closely related sequence ARF19) is a target for SUMOylation. Objective 2 aims to discover whether ARF7 SUMOylation blocks DNA binding causing a reduction in auxin-dependent lateral root initiation. Objective 3 will determine where and how ARF7 SUMOylation blocks lateral root initiation employing ARF7 tissue specific expression and ChIPseq analysis to reveal the mechanistic basis and target genes mediating LR hydropatterning, respectively. Objective 4 addresses how the SUMOylation machinery is controlled on wet and dry root sides to create an auxin response gradient that patterns LR branching. Objective 5 will probe whether hydropatterning & ARF SUMOylation represent highly conserved mechanisms in vascular and non-vascular land plants.

Who will benefit from this research?
- Life science researchers
- Agronomists and plant breeders
- Mathematicians and computer scientists
- Industrial collaborators
- Members of the public

How will they benefit from this research?
The project will generate a number of new and innovative experimental tools, data resources and models that a wide spectrum of researchers from other disciplines would be interested in employing. For example, Life Scientists could employ similar approaches to study SUMO-regulated processes in other biological systems; plant breeders and agronomists will use the information generated about SUMO and its target genes and processes in breeding studies and/or to design new approaches to manipulate root branching in crops, forestry and horticultural varieties; researchers in the areas of mathematics and computer sciences would use the multicellular models and software tools generated, respectively. This award would also help establish a knowledge base that will allow by Industrial collaborators, to be explored, helping generate IP and new products with the information. Members of the public would gain access to 3D images of root systems from a diverse collection of vascular and non-vascular plants via a web-based interface developed as part of this project.
Data generated during the project will be stored in accordance with UKAS guidelines and published in peer-reviewed journals. All biological materials generated will be deposited at the Nottingham Arabidopsis Stock Centre (NASC); whilst models would be downloadable from the Edinburgh-based Plant Model Repository and then, following their publication, the Biomodels database at EMBL.
The project will also help train researchers experienced with working as part of a multidisciplinary team. This multidisciplinary expertise will uniquely position them for employment in the UK Life Science and Pharmaceutical Industries.
In terms of timescales of benefits, selected data, materials and models generated would be made publically available during the period of the award as outlined above and in accordance with our data release statement (see section 1b of the case for support). Staff would be available to enter the UK work force in 2018-2020. Application of findings made by the award to create, for example, new products and IP, is anticipated to be on the scale of 5-10 years.
Engagement with end users and beneficiaries about the project:
The PI, co-Is and PDRAs will disseminate their results at scientific conferences, through published journal articles and at our annual CPIB Research Showcase meeting with Industrial collaborators, such as Syngenta and Unilever.
A website providing 3D images of root systems from a diverse collection of vascular and non-vascular plants will be made available for public access.