Traits and technologies to boost North African protein self-sufficiency (BEANS4N.AFRICA)

Lead Research Organisation: University of Reading
Department Name: Sch of Agriculture Policy and Dev


Faba bean is a grain legume whose nutritional value, particularly its high protein content, has earned it the nickname "poor man's meat" and for hundreds of millions of inhabitants of North Africa, the Nile Valley and the Middle East, it is the dominant source of staple dietary protein. Furthermore, in times when sustainable agricultural productivity is more important than ever, faba bean stands out as THE grain legume that combines very high yield potential, low environmental impact due its ability to fix its own nitrogen fertilizer in its root nodules, high nutritional value and widespread cultural acceptance.
Unfortunately, production of faba bean in North Africa has undergone a long-term decrease, simply because it is grown on far less land than just a few decades ago. The major reason for this alarming abandonment of areas previously planted to faba bean is not the result of a fall in demand but due to the spread of a parasitic weed known as broomrape (Orobanche). Broomrape is unable to photosynthesize and must attach itself to a host root system in order to develop and reproduce. The inability to eradicate it from infested soil arises from the fact that it produces up to two hundred thousand tiny seed per flowering head that can lie dormant for decades in the soil until triggered to germinate and attach when the chemical signature of a nearby host root is detected.
Fortunately, there are researchable solutions to equip the faba bean to live and thrive in the presence of Orobanche seed, but to succeed in the battle on the ground, there is a need to take action on several fronts. This project recognises faba bean as a key crop underpinning the most basic level of food security in North Africa and puts forward an integrated, multi-disciplinary programme of research that addresses the faba bean self-sufficiency issue at three different levels.
Firstly, we propose immediate investment in high throughput genetic profiling technology, which we will put to use in creating a map of the six chromosomes of the faba bean genome that is orders of magnitude more detailed than any currently available. This technological step change will mean many previously untackled problems such as finding genes that confer resistance or tolerance to a range of pests, diseases and stresses will become feasible. However, on its own, this technology would have limited relevance to the nutritional and economic welfare of the developing world.
Therefore, our second level of activity is to deploy this new mapping technology in partnership with some of North Africa's best breeders and geneticists to locate genes that confer two distinct mechanisms for thriving in the presence of broomrape: one mechanism involves removing the chemical signals that trigger parasite germination, the second mechanism involves improved ability to compete with the parasite after it has attached to the root. We will complement this gene hunt (which will improve future prospects for accelerated breeding of highly broomrape-tolerant faba bean protected by both mechanisms) with capacity-building work using two traits which can be efficiently selected for already - one a novel faba bean herbicide resistance that will permit treatment of the crop with herbicides that kill the broomrape and not the crop, and the second, removal of an anti-nutritional factor called vicine that causes a serious hemolytic disorder called favism in predisposed individuals constituting 5-10% of the population.
Thirdly, because no breeding achievements actually make a difference without widespread uptake of new varieties, we integrate here a thorough socio-economic study that will produce recommendations to the project participants on what and how to deliver their breeding and agronomy innovations to maximise uptake and more generally to governments and the foreign aid community to highlight bottlenecks and potential solutions in the rollout of new varieties and agronomy advice

Technical Summary

Uncontrolled spread of the parasitic weed, Orobanche crenata, across North Africa has led to a long-term decline in production of faba bean - a staple protein source - that impacts economic and nutritional welfare of smallholders and urban poor across the region.
We propose a multi-disciplinary research program focused on this key legume, together with partners in Egypt and Tunisia, to simultaneously address: 1. the need for an efficient, high-throughput genotyping platform to make rapid progress in quantitative genetics, 2. The opportunity to exploit new discoveries and genetic resources that promise to deliver major breakthroughs in our understanding of the genetics of host tolerance to Orobanche, 3. the desire of well-trained geneticists in our partner institutes in Egypt and Tunisia to partner directly with the UK to deploy existing traits and technologies and 4. the recognition that adoption of new traits and varieties can be improved through a better understanding of barriers to uptake.
Specifically, we will design and validate a 50K SNP genotyping array and use it do develop a high resolution genetic map based on a new multi-parent mapping population. High resolution genotyping and precision phenotyping of the Orobanche-faba interaction under controlled conditions will be combined to genetically dissect two distinct tolerance mechanisms - low strigolactone exudation and greater post-attachment competitive ability. Beside these mapping studies, we will also initiate a capacity-building breeding pipeline with our Egyptian and Tunisian partners to introgress two traits of immediate value - resistance to a sulfonylurea herbicide and low vicine-convicine (anti-nutritional) content - into locally adapted backgrounds. Finally, a socio-economic study of the agri-innovation systems in Tunisia and Egypt will ensure a better understanding by project participants of end user needs and involvement of stakeholders in designing ways to increase adoption rates and impact.

Planned Impact

The overarching impact this project has been designed to deliver is to secure stable, home-grown supplies of nutritious and affordable faba beans, traditionally widely grown and hugely valued across North Africa as a protein-rich and satisfying staple food, earning it the moniker of "poor man's meat".
The project works across disciplinary boundaries with inputs from life sciences, social sciences and economics to act across the whole agronomy and breeding innovation pipeline in two contrasting North African countries, Egypt and Tunisia to build the capacity of breeding to deliver better solutions to the challenges faced, faster.
The first area of impact surrounds the adoption of the ultimate products of the research proposed here: new varieties with combinations of Orobanche tolerance mechanisms and herbicide resistance. Such varieties have the potential for faba bean production to resume in heavily infested areas, achieving high yields and depleting the Orobanche seed bank year on year. To achieve this high level impact we envisage activities to ensure that marker-assisted breeding can be perpetuated in our current partner countries and others beyond the timescale of the project by facilitating planning for transfer of marker-based selection technologies to Tunisia and Egypt and by holding a workshop to involve non-project participants in sharing our experiences. We also envisage working on involving in-country stakeholders in gathering evidence to demonstrate the value of the traits being introgressed. Using the low vicine-convicine trait as an example, we plan to generate collaborations with an Egyptian University hospital which screens and treat favism sufferers to work with us on assessing the safety of our low vicine breeding lines.
The second area of impact is in breaking down barriers to uptake of varietal and agronomic innovations. Here the approach involves activities to partner with and widen the scope of extension projects already up and running, to extend the socio-economic study to a targeted engagement of key stakeholders and to use web and social media to disseminate and engage in interactive discussion with the wider public.
Thirdly, a desirable legacy of this project would be if our developing country partners feel empowered and capable of proposing quantitative genetics research into other traits of interest, in which UK collaboration might figure in a supportive role or not at all. Towards this end, our Tunisian and Egyptian partners will write research proposals by the end of this Foundation Award that embody their enhanced capacity to undertake internationally competitive underpinning research.
Description An array-based high-throughput genotyping assay carrying over 50,000 features (SNPs) was successfully developed for faba bean. At least 30,000 SNPs were polymorphic and to date over 1,000 genotypes have been analysed. Based on this new genotyping tool, a new high density genetic map with locations of c.14,000 SNPs was developed. We have also genotyped a panel of inbred lines and demonstrated the ability to conduct genome-wide association scans.
We fine-mapped the VC1 gene controlling levels of the anti-nutrients vicine and convicine, which cause favism in genetically predisposed humans, contributing to the discovery of an unsuspected biosynthesis pathway of these secondary metabolite and obtained perfect markers with which to introgress the low vicine trait into N. African bean germplasm.
Efforts to develop herbicide-resistant faba bean lines were superceded by the release in Australia of a variety expressing very effective imidazolinone resistance and this trait source and the perfect marker associated with it have been adopted with the goal of introgressing the trait into N. African breeding programmes.
Highly controlled Orobanche resistance screening systems were developed in Tunisia, rather than in Egypt as first planned, and used to screen breeding populations for tolerance to the two different Orobanche species present in Tunisia. Several lines with novel combinations of quality and Orobanche tolerance were found.
Field-based screening in Egypt has resulted in the discovery of a new useful source of Orobanche tolerance and earliness which will be registered as a breeding line in Egypt.
In parallel with crop pre-breeding and breeding activities, a detailed socio-economic study of the Tunisian innovation system and farmer's awareness and motivation to adopt new varieties and the importance they attach to specific traits led to an increased understanding of the most productive intervention points to accelerate the pace of innovation in faba bean production systems.
Finally, the capacity-building objectives of the programme were highly successful in both partner countries; enhancing both the underpinning infrastructure needed to underpin traditional faba bean breeding methods and the skills and infrastructure underpinning molecular breeding.
Exploitation Route We plan to make the high-density genotyping array publicly available as a Life Technologies Axiom catalogue array, at which point it will be available for all public and private entities for use in their genetics and breeding programmes for the purposes of GWAS, QTL and gene mapping, parent selection and genomic selection.

A number of UK and international projects will use our Axiom array as a commonly adopted genotyping platform.
Sectors Agriculture

Food and Drink

Description The high-throughout SNP array has been used by private plant breeders in Europe to underpin genomics-assisted breeding approaches, which at the outset of the project were in their infancy in faba bean. INRAT - the Tunisian National Agricultural Research Agency - has, as a result of the project, been able to commence molecular breeding for low vicine faba bean varieties. The Egyptian ARC-Field Crops Research Institute has obtained new sources of parasitic weed resistance to enhance its varietal production pipeline and has also begun looking into the options for molecular breeding of traits such as low vicine which cannot be selected using traditional breeding methods.
First Year Of Impact 2019
Sector Agriculture, Food and Drink
Impact Types Economic

Description GCRF Agri-tech Catalyst Seeding Award "Bridging the gap between the research and release of varieties containing novel traits in Tunisia"
Amount £142,000 (GBP)
Funding ID GCRF-SA-2020-Reading 
Organisation United Kingdom Research and Innovation 
Sector Public
Country United Kingdom
Start 03/2020 
End 09/2021
Description Pulse Crop Genetic Improvement Network
Amount £1,300,000 (GBP)
Funding ID CH0110 
Organisation Department For Environment, Food And Rural Affairs (DEFRA) 
Sector Public
Country United Kingdom
Start 02/2018 
End 01/2023
Title Axiom 50K SNP genotyping array for faba bean 
Description A database containing in silico predicted SNP polymorphisms within Vicia faba coding sequences was created by mining public transcriptome datasets from eight distinct faba bean genotypes. From this SNP database, 57,529 high confidence markers covering 15,687 separate genes were selected to tile on a genotyping array. The genotyping array has been manufactured by Life Technologies as an Axiom array and validated by hybridisation with 384 diverse faba bean accessions. Preliminary results show approx 28k markers are classified as high resolution polymorphic in the initial set of samples. This number could increase as additional populations are genotyped. 
Type Of Material Technology assay or reagent 
Year Produced 2018 
Provided To Others? Yes  
Impact Separate collaborations were developed with the Crop Development Centre at the University of Saskatoon and NPZ Innovations, dominant breeders of commercial spring faba bean varieties in Canada and Europe respectively, to genotype representative lines from their respective breeding programmes. The 50K array therefore shows promise to become a standard genotyping tool facilitating easy cross-referencing of research results across borders. 
Title Axiom 50K v2 SNP genotyping array for faba bean 
Description An expanded database containing in silico predicted SNP polymorphisms within Vicia faba coding sequences was created by merging SNPs from three independent SNP mining platforms (two provided by project partners from Aarhus and INRA respectively). After removal of redundant SNPs, 57,312 high confidence markers covering >30,000 separate genes were selected to tile on a genotyping array. The genotyping array has been manufactured by Life Technologies as an Axiom array and validated by hybridisation with 1,920 diverse faba bean lines and members of mapping populations to date. 
Type Of Material Technology assay or reagent 
Year Produced 2020 
Provided To Others? Yes  
Impact Increased gene coverage of high density SNP genotyping platforms. 
Description Design of a multi-species legume genotyping SNP chip 
Organisation State Government of Victoria
Department Agriculture Victoria
Country Australia 
Sector Public 
PI Contribution My research team contributed sequences of validated and informative faba bean SNPs and related metrics such as allele frequencies in advance of publication.
Collaborator Contribution Agriculture Victoria Research (AVR) led an international consortium of research groups with data or technology relevant to high density, high throughput genotyping of the main Australian legume crops including its own in silico SNP mining. AVR will produce the multi-species chip, which will primarily be used in Australian legume breeding programmes.
Impact Not yet known as activity is just started.
Start Year 2020
Description Design of a v2 Axiom genotyping array for faba bean 
Organisation Aarhus University
Department Faculty of Agricultural Sciences
Country Denmark 
Sector Academic/University 
PI Contribution Validation of 30,000 SNPs from the v1 array. Integration of SNP information from all partners and design of a v2 array.
Collaborator Contribution Provision of deep transcriptome reference (Aarhus) and SNPs discovered from re-sequencing of 200 faba bean accessions (INRA-Dijon).
Impact v2 Axiom 50K array
Start Year 2019
Description Design of a v2 Axiom genotyping array for faba bean 
Organisation French National Institute of Agricultural Research
Country France 
Sector Academic/University 
PI Contribution Validation of 30,000 SNPs from the v1 array. Integration of SNP information from all partners and design of a v2 array.
Collaborator Contribution Provision of deep transcriptome reference (Aarhus) and SNPs discovered from re-sequencing of 200 faba bean accessions (INRA-Dijon).
Impact v2 Axiom 50K array
Start Year 2019
Description Dissemination Workshop with Tunisian Crop Innovation System stakeholders 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Policymakers/politicians
Results and Impact A virtual stakeholder engagement and policy workshop entitled "Opportunities and constraints for the faba bean production system in Tunisia" was conducted for 29 October 2020. The agenda for the workshop was divided between talks by researchers from the UKRI-funded BEANS4N.AFRICA programme disseminating the main findings from the project both in terms of crop improvement and the main factors identified in studies of the Tunisian innovation system and farmer perceptions and motivations in relation to legume crop production and a round-table discussion of opportunities and constraints. Participants included key institutional, industry and government stakeholders in the Tunisian legume crop production sector. Of importance was the presence of the Ministry of Agriculture (responsible for the national strategy for cereals which involves subsidising the growth of faba beans for soil fertility), SOSEM (the private sector seed producer who have just released the first certified faba bean seeds in the country) and INGC (the extension body who are key in reaching farmers).
Year(s) Of Engagement Activity 2020
Description Invited talk to industry representative group (Pulse Crop Genetic Improvement Network Stakeholder Workshop) 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Industry/Business
Results and Impact Gave talk entitled "Increasing diversity in faba bean" to a virtual audience of over 50 assembled stakeholders of the UK pulse improvement community; featuring updates on the measurement of diversity with SNP genotyping tools and the discovery of a key gene in the biochemical pathway to production of the anti-nutrients vicine and convicine. This included industry representatives from the breeding, agronomy, agrochemical, food processing and manufacturing sectors as well as representatives from Defra and UKRI responsible for agricultural policy and research underpinning sustainable agricultural production. Plans for stakeholder-driven research were advanced at the meeting.
Year(s) Of Engagement Activity 2020
Description Invited talk to pulse industry representative group 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Industry/Business
Results and Impact Talk entitled "Overview of industry-academia exchanges related to legume crop improvement" at the Defra-funded Pulse Crop Genetic Improvement Network Annual Stakeholder Meeting at Belton Woods, Lincolnshire on 14th November 2019. This included reporting of a survey of industry research needs, an update on public-private collaborations and projects which had recently formed in response to these needs and highlighting of opportunities for innovation in pulse cropping and end uses arising from recent research. Follow-up meetings that have spawned a potential Standalone LINK project resulted.
Year(s) Of Engagement Activity 2019