Characterisation of the molecular and cellular mechanisms controlling lateral root emergence using an integrative-systems based approach

Food security is a major global issue. Significant improvements in crop yields are urgently required to feed the dramatically increasing world population by 2050. Our industrial partner has recently discovered a series of yield enhancing agrochemicals that increase crop yield by promoting root growth and branching. Increasing the number of root branches (termed lateral roots) increases the water uptake and acquisition of nutrients in crops and therefore understanding the regulation of lateral root development is therefore of vital agronomic importance. Lateral root (LR) development can be divided into 2 distinct processes; (A) formation (i.e. new roots forming deep within the centre of the main root); and (B) emergence (i.e. when new roots which form deep inside the main root need to push through the surrounding tissues before entering the soil). Research has focused largely on studying LR formation. However, recent evidence suggests that LR emergence is an important checkpoint for root branching which is regulated by nutrients such as nitrate and phosphate and hormone signals such as auxin. We have recently shown that auxin originating from new LR acts as a local signal that promotes overlying cells to separate, enabling new roots to emerge. We have identified ~560 genes that auxin regulates to cause lateral root emergence. The effect of auxin on LR emergence is very complicated and appears to involve about 560 different genes. To help us deal with this complexity, we will employ a new approach termed Systems Biology in which biologists and mathematicians work closely together. This involves generating a large body of experimental information about these different genes which is then integrated into a mathematical model. Auxin regulates LR emergence 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 controls LR emergence at the gene, cell and tissue level. Establishing this knowledge base will enable us to determine exactly how the root-growth-promoting agrochemicals affect LR development. The knowledge gained from this study will help scientists understand how best to manipulate root growth and enhance crop yield.

The project will adopt a systems approach to study lateral root emergence. Unlike previous genetic studies, our systems approach will provide a deeper understanding of how components of the lateral-root-emergence pathway interact at the network/cellular/tissue levels. The research programme has 4 clearly defined objectives. Objective 1 will employ systems approaches to determine how and when the auxin signal reaches the cells in tissues overlaying lateral root primordia. Objective 2 will assemble new and existing components of the auxin transport and signalling machinery and their downstream targets into the LR emergence regulatory network and employ mathematical modelling to investigate the dynamics of the proposed networks and pinpoint missing components. Objective 3 will investigate the relative importance of the three key biomechanical processes (i.e. hydrostatic & osmotic potential differences; cell-wall softening; and adhesive forces between cells), how they are co-ordinated and how they interact during LR emergence employing a multiscale mathematical model that will include water fluxes, cell-wall remodelling, tissue stresses and cell growth and separation. Objective 4 will build on this knowledge base and exploit recent advances in imaging roots in soil and agar, together with other Arabidopsis root systems biology resources at Nottingham, to determine how a series of novel agrochemicals provided by our industrial sponsor promote root growth. This ambitious project demands researchers with skills in Arabidopsis molecular genetics, plant molecular cell biology and mathematical and biomechanical modelling. All of the named co-investigators and PDRAs on this grant have gained invaluable experience of the systems approach whilst working at CPIB (2007-2010). The multidisciplinary expertise, resources and tools that have been assembled for this project uniquely position us to create, test and validate our lateral root emergence model.

Who will benefit from this research? This BBSRC Industrial Partnership Award (IPA) will establish a knowledge base that will allow the modes of action of a series of root growth promoting agrochemicals developed by our Industrial Partner, Syngenta, to be systematically explored, helping generate IP and new products with the information. The project will also generate a number of new and innovative experimental tools, data resources and models which a wide spectrum of researchers from other disciplines would be interested in employing. For example, Life Scientists could employ similar approaches to study multi-cellular processes in other biological systems; researchers in the areas of mathematics and computer sciences would be interesting in using the multiscale models. How will they benefit from this research? The research will enable scientists at our Industrial Partner, Syngenta to understand how their novel agrochemicals improve root function for enhanced crop performance. These outputs provide practical solutions for improving crop performance and help deliver food security, a strategic priority area supported by the BBSRC. 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 agreement with Syngenta (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, following their publication from the Biomodels database at EMBL. 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 above and in accordance with our data release agreement with Syngenta (see section 1b of the case for support). Staff would be available to enter the UK work force in 2012. 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, through published journal articles and in reports and meetings with our Industrial partner, Syngenta.