Mapping genetic and cellular interactions during growth of a simple plant system

Global agriculture is founded on a few crop species, the earliest of which were domesticated by Neolithic farmers. They have been subject to selection and breeding for millennia, to produce plant forms with better agronomic traits. Many of the genetic changes associated with crop domestication have been mapped precisely, to relatively few genes. These plant varieties now produce billions of tonnes of food, materials and chemicals each year. Today, radical changes are underway for engineering of plants. New gene editing techniques have allowed genetic engineers to recapitulate ancient traits and transfer them to new species. We face the prospect of being able to systematically reprogram the growth and final form of any plant, and harness the functional diversity of plant species that have not been domesticated.

But, while we have evermore-facile access to the DNA code that must be used to reprogram plant systems, the interconnections between genetic code, regulatory networks, cells and physical processes that drive emergent patterns of plant growth and form - remain ill-defined and out-of-reach for biological engineers. This proposal aims exploit a uniquely simple plant system to tackle the challenge of better understanding growth. We will use Marchantia polymorpha gemmae as a model system for direct visualisation of apical growth and manipulation of regulatory dynamics at different, interacting scales of molecules, cells, tissues and organism. We will separate interacting components using laser microscopy, in order to map functional imnteractions between cells. In addition, we are generating new markers for gene expression, and will use these to draw connections between gene activities and cell interactions.

Marchantia has been developed as a simple plant system is haploid and has an open form of development that allows direct visualisation of tagged gene expression and cellular growth in living tissues. The basal plant system is fast and easy to work with. It is easy to culture, regenerate and transform. It has a simple cellular architecture and streamlined genome with highly reduced gene redundancy. We have developed standardised DNA parts and automated assembly. Engineering systems are in place to facilitate the design of modular DNA parts and rapid assembly of large-scale genetic circuits. We plan to map cellular interactions and interdependencies that regulate patterns of cell proliferation, differentiation and branching across the meristem in Marchantia gemmae, using laser dissection and cell-fate markers.

We will apply gene editing tools and conditional complementation to allow marked clonal analysis of loss of gene function and phytohormone interactions in Marchantia gemmae, to develop and test models for systematic rewiring of Wuschel-Clavata and auxin-cytokinin regulatory networks during growth of this simple plant.

Interdisciplinary training and capacity building: Modern approaches to biology are are providing low-cost, breakthrough tools and technologies such as (i) standardised, modular DNA parts and rapid assembly of genetic circuits for reprogramming biological systems; (ii) access to simple biological systems, (iii) low-cost, customisable instrumentation for interdisciplinary research projects and (iv) legal frameworks and repositories for the free exchange of genetic materials. These new technologies are relatively low-cost, and allow radical new approaches to education and training in both the UK and low resource environments. This has led to my establishment of Biomaker, a programme for interdisciplinary project-based training and application development (https://www.biomaker.org). The Biomaker programme uses accessible hardware and visual programming to facilitate teamwork between biologists, computer scientists and engineers. Teams are provided with starter kits and technical resources that allow them to design and construction of low-cost instrumentation for biological experimentation and field applications. We have begun to implement this programme with key partners located in African institutions, to build local expertise and capacity through knowledge sharing and exchange of open-source tools and materials. Further, the outputs of Biomaker projects are being collected on an online platform (https://www.hackster.io/biomaker). This provides a free mechanism for documentation and global sharing of projects. We hope to use this funding proposal to expand this project. Accessible learning and resource sharing has a beneficial impact on training and learning systems in African universities, community labs and industry. The critical importance of this kind of knowledge transfer for emerging bioeconomies was highlighted in our GCRF report on "Capacity building for the bioeconomy in Africa" (https://www.openplant.org/reports/). Further, the adoption of frugal approaches to open, project-based learning will have major benefits for interdisciplinary teaching in UK schools and universities.

I have established of Biomaker, a programme for interdisciplinary project-based training and application development (https://www.biomaker.org). The Biomaker programme uses accessible hardware and visual programming to facilitate teamwork between scientists, but also includes community participation. Teams are provided with starter kits and technical resources that allow them to design and construction of low-cost instrumentation for biological experimentation and field applications. We have begun to implement this programme with key partners located in African institutions, to build local expertise and capacity through knowledge sharing and exchange of open- source tools and materials. Further, the outputs of Biomaker projects are being collected on an online platform (https://www.hackster.io/biomaker). This provides a free mechanism for documentation and global sharing of projects. We hope that these kinds of accessible learning and resource sharing will have a beneficial impact on training and learning systems in African universities, community labs and industry. The critical importance of this kind of knowledge transfer for emerging bioeconomies was highlighted in our GCRF report on "Capacity building for the bioeconomy in Africa" (https://www.openplant.org/reports/). Further, the adoption of frugal approaches to open, project- based learning will have major benefits for interdisciplinary teaching in UK schools and universities.