IDP BRIDGES Project Descriptions

Guillaume Lacavé

Growth and bioactive properties of native potatoes from Chile: Ancestral genetic resources for modern human needs

Advisors: Prof. Achim Walter and Dr. Eduardo Perez, ETH Zurich

Plant genetic resources are the keystone of the creation of any new plant variety. They are crucial for introducing new traits valuable for the agro-food system. For instance, farmers are highly interested in varieties resistant to diseases and the industry is concerned with the uniformity of the product, as well as its protein and starch contents. In the field of logistics, resistance to transport plays a major role. Finally, consumer’s demand is today mainly focused on traits related to specific uses, taste and conservation.

The objectives of our work were to assess the potential of native Chilean potatoes to provide interesting traits regarding resistance to drought stress, and health  benefits thanks to antioxidants content or resistant starch. These native varieties, also called landraces, are an important heritage of Chile, created by ancestral farming systems throughout generations of farmers. Our results showed a high diversity in the response of the landraces to drought stress in the field. Regarding nutrition traits, a broad spectrum of contents in anthocyanins, polyphenols, starch, resistant starch, proteins contents could be described in Chilean landraces, as well as interesting antioxidant potential. Though the impact of drought was observed on  the yield of potatoes, no impact was detected on the concentration of the different bioactives analysed (anthocyanins, polyphenols, starch, resistant starch).  Additionally, the receptivity of the Chilean market to new potato products was also  investigated through a stakeholders and consumer’s analysis in Chile. This study focused on specific marketing advantages such as local origin, attractive colours and high antioxidants content. The results showed an interest of the potato market for innovative products, including products rich in antioxidants.

Associated Partner:

María Elvira Zúñiga, Director of Regional Centre for Studies in Food and Health (CREAS, Centro Regional de Estudios en Alimentos y Salud, Valparaíso, Chile). CREAS  is a research, scientific and technology Centre located in Valparaíso. It is currently a nonprofit private corporation. One of the utmost purposes of CREAS is to establish itself as an excellence Centre of technological research, focused in the strengthening of healthy and functional food production in its area.

 

Devang Mehta

Engineering virus resistance in cassava: Towards a sustainable production system in Africa

Advisor:  Dr. Hervé Vanderschuren, ETH Zurich

Cassava is a staple food crop for almost a billion people worldwide and especially in sub-Saharan Africa. Unfortunately, cassava production in Africa is severely limited by the effects of cassava mosaic geminiviruses (CMGs). Genetic engineering thus holds great promise for rapid improvement of cassava varieties, and without promoting a reliance on chemical measures to limit insect vectors which transmit damaging viruses. Unfortunately, DNA viruses are often fast-evolving species and to-date no successful release of transgenic plant resistant to DNA viruses has been carried out.
In my project we sought to study the field effectiveness of engineered virus resistant cassava plants. Our results from a confined field trial of these transgenic plants in Kenya indicate that transgenic plants displayed moderate resistance in the field as compared to controlled lab experiments. We have subsequently worked on  developing a novel long-read enrichment sequencing approach to precisely sequence the geminiviruses that infected our plants in the field. The results from this sequencing experiment will provide us with additional insights into the populations of geminiviruses present in Africa, as well as populations of geminiviruses present in individual plants, and the effect of our transgene on these populations. Additionally, we have developed new transgenics, using both RNA silencing and CRISPR/Cas9, which are being assessed for resistance to the CMGs in lab experiments. The long term vision for my project is to disseminate transgenic sources of resistance which can help farmers in sub-Saharan Africa sustainably deal with the endemic problem of cassava geminiviruses. We also plan on working with our partners in South Africa to help develop cassava as a commodity crop for starch production, leading to greater economic returns for farmers who currently use cassava as a subsistence crop with very poor marketability.

Partner: 

Professor Marie Emma Christine Rey, University of the Witswatersrand, South Africa (Plant Biotechnology Programme). Wits, a world-class research university in Africa, is renowned for its commitment to academic and research excellence. It contributes to the global knowledge economy and local transformation through the generation of high level, scarce skills and innovative research. At the forefront of a changing society, Wits is an engaged institution, dedicated to advancing the public good. It promotes intellectual communities and attracts talented students, distinguished academics and thinkers from around the globe.

Silvia Turco

Small RNA-omics for diagnostics: Improve measures and management practices of viral disease

Advisor: Dr. Mikhail Pooggin, University of Basel

In modern agriculture, horticulture and farming, it is critical to assess the risk of emerging plant infections and to control the spread of plant viral diseases, which requires a fast and reliable virus diagnostic and genome reconstruction tool.

The siRomics approach based on small RNA sequencing and bioinformatics analysis was used for virus detection and genome reconstruction. In a potato sample from a local shop, a combination of RT-PCR and bioinformatics was used to reconstruct two closely related strains of the same Potato virus Y. In another sample, a complex of Potato virus Y and Potato virus X was identified. In collaboration with Agroscope, many more samples have been analyzed. As expected, grapevine samples showed a crowded virome, including viroids. In cherry trees affected by little cherry disease, we confirmed that the presence of two strains of Little cherry virus in one of the samples, induce more severe symptoms compared with the sample where only one virus was detected. In a fig tree exhibiting virus-like symptoms coming from a private garden, a local isolate of Fig mosaic virus was identified and reconstructed. Finally, in the forest bush plant Ligustrum vulgare (privet) showing yellow mosaic disease, a totally novel virus distantly related to Barley yellow strip virus and Lychnis ringspot virus was identified, fully reconstructed and named Ligustrum mosaic virus. The siRomics approach was also used to evaluate the cross-protection in tomato plants pre-inoculated with a protective strain of Pepino mosaic virus against a more severe local isolate. The results of our study are informative for further understanding the mechanisms of RNA silencing-based antiviral defenses, which would contribute to basic research in the field of plant-pathogen interaction, and for developing novel strategies of virus control, which could potentially be implemented in the future in Swiss agriculture though our recommendations to the policy-makers.

Partner:

Olivier Shumpp, Agroscope, Nyon, Switzerland is the Swiss centre of excellence for agricultural research, and is affiliated with the Federal Office for Agriculture (FOAG).

Claudia Hahn

Effects of seasonal drought on the productivity of grasslands: Recommendations for a sustainable fodder production in a changing climate

Advisor:  Prof. Ansgar Kahmen, University of Basel

The response of grassland productivity to projected future increases in extreme weather events, such as droughts, is of high interest. In particular, the timing of a drought events in the course of the growing season and its impact on the functioning of the ecosystem remains unclear.

In our experiment drought had an impact on the seasonal productivity of highly managed grasslands in every season. However, absolute growth was reduced under spring drought more than under summer or fall drought. Most interestingly, though, the total annual biomass production (ANPP) was only affected by summer drought events, while spring and fall drought events did not lead to a reduction of ANPP. This surprising pattern was caused by biomass production levels in the post-drought phase after a drought event exceeding the productivity of the control. However, under future climate change agricultural production is at stake. Understanding the effects of extreme weather events on yield will help stakeholders to make future fodder production more predictable and, thus, sustainable. In addition, the individual
responses of different grassland species on drought events occurring at different times in the growing season will help farmers and seed companies to design adapted seed mixtures that will help to sustain productivity in a more variable climate. To successfully integrate our results into actual policy work we are liaising closely with the AGFF, which is an association of farmers and other institutions interested in fodder production. The AGFF regularly organises information events, field excursion or other events to inform farmers and other stakeholders about recent research and state of the art farming practices.

Partners:

Andreas Lüscher, head of research group Forage Production / Grassland Systems (Agroscope), and Willy Kessler, managing director, Arbeitsgemeinschaft zur Förderung des Futterbaues (AGFF, Swiss Grassland Society)

Agroscope is the driving force in agricultural research for sustained economic activity in the agricultural, nutritional and environmental sectors. Agroscope develops scientific knowledge and basic technical principles for agricultural and environmental policy decisions and their legal implementation. AGFF links research with the extension services and grassland farming, and transfers knowledge and innovation for an economically and environmentally friendly grassland use into practice.

Arianna Nigro

Revealing the importance of sugars for plant performance: Development of a high-throughput phenotyping protocol

Advisor: Dr. Diana Santelia, University of Zurich

In plants sugar transporters localized at the cellular membrane mediate the  exchange of sugars. Sugar Transport Proteins (STPs) are one of the major classes of sugar transporters in Arabidopsis thaliana.

Using the quantitative high-throughput phenotyping protocol developed at Photon Systems Instruments (PSI, Czech Republic) (Awlia et al. 2016), we show for the first time that Arabidopsis plants lacking both STP1 and STP4 transporters are significantly impaired in growth and photosynthesis. These plants have also lower capacity to take up carbon dioxide through stomata – pores on the leaf surface –, partially explaining their reduced growth and photosynthesis. Our scientific achievements result from the successful application of cutting-edge technology to basic research. Working at the science-innovation interface has made possible to combine technological advances with scientific knowledge, overcoming previous difficulties and achieving the foreseen goals. Different missions and languages embraced by academia and industry can constitute a challenge in the decision-making process for the development of the project. The main outputs of this project are knowledge generation together with the creation and validation of standardized methodological protocol now integrated in the portfolio of the screening approaches offered by PSI.

Partner:

Klara Simkova, Chief Scientist for Technical Support, PSI, Czech Republic. For over twenty years PSI has been specializing in the design and manufacture of sophisticated, high-end instrumentation for research in biological sciences. The current product lines include: chlorophyll fluorescence techniques, advanced Chl and GFP imaging, intelligent photobioreactors, growth chambers and algal incubators,  plantscreen and plant phenotyping systems customized to users' needs, wide range of compact, hand-held instrumentation. PSI products are based on the latest techniques and components used in scientific programs in many countries throughout the world.

Wuyan Wang

Developing starch diversity in the orphan crop tef: Improve breeding programs in Africa

Advisor: Prof. Dr. Samuel Zeeman, ETH Zurich

Tef (Eragrostis tef) is an important food grain in Ethiopia, where it is used to make injera or keyta. Tef seeds have high fiber, iron, and are gluten-free. Yet tef lacks diversity in its grain starch properties.
To address this, we are using reverse genetics (TILLING and high-throughput DNA sequencing) to find new tef lines with altered starch. We found six lines with mutations in the Granule Bound Starch Synthase 1 gene. By sequencing many starch related genes amplified from pooled genomic DNA of 4000 plants, a single  nucleotide polymorphism (SNP) database can be established. Validation of these SNPs is presently ongoing. The essential role of tef as a crop in Ethiopia and the  increasing demand for tef products in global food market underscore the significance of our research work towards its improvement. In the future, tef varieties with altered starch properties from our project can have long-term impact, enhancing the use and value of tef within and outside Ethiopia. Furthermore, if successful our program can serve as a flagship case in Ethiopia, demonstrating that international scientific collaborations can bring real benefits to ordinary people. The cooperation with the Ethiopian Institute of Agricultural Research offers us the possibility to transfer our scientific outputs to society. With bringing new tef varieties into their breeding program, increasing amount of high quality tef with new starch traits will be selected out and be chosen by the local farmers. Thus, then the food market will also be enriched both at the national and international level.

Partners:

Dr. Zerihun Tadele, University of Bern, and Dr. Assefa Kebebew, The Ethiopian Institute of Agricultural Reasearch ( EIAR). The research group of crop breeding and genomics in University of Bern focus on improving economically important but under-researched crops from developing world. Currently they implement a modern improvement technique to develop lodging resistant and drought tolerant tef cultivars. EIAR provides strong leadership in coordinating research within the Ethiopian Agricultural Research System (EARS), by taking a leading role in influencing agricultural policy development.

Michael Thieme

Unlocking sealed genetic resoures: Making use of epigenetics in plant breeding

Advisors: Dr. Etienne Bucher and Prof. Thomas Boller, University of Basel

Plant genomes consist in large parts of repetitive elements that are capable of making new copies of themselves under certain conditions (transposable elements). Interestingly, some of these elements can serve as genetic sensors for external stimuli such as heat stress, making them in theory a powerful tool for plant breeding. However, to avoid their uncontrolled proliferation under normal growth conditions these elements are strictly repressed by the plant.
During my PhD project, I discovered a key regulator at the origin of TE-silencing that can easily be targeted with a simple drug application. Thus, I developed a method to open a so far sealed endogenous genetic resource that can now be used for plant breeding. My findings significantly contributed to the development of a highly innovative and patented approach for plant breeding that could contribute to food security of a growing population under changing environmental conditions. Cultivation of more efficient and stress tolerant crops would come along with a decreased need for pesticides and fertilizers. Hence, our approach that fully relies on the stimulation of endogenous genetic resources could be of particular interest to achieve the main objectives of organic farming. To bring this new method to the market, evidence is needed for the scientific progress but also as a basis for a successful dissemination to and discussion with identified stakeholders such as breeders, farmers and consumers. A positive perception of these stakeholders will be essential for establishing this approach and to be considered in political decision-making. Therefore, a socio-economic assessment of acceptance of this technology by stakeholders will be the next step.

Partner: 

Dr. Monika Messmer, Research Institute of Organic Agriculture (FiBL). FiBL is an independent, non-profit, research institute with the aim of advancing cutting-edge science in the field of organic agriculture.

Timothy Sykes

Molecular breeding strategies: Control pollination for improved forage and turf grass breeding

Advisor: Prof. Dr. Bruno Studer, ETH Zurich

Grasslands are important agro-ecosystems; worldwide, they account for 80% of milk production and 70% of meat production. Perennial ryegrass (Lolium perenne L.) is a major component of temperate grassland systems and accounts for almost 50 per cent of total grass production, making it the most important grass species in Europe. In forage grasses, biomass is the primary yield target, but despite intensive breeding efforts over the last decades, increases in biomass yield are below that of major crop species.
My research has focussed on the restoration of cytoplasmic male sterility in perennial ryegrass (Lolium perenne L.). This trait is important for plant breeders as it allows pollination-direction control during the commercial production of potentially  higher yielding hybrid seed. My research has identified the genomic regions likely responsible for fertility restoration and I am currently developing molecular markers that will allow breeders to quickly identify if their plants are carrying the gene responsible for fertility restoration, ultimately speeding up the breeding process. As I am working within molecular plant breeding techniques I have been actively involved in the policy debate surrounding the emergence of these new plant breeding techniques. I have organised and moderated a stakeholder debate at Europe’s premier plant breeding and research conference (EUCARPIA), as well as being interviewed for Swiss national radio and newspapers. This has culminated in being chosen by the Swiss Academies of Science to represent Switzerland at the European Academies Science Advisory Council’s working group on genome editing, providing science-policy advice to the European parliament.

Partner:

Dr. Torben Asp, Department of Molecular Biology and Genetics at Aarhus University, Denmark, and The Norddeutsche Pflanzenzucht Hans- Georg Lembke AG is a medium-sized, privately-owned, plant breeding company located in Hohenlieth (Schleswig-Holstein) and Malchow-Poel (Mecklenburg-Vorpommern) in Germany.

Lisa King

Biodiversity conservation in the tropics: Investigate transition and development pathways of commodities

Advisor: Dr Jaboury Ghazoul, ETH Zurich

The availability and quality of land use data has improved considerably, however, we remain limited in the recommendations, we can make given that much important information is still not readily available from satellite imagery. Better  understanding local dynamics and ensuring the implementation of research recommendations remain an ongoing challenge.
Within this project, we modeled the competing demands for land from agricultural commodity crop development in Indonesia, specifically palm oil, rubber and cocoa. The main results were that there is an important potential for continued land conflicts given the overlap in areas of high suitability for the crops studied, and the overlap with existing crops essential to food security. Current governmental and voluntary conservation measures have the potential to protect large areas of forest, however, this will depend on their effective implementation and whether differences in sustainability standards in different industries can be reconciled. Evidence is necessary to ensure that policies for reducing  deforestation and biodiversity loss are effective in achieving their intended effects, including the mitigation of unintended side effects. My work highlighted that without better integration of conservation initiatives with regards to agricultural commodity development, environmental degradation will continue.

Partner: 

Professor David Wilcove, Ecology and Evolutionary Biology and Public Affairs, Princeton University. Princeton University's Program in Science, Technology and Environmental Policy (STEP) is based in the Woodrow Wilson School of Public and International Affairs with strong ties to the Princeton Environmental Institute.

Charlotte Pavageau

Co-production of pollination services in coffee plantations: Developing sustainable management scenarios

Advisor: Prof. Jaboury Ghazoul, ETH Zurich

Designing optimal land-use is a key challenge for decision makers and policies aiming at promoting sustainable development for a given region. However, optimal land-use planning is very uncertain and embedded with high complexity. Thus, research on modelling landscape-scale ecosystem services and land-use planning, contribute to this debate.
My PhD project focused on how the landscape is driving pollination services in a coffee growing region. We underlined the importance of land-use mosaic, in particular the imbrication of agroforests and forest fragments, as well as local management practices to attract pollinators in coffee plantations. Besides, we developed two alternative management scenarios potentially impacting pollination service: a better coordination between farmers by irrigation scheduling and nesting site conservation. We explored how pollination services and crop production could  be optimized under those two scenarios. While coordination between farmers displays higher benefits, the implementation of such strategy would pose many  challenges, from the integration of many individual decisions to the creation of dedicated institutions. This scenario is also associated with uncertain risks for the production of coffee, as well as other environmental impacts on forest cover. My work is helping to assess the consequences and risks of different scenarios, using the example of pollination service. We started to overcome these challenges by using participatory approaches such as stakeholder workshop with farmers and local authorities and information leaflet to share different views on the future of agricultural landscapes.

Partner: 

Prof Uma Shaanker (ATREE). ATREE is a non-profit organization working to conserve India’s biodiversity. It’s mission is to promote socially-just environmental conservation and sustainable development by generating rigorous interdisciplinary knowledge that engages actively with academia, policy makers, practitioners, activists, students and wider public audiences.

Yuanyuan Huang

Fixing carbon in subtropical forest to mitigate climate change: How to transfer the knowledge to farmers

Advisor: Prof. Dr. Bernhard Schmid, University of Zurich

Forest ecosystems contain the majority of the carbon stored in terrestrial ecosystems, and play an important role in helping mitigate climate change. A central question in biodiversity research is how experimental manipulations of plant diversity affect primary productivity including carbon storage. Grassland experiments have shown a positive relationship between the two variables, but it is not clear if the same holds for forests.
We tried to understand whether more diverse forests provide more forest ecosystem services. With observational studies, we found that biodiversity can promote tree growth in natural forest. By monitoring tree growth of around 13.000 trees in 512 plots with six biodiversity levels (1, 2, 4, 8, 16 or 24 species) for four years (2013–2016) in a field-manipulated experiment, we discovered that more diverse plantations during the initial 7 years of growth accumulated more biomass, and this positive diversity effect increased with time. It turned out pathogens and  herbivores inhibited productivity more in low than in high diversity. Thus, it is important to take species’ richness into account in afforestation. Our results can be directly linked to on-going assessments that sup-port forest policy design,  strengthening the science - policy interface for the conservation and sustainable development. We carried out questionnaire surveys and interviews with stakeholders in five villages near the field site to obtain a good understanding of their attitudes toward forest ecosystem and biodiversity. We also built up a micro-blog, through which people can receive information about «biodiversity and forest ecosystem functioning» on their mobile phones. However, it is not easy to successfully integrate decision makers into the project without any immediate practical profits for them.  This causes some difficulties to translate the scientific data into actual management decisions.

Partner: 

Prof. Keping Ma, Institute of Botany, Chinese Academy of Sciences (IBCAS). The Institute of Botany of the Chinese Academy of Sciences (IBCAS) is one of the oldest comprehensive research institutions in China, which has led the development of plant science in China since its establishment in 1928. The institute has received three first-level National Natural Science Awards, as well as more than 160 awards at the national and provincial level.

Constantin Pöll

Recent biodiversity changes in managed grasslands in the Swiss mountains

Advisor: Prof. Jürg Stöcklin, University of Basel

Agriculturally used grassland in mountain areas are among the most species rich habitats in Europe. In addition to natural gradients, i.e. spatial and temporal variation, different types of land use have shaped the landscape and thereby the biodiversity of grasslands. Mowing or grazing, the intensity of land uses, the amount of fertilizers and the accessibility of parcels are important determinants of grassland biodiversity. Socio-economic and associated land use changes are a major threat for this diversity. Great efforts are necessary to protect the existing biodiversity because of its importance for the stability of ecosystems and the many directly and indirectly associated ecosystem services.

In my study I am using biodiversity data from grassland parcels of the Swiss Alps and the Swiss Jura recorded 10 to 15 years ago. In the same geographical positions with the same methods, I record plant diversity again. Biodiversity changes will be evaluated by comparing new and old plant diversity data, i.e. species number and composition. By interviewing farmers, I reexamine for each parcel the socio-economic drivers and recent changes in land use. This approach allows evaluating effects of land use and socio-economic factors on plant diversity. Land users are involved in the project from the start and will, together with local and federal authorities be involved in the formulation of recommendations for measures and improvements of incentives to maintain biodiversity.

Lukas Schütz

Reliability of biofertilizers: Improving food security and nutrient use efficiency

Advisor: Prof. Thomas Boller, University of Basel

Microbial inoculants or biofertilizer are a promising tool for future agriculture. Biofertilizer exist in various forms such as rhizobia, azospirilla, or mycorrhiza. Particularly in dry regions, the use of these microorganisms may provide a potential solution to improve water and nutrient use efficiency. However soils are highly diverse in their composition and soil biota which makes the inoculation success hard to predict.

My PhD thesis is dedicated to the application of biofertilizers mostly to South India, and my results support the successful application of biofertilizers in this region. My research topic is the use of biofertilizers such as arbuscular mycorrhizal fungi (AMF) in a pigeon pea-finger millet mixed cropping system in South India. In my experiments, I studied the complex interactions between the two plant species, arbuscular mycorrhizal fungi and soil fertility. I could show that AMF species differ in their ability to spread through soil to colonize neighboring plants, and also in their  ability to promote the growth of the plants. Furthermore, I conducted a meta-analysis of 171 field studies to compare the yield responses of various crops and their phosphorus and nitrogen use efficiency in response to biofertilizers. We identified key factors like pH and soil carbon influencing the success of biofertilization. However, the study of soil biodiversity is only at the beginning and the success of biofertilizer application is still difficult to predict. In the future, there will be more tools and better soil maps to study the soil community and develop a better understanding of their interactions with plants and biofertilizers, which will advance this field furthermore.

Partner:

Paul Mäder, Research Institute of Organic Agriculture (FiBL). FiBL is an independent, non-profit, research institute in the field of organic agriculture. FiBL’s research team works together with farmers to develop innovative and cost-effective solutions to boost agricultural productivity while never losing sight of environmental, health and socio-economic impacts. Alongside practical research, FiBL gives high priority to transferring knowledge into agricultural practice through advisory work, training and conferences.

Margarida Sofia Nobre

Evaluating the potential of apomixis for sustainable agriculture and food security

Advisor: Prof. Dr. Ueli Grossniklaus, University of Zurich

Apomixis, the asexual reproduction through seed, leads to the formation of offspring that are clones of the mother plant. Apomixis occurs naturally in about 500 species of flowering plants spread over diverse taxonomical groups, some ancient lineages, some more recent. The exact way the clonal seed is formed also varies from one species to another. It is evident, then, that the process must have arisen independently in each group. By reproducing clonally, a plant’s features will remain unchanged (as opposed to having a mix of the features of both parents). In nature, this allows the colonization of specific niches, often harsh growing conditions, to which those features are particularly suited. For agriculture, however, the appeal is in the genetic fixation of hybrids and thus hybrid vigor. Hybrids, generated by crossing to distinct inbred parental lines, perform better in the field, showing a higher robustness against biotic and abiotic stresses and producing higher yields. However, hybrids are either sterile or lose their advantages in the following generation, so the original cross must be recreated every season, to great cost in time and money. Therefore, the harnessing of apomixis in crops has been a long sought-after goal to preserve hybrid vigor via clonal seed production. Apomixis is considered a consequence of the misregulation of genes (in time and/or space) regulating sexual reproduction. It is well known that hybridization events lead to metastable changes in gene expression, such that one can postulate that apomixis might result from hybridization. Indeed, most apomictic species either are allopolyploids, i.e. hybrids of two distinct species, or have gone through a period of allopolyploidization in their evolutionary history. Since such primary hybrids are often sterile, apomixis could be a way to overcome sterility. Apomictic seeds are formed in various ways. In common, they must avoid meiosis (apomeiosis) to end up with a diploid embryo sac (containing the egg cell that will become the embryo, and the central cell that will become the endosperm) that will not require fertilization of the egg cell to develop into an embryo (parthenogenesis). This can either happen by independent means (autonomous apomixis), or require fertilization of the central cell (pseudogamous apomixis). In this project, we worked with the genus Boechera. These mountain plants are the closest relatives to the model system Arabidopsis thaliana in which apomixis occurs. Importantly, in the Boechera genus there are species that reproduce sexually, apomictically, or one or the other in a gradual and facultative way. Moreover, while many  species are polyploid, apomixis was also reported at the diploid level, simplifying molecular analyses. We looked into genes that, when mutated in Arabidopsis, display elements of apomictic reproduction. We compared the sequence and structure of those genes between several Boechera species to look for a possible correlation with the mode of reproduction and their evolutionary history. Some of these genes have striking differences that signify the production of completely different versions of the encoded protein. This would have significant implications for the development of the reproductive cells and may sway their path towards one or another reproductive mode. The next steps will be to assess the functionality of these proteins. Can we change the way a plant reproduces by inserting one version of the corresponding gene into another species? This is yet to be seen. But if it works, we will be one step closer to understanding apomixis, and perhaps one step closer to engineering it in economically valuable crops.
 

Contribution at the interface of S&P / S& Innovation
When talking about evidence-based decision making, the most immediate thought is of policy decisions based on scientific data. But research itself can (should) be based on evidence and prior knowledge, and funding and project management decisions are made with this information in mind. In any company, a project that aims to develop a product includes an analysis of the intellectual property surrounding the possible outcome: what are the patents involved in the necessary enabling technologies, who owns them, who can be a competitor or a collaborator. Such a study is called a patent landscape, and millions are spent by companies in establishing these landscapes for each product they intend to develop and market. In the sciences, such a landscape is a necessary but often overlooked step in developing a project. Too often, an academic research proposal aiming to pursue a promising innovation that could bring benefits to society cares only for the discovery itself and not the future use of it. At most, institutions encourage the patenting of the discovery, and funding organisms are satisfied with that prospect. But no innovation can be used in a vacuum; a marketable product will involve dozens (if not hundreds) of steps in its production that will, themselves, also be under patent protection. That academic researchers disregard patent landscaping is easily understandable: they might simply be ignorant of the existence of such a thing, or they might know how patents are dense with obscure legal language, and that wading through a sea of patents is cumbersome and time-consuming, when there are experiments to carry through and articles and grant proposals to write, not to mention that there is also very little external encouragement to produce a patent landscape. But academic researchers, and especially those in plant and agricultural research with clear translational aspects, cannot afford to ignore this task. How then is this to be encouraged into common practice?

The answer lies in sharing.

CAMBIA, the organization at which I worked during the secondment to their offices in Canberra, has been developing and improving free online platforms dedicated to serve whoever wants to research and analyse patent documents. On their main patent platform, the Lens (lens.org), anyone can easily search and read millions of full-text patent documents from around the world, as well as see their legal status. Users are able to browse, collect documents, and perform basic analysis on their groups of patents of interest, all free of charge. The Lens is continually improved via user feedback, and its developing team continues to negotiate access to more full-text documents from as many patent jurisdictions as possible. During my time with CAMBIA, I worked on drafting a patent landscape for the use of apomixis as a technology, that is, the technological path to producing a plant that has been engineered to reproduce apomictically. I served as well as a benchmarker, by brainstorming and suggesting improvements to the platform based on my user experience. The goal is to develop the Lens to a platform that is as user-friendly as possible, and that helps the users navigate the patent sea even without much previous knowledge. The vision for the future is to expand the Lens into a user-content driven repository of landscapes, where landscapes can be shared and improved upon by the community of users, so that the act of patent landscaping can be just a matter of assembly, improvement, and fact-checking, saving time and making the process easier and less daunting, and ultimately making it an ordinary part of project planning.

Partner:

Dr. Richard Jefferson, CEO of CAMBIA (CAMBIA). CAMBIA's mission is to democratize innovation: to create a more equitable and inclusive capability to solve problems using science and technology. Their institutional ethos is built around an awareness of the need and opportunity for local commitment to achieving lasting solutions to food security, agricultural, public health and environmental problems, envisioning a situation in which the broadest community of problem solvers are empowered with new technologies to become innovators in developing their own solutions to the challenges they face - solutions for which they feel ownership.