Root SAT-NAV: uncovering the molecular mechanisms guiding root angle in soil

Food security represents a major global issue. Crop production has to double by 2050 to keep pace with global population increasing to 9 billion. This target is even more challenging given the impact of climate change on water availability and the aim to reduce fertilizer inputs to make agriculture become more environmentally sustainable. In both cases, developing crops with improved water and nutrient uptake efficiency would contribute significantly to the solution. Root architecture critically influences nutrient and water uptake efficiency. For example, phosphate uptake efficiency could be significantly improved by manipulating root growth angle to better explore the topsoil where it accumulates. Despite this knowledge, the genes that regulate root angle in crops remain to be identified. Root angle is primarily regulated by the gravitropic response. However, other directional signals like water gradients induce roots' stress-activated-tropisms navigation (SAT-NAV) system when encountering drying soil. Despite their obvious importance, it is currently unclear how hydrotropism interacts with gravitropism to enable roots to forage for water. Understanding the genetic and environmental regulation of root angle is therefore of vital importance to crop improvement.

Together with our collaborators, we have recently shown that root tips respond to changes in gravity or moisture by forming gradients of the plant hormones, auxin and ABA, respectively. After a gravity stimulus, auxin accumulates on the lower side of roots, inhibiting cell growth and causing roots to bend in the direction of gravity. We suspect that ABA functions in a similar way to direct root growth towards water. How do these hormones cause these changes? We have identified ~570 genes that auxin regulates to cause root bending. The effect of auxin on root bending is therefore very complicated. To help us deal with this complexity, we will employ a new approach termed Systems Biology that brings together the best of Biology and Maths. This involves generating a large body of experimental information about these different genes and the processes they control that is then integrated into mathematical models. Auxin regulates root bending by inducing responses in many different cells and tissues. Our model therefore has to include information not just about a list of genes but also consider their behaviour in many different root cells and tissues. We then need to determine how realistic our root model is, by designing experiments to test its ability to accurately predict real results. The model can then be used to test ideas and provide new insight about how auxin (or ABA) controls root bending at the gene, cell and tissue level. It will be very important to test whether our findings in the lab are relevant to soil. We will address this important question by exploiting new advances in non-invasive imaging to monitor root growth in soils using X-ray micro Computed Tomography (CT). Using this new imaging capability we will test the impact of altering root gravitropism and hydrotropism on root water and nutrient uptake efficiency in rice. The knowledge gained from this study will help scientists understand how best to manipulate root angle and enhance crop yield.

Roots employ directional signals to explore the soil environment and acquire anchorage and resources. Root angle is primarily regulated by the gravitropic response. However, other signals like touch and water/oxygen gradients induce roots' stress-activated-tropisms navigation (SAT-NAV) system when encountering compacted, drying and water logged soil, respectively. Despite their importance, it is currently unclear how these signals and their tropic responses interact and override root gravitropism.

This project aims to uncover the mechanistic basis and functional importance of gravitropic and hydrotropic responses in roots of Arabidopsis growing on agar and crops growing in soil. Unlike previous genetic studies, our multidisciplinary approach will help develop a deeper understanding about how these directional signals and components of their tropic response pathways interact to control root angle. The experimental programme is broken down into 3 clearly defined objectives:

- Objective A will employ systems approaches to characterise the signals, networks and cellular mechanisms controlling root gravitropic and hydrotropic responses.
- Objective B will determine how these tropic response pathways interact to control root angle and regulate the biomechanics of organ curvature employing a multiscale mathematical model that will include hormone signalling, water fluxes, cell-wall remodelling, cell growth and tissue stresses.
- Objective C will employ microCT imaging of roots in soil to uncover the roles and relative importance of gravitropism and hydrotropism, exploiting recent advances at Nottingham

The knowledge gained from this study will be very relevant to the BBSRC Highlight Area "effects of environmental change on the soil-water interface: implications for food production and water supply".

Who will benefit from this research? This BBSRC Award will help establish a knowledge base about the genetic regulation of root angle that will benefit breeders by generating molecular markers to select for root traits. Project results can also be exploited in other current grants with industrial collaborators. For example, in the BBSRC IPA award (BB/H020314/1) the modes of action of a series of root growth promoting agrochemicals developed by our Industrial Partner, Syngenta, are being explored.

The microCT technology and newly developed imaging tools employed in this project will facilitate deep phenotyping for root traits in crops. The PI and several of the CI/RCIs are part of the Nottingham hub for the new European Plant Phenotyping Network (EPPN) that will enable other European researchers access to these and other facilities.

The project will also generate a number of new and innovative experimental tools, data resources and models that a wide spectrum of researchers from academic and commercial organisations would be interested in employing. For example, Life Scientists are likely to use the new imaging tools, such as the vertical imaging confocal, and image analysis software, such as CellSeT and RootTrace. Researchers in the areas of mathematics and computer sciences would also be interested in using the multicellular models.

How will they benefit from this research? The research will enable scientists at commercial collaborators to understand how to improve root function for enhanced crop performance. These outputs provide practical solutions for improving crop performance and help deliver food security, and is very relevant to the BBSRC Highlight Area effects of environmental change on the soil-water interface: implications for food production and water supply

Data generated during the project will be stored in accordance with UKAS guidelines and published in peer reviewed journals in accordance with our data release statement (see section 1b of the case for support). 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. Image analysis tools will be deposited on www.sourceforge.com where researchers can download code. Note: RootTrace has been downloaded over 1500 times, to date.

The project will also generate researchers experienced with working as part of a multidisciplinary research 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 in accordance with our data release agreement (see section 1b of the case for support). Staff would be available to enter the UK work force in 2015. 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-I's and PDRAs will disseminate their results at scientific conferences, via the CPIB website, and through published journal articles.