Modelling and manipulation of plant-aphid interactions: A new avenue for sustainable disease management of an important crop in Africa

Lead Research Organisation: University of Cambridge
Department Name: Plant Sciences

Abstract

In Eastern and Central Africa beans are a vital crop because they enrich the soil with fixed nitrogen (an indispensable natural fertilizer), which in turn supports the cultivation of other important crops such as corn (maize) and cassava. Beans are an essential part of the regional diet because they are rich in protein and crucially important micronutrients like iron and zinc. Since beans are predominantly grown and traded by women, this crop provides additional direct economic benefits to women and their children. Unfortunately, a number of viruses attack bean plants, causing severe crop losses from disease. Although there are a few bean varieties with resistance to one of these viruses (called bean common mosaic virus), a closely related virus that occurs widely in, and is indigenous to, Africa (bean common necrotic mosaic virus) causes plants of these 'resistant' lines to die. Thus, it is important to develop new strategies to defend this vital crop.


Our approach is to attack the insects (aphids) that transmit these viruses from plant to plant. We have found that aphid-plant interactions are controlled in large part by the plant's 'small RNA pathways'. Small RNA pathways are a recently discovered regulatory system used by plants and many other organisms to control the expression of their own genes as well as to fight off disease. The discovery of small RNA pathways has revolutionized biology and medicine. In plants, small RNA pathways control, among other things, the production of natural signal chemicals that attract or repel insect pests, including aphids. Intriguingly, viruses produce factors called 'silencing suppressors' that modify small RNA pathways. We have found that silencing suppressors affect the interactions of virus-infected plants with aphids in a way that is likely to enhance the rate at which these insects acquire viruses and transport them to other plants. We have assembled a team of scientists based in Uganda, Kenya and at two centres in the UK to translate these findings from the laboratory to the field and exploit them for protection of beans. However, aphids and the viruses they transmit are problems for all major crops and the work will yield vital data for the wider field of crop protection.

Our multinational team will collaborate to:

A. Identify potential factors involved in mediating plant-aphid communication in plants: small RNAs, the genes they control, and the chemical signals whose production they regulate.

B. Use the modelling methods provided by the discipline of mathematical epidemiology to help us design experiments (under lab and later field conditions) to predict how altering the attractiveness of plants (whether engendered by changes in the plant or deployment of signal chemicals as traps or decoys) could be used to help minimize or prevent the transmission of viruses.

C. Utilize the work from 1 and 2 to design experiments to test the effects on virus transmission of modifying plant responses to aphids or utilization of purified signal chemicals to trap or deter aphids under controlled and simulated field conditions.

D. To achieve impact by disseminating information gained from our work to African crop scientists, growers and consumers through the Pan-Africa Bean Research Alliance, a network of the national bean research programmes of 28 African nations.

Technical Summary

Our overall objective is to assess potential risks/benefits for disease management (using epidemiological modelling with experimental validation) from identifying and adapting the knowledge/tools (including gene sequences/semiochemicals/epidemiological models) from studying viral suppressor of RNA silencing-mediated effects on aphid-plant relations to develop 'push-pull'-type systems to protect bean. However, aphids are important pests and disease vectors affecting all major crops, meaning our results will have wide applicability. Our collaboration will translate work from model systems (Arabidopsis and tobacco) to a vital crop (bean) with uniquely African viral disease problems (with emphasis the combined effects of bean common mosaic virus and bean common necrotic mosaic). Key objectives/activities are listed with lead researcher(s) and time-scales indicated in parentheses.

1. Epidemiological modelling (Yrs 1-4, CAG, Cam)
2. Validation and exploration of modelling predictions in controlled conditions (Yrs 1-4, Cam)
3. Field surveys and data collection in Uganda (Yr. 1) and experiments utilizing data from 1 and 2, and field samples (Yrs. 2-4)(MA, CIAT)
4. Analyzing the effects of silencing suppressors on bean mRNA and small RNA profiles (Yrs 2-4) (JH, AD, BecA; DB, Cam)
5. Metabolite analyses to identify semiochemicals produced by bean that influence plant-aphid interactions (Yrs 2-4, Rothamsted)
6. Initiating pathways to impact activities via the Pan-Africa Bean Research Alliance, a network of the national bean research programmes of 28 African nations (Yr3/4; Lead: MA, CIAT).

Planned Impact

The project focuses on development of solutions to problems caused by viruses and the aphids that transmit them in bean. Bean (Phaseolus vulgaris) is an important crop because: it is a primary source of protein and trace elements in the East and Central African diet; it is a vital intercrop required for high yields and biotic and abiotic stress resistance in other crops including maize and cassava, and because it is of particular economic as well as nutritive value to women and children in the region. But the project will generate outputs (epidemiological models, genes, and gene sequences, and semiochemicals) that will be useful for addressing aphid and virus problems in any crop in any region, especially in the face of the treat to food security posed by spread of insecticide resistance, and the emergence of novel aphid-vectored diseases. Impact will be achieved through four interrelated activities.

1. Impact through Capacity Building The project enables BecA and ECABREN to expand research beyond their respective ILRI and CIAT core-funded activities but in line with priorities developed in consultation with African national partners both in the public and private sectors (see Letters of Support from NARO, Uganda and FICA Seeds Ltd., Uganda). Impact will be achieved through training of personnel at all levels especially the training of a PhD student and the Kenya and Uganda-based PDRAs in state-of-the-art methodologies. The project will also enhance the ability of UK partners to contribute to future North-South collaborative projects.

2. Impact through Publication and Dissemination of Scientific Results including novel epidemiological models, transcriptomic and metabolomic datasets and semiochemicals, peer-reviewed papers and conference presentations.

3. Achieving Impact with Growers, National Research Organizations (NAROs), and Industry in the African arena utilizing the Pan Africa Bean Research Alliance's excellent network to feed information/tools to end-users (primarily small-holder growers including a high proportion of women). PABRA has a strong track record for participatory monitoring and evaluation in assessment of impact using results-based indicators to track project achievements and progress towards positive economic and social goals. We will closely with Dr Robin Buruchara, PABRA co-ordinator (based at CIAT Kampala) on this phase.

4. Achieving Impact: Public communication and engagement in the UK by engagement with the public through existing arrangements at Cambridge and Rothamsted Research.

Publications

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Carr JP (2019) Plant defense signals: Players and pawns in plant-virus-vector interactions. in Plant science : an international journal of experimental plant biology

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Groen SC (2017) Engineering resistance to virus transmission. in Current opinion in virology

 
Description The initial field trials - and follow up work in progress (see Section 3 above) - suggest that mixtures of
differentially aphid attractive/repellent grower-preferred common bean cultivars (potentially utilising existing
available resistant cultivars present at a minimal frequency) could provide a viable, low tech approach to
inhibiting the spread of aphids, and potentially of viruses, within mixed cropping systems, which are
prevalent in east and central Africa.
Exploitation Route As work on this progresses, information on these approaches will be
pipelined to stakeholders by via the Pan-African Bean Research network though collaborators at CIAT.
Sectors Agriculture, Food and Drink

 
Description 2014 Gerardine Mukeshimana, the Postdoctoral Scientist working on this project at the BecA-ILRI Hub, was appointed Minister for Agriculture and Animal Resources in Rwanda in July 2014. At BecA, besides the bean project research activities, Dr. Mukeshimana was also involved in efforts in building the capacity of institutions and individuals in the African national research systems in biosciences-related crop research through knowledge transfer and resource mobilization. Before her ministerial appointment, she presented a poster on this project at the MPMI conference held between 6th -10th July 2014 in Greece. 2016-onwards. http://hub.africabiosciences.org/media-center/news/402-beca-ilri-hub-scientist-gerardinemukeshimana-appointed-minister-for-agriculture-and-animal-resources-in-rwanda Since then, the BecA-ILRI Hub team has worked with Dr Mukeshimana in her role as Minister to outline and begin implementing a more comprehensive capacity building and research program for Rwanda. In experiments under controlled conditions in which CMV-infected, aphid-infested plants were placed in proximity to mixtures of non-infected plants of Arabidopsis accessions with differing intrinsic levels of attractiveness to M. persicae, we showed that aphid migration and aphid-mediated CMV transmission can be manipulated to either enhance or inhibit spread of the insects themselves and of the virus that they carry (Bravo, Donnelly, Pate et al. unpublished). This is shown by simple experiments with Arabidopsis using Col-0, an accession that is less attractive to M. persicae than accession Ei-2. If CMV-infected plants at the start of the line (position '0') are infested with M. persicae & placed next to lines of uninfected plants, aphids migrate furthest and transmit the virus to the most plants if 'Plant 0' is of a less attractive line and adjacent plants are attractive (Ei-2, for example). This work moved on to more complex '2-dimensional' plant arrangements, which backed up the results of the 'line' experiments, showing that aphids spread and virus transmission could be inhibited or promoted, depending up the plant mixture and spatial arrangements used. Inclusion of resistant plants (using transgenic plants that are resistant to CMV) showed that it is not necessary to have 100% resistant plant populations to 'sanitize' (i.e. allow the vector to lose any inoculum) aphids so that they cease to transmit virus. This opens the way to devising seed mixtures that can inhibit virus infection whilst avoiding placing selective pressures on viruses to overcome resistance, while the method also avoids applying any selective pressure on the vectors. We believe this could be the basis of new sustainable crop protection practices that would be compatible both with smallholder, mixed cropping cultivation or with larger scale commercial farming. This data was used as proliminary finding in seeking further funding under GCRF. 2016/2017. Dr. Wamonje completed the bioinformatic analysis of our aphid viral metagenomics and molecular identification of aphids present in aphids present in smallholder farmers' fields in Kenya (from his field surveys with JPC in 2014). He used a PCR-based technique to identify aphids prevalent in smallholder bean farms and next generation sequencing shotgun metagenomics to examine the diversity of viruses present in aphids and in maize leaf samples. Samples were collected from farms in Kenya in a range of agro-ecological zones. Molecular species identification using PCR and Cytochrome oxidase 1 (CO1) gene sequencing showed that Aphis fabae was the sole aphid species present in bean plots in the farms visited. Sequencing of total RNA from aphids using the Illumina platform detected three dicistroviruses. Maize leaf RNA was also analysed. Identification of aphid lethal paralysis virus (ALPV), Rhopalosiphum padi virus (RhPV) and a novel Big Sioux River virus-like dicistrovirus in aphid and maize samples was confirmed by RT-PCR. Phylogenetic, nucleotide and protein sequence analyses of eight ALPV genomes revealed evidence of intra-species recombination with the data suggesting there may be two ALPV lineages. Analysis of BSRV-like virus genomic RNA sequences revealed features that are consistent with other dicistroviruses and that it is phylogenetically closely related to dicistroviruses of the genus Cripavirus. The discovery of ALPV and RhPV in aphids and in plants (which these viruses use as a reservoir for infection of feeding aphids) further demonstrates the broad host range of these dicistroviruses. This is the first report of these viruses being isolated from either host. Our BSRV-like sequences are potentially a novel dicistrovirus infecting A. fabae. The work has potential for the future development of biocontrol of aphids and has been drafted for journal submission (see Wamonje et al. 'Metagenomics of aphids present in bean and maize plots on mixed-use farms in Kenya reveals low aphid diversity and existence of three Dicistroviruses including a novel Big Sioux River virus-like dicistrovirus' Virology Journal 2017) and constitutes part of Dr Wamonje's PhD thesis. An additional capacity building benefit of the research was that we were able to offer the filed technician of our CIT-Uganda partners, Mr Warren Arinaitwaye, a Cambridge in Africa PhD studentship. He began his studies on aphid-plant-virus interactions in October 2017.
First Year Of Impact 2014
Sector Agriculture, Food and Drink,Education
Impact Types Societal,Policy & public services

 
Description Cambridge-Africa Alborada Research Fund
Amount £6,260 (GBP)
Organisation University of Cambridge 
Department Alborada Research Fund
Sector Charity/Non Profit
Country United Kingdom
Start 10/2015 
End 09/2016
 
Description Isaac Newton Trust
Amount £19,202 (GBP)
Funding ID Newton Trust Grant reference no. 12.07(1) 
Organisation University of Cambridge 
Sector Academic/University
Country United Kingdom
Start 10/2012 
End 12/2012
 
Description Biosciences east and central Africa Hub at ILRI Nairobi Kenya 
Organisation CGIAR
Department International Center for Tropical Agriculture
Country Colombia 
Sector Charity/Non Profit 
PI Contribution This lab and partners work on a SCPRID-funded programme to apply outputs of previous BBSRC-funded projects on virus and virus-plant-aphid interactions (respectively BB/D008204/1A viral counter defence protein as a probe for cross-talk or functional overlap between host defence pathways and BB/F014376/1 Subversion of insect resistance: A novel role for a plant viral silencing suppressor ) to investigate how the transmission of viruses by aphids might be disrupted in an African context. The programme is explained in layperson terms at http://www.bbsrc.ac.uk/web/FILES/Publications/1210-scprid.pdf
Collaborator Contribution The cambridge group provides experimental (Carr, Baulcombe) and Modelling (Gilligan) expertise. Rothamsted (Bruce, Pickett) provides expertise in semiochemicals. BecA-ILRI provide expertise in application of biotech in an African context and CIAT expertise in bean as a crop and fieldwork.
Impact The grant is still in progress- two annual reports have been provided to BBSRC via Amanda Read (BBSRC, SO) A number of publications/meeting abstracts have been generated - submitted elsewhere in this (complicated) system.
Start Year 2013
 
Description Biosciences east and central Africa Hub at ILRI Nairobi Kenya 
Organisation Rothamsted Research
Country United Kingdom 
Sector Academic/University 
PI Contribution This lab and partners work on a SCPRID-funded programme to apply outputs of previous BBSRC-funded projects on virus and virus-plant-aphid interactions (respectively BB/D008204/1A viral counter defence protein as a probe for cross-talk or functional overlap between host defence pathways and BB/F014376/1 Subversion of insect resistance: A novel role for a plant viral silencing suppressor ) to investigate how the transmission of viruses by aphids might be disrupted in an African context. The programme is explained in layperson terms at http://www.bbsrc.ac.uk/web/FILES/Publications/1210-scprid.pdf
Collaborator Contribution The cambridge group provides experimental (Carr, Baulcombe) and Modelling (Gilligan) expertise. Rothamsted (Bruce, Pickett) provides expertise in semiochemicals. BecA-ILRI provide expertise in application of biotech in an African context and CIAT expertise in bean as a crop and fieldwork.
Impact The grant is still in progress- two annual reports have been provided to BBSRC via Amanda Read (BBSRC, SO) A number of publications/meeting abstracts have been generated - submitted elsewhere in this (complicated) system.
Start Year 2013
 
Description Role of aphids in the transmission of a suspected viral disease and the disease's impact on the growth and yield of cabbage in Ghana 
Organisation University of Ghana
Country Ghana 
Sector Academic/University 
PI Contribution A new disease in Ghana affecting the cabbage cash crop has been noted. Likely viral aetiology and associated with unusual build up of aphids on diseased plants. The team aims were as follows: 1. Identify the pathogen causing a novel disease of cabbage in Ghana 2. Elucidate the role of aphids in transmitting this disease 3. Assess the impact of this disease on the growth and yield of cabbage in Ghana
Collaborator Contribution Helped with field surveys, site locations and transport.
Impact Work in progress.
Start Year 2015