Durable rice blast resistance through genomic analysis of the host-pathogen interaction

Lead Research Organisation: University of Exeter
Department Name: Biosciences

Abstract

Rice provides 23% of calories consumed by mankind, and this figure is even higher in many developing countries. In fact, rice is the primary dietary staple for at least 70% of the world's poorest people. In Sub-Saharan Africa, most countries have adopted rice as a strategic crop in their food security policies in order to meet the needs of their growing urban populations. One of the biggest constraints on rice production in Sub-Saharan Africa is a devastating disease called rice blast. This disease can cause losses of up to 50% of the rice harvest in these regions, causing severe economic problems for farmers and leading to rice shortages and a greater need for importation of rice at high prices. This project aims to characterise populations of the pathogen that causes rice blast using genome sequencing, in order to determine its variability and capacity to cause disease on the most widely grown rice varieties. We then aim to use this knowledge to identify novel sources of resistance from world-wide rice stocks and, in particular, rice varieties especially bred to thrive in African growing conditions. We will then use modern, marker-assisted plant breeding approaches to create durably resistant rice varieties for use by growers in Sub-Saharan Africa. During the course of the project we will carry out training of four post-doctoral research fellows, who will spend significant amounts of time working in the region, and who will disseminate skills in molecular genetics, genomics and bioinformatics. We will also train two PhD students from Sub-Saharan Africa who will work in each member laboratory and receive training in modern genetic and genomic techniques applied to controlling one of the world's most devastating plant diseases.

Technical Summary

The aim of this project is to use a combination of next generation DNA sequencing and genome wide association studies to carry out genotypic and phenotypic diversity studies of the rice blast pathogen, Magnaporthe oryzae, in Africa. This information will be used to identify novel sources of rice blast resistance that will be deployed through marker-assisted rice breeding programmes to produce high yielding, locally-adapted rice cultivars with durable disease resistance. Specifically, the target countries will include Kenya, Uganda, and Burkina Faso where rice blast remains a major disease constraint that significantly impacts grain yields. The overall goal of this project is to develop a strategic and efficient method to breed for improved disease resistance based on pathogen diversity and availability of host resistance genes. The project will bring together leading international scientists from the rice blast research community with complementary expertise in pathogen biology and genomics (Talbot, Mitchell), rice blast resistance genetics and breeding (Correll, Wang) and local expertise in rice blast resistance deployment and rice breeding (Wasilwa, Okori, Harvey, Ibrahima). This international team is well-equipped to carry out the fundamental science proposed, but also to translate the findings into durable resistance that will impact directly on farmers' ability to grow rice successfully in resource-poor regions of Africa. The overall objective of the project is to gain a thorough understanding of the phenotypic and genotypic diversity of the regional rice blast pathogen population in order to guide introgression of multiple sources of resistance into New Rice for Africa (NERICA) rice lines and other high performance rice cultivars using marker assisted breeding.

Planned Impact

Immediate outputs of this research will be in the form of technologies, training, knowledge and processes. The research will involve leading research laboratories from
the UK and USA, coupled with resources and knowledge from global rice research centres (WARDA and IRRI). Key training will be provided to students and researchers from three African countries; Kenya, Uganda and Burkina Faso. National institutions (KARI, Makerere University) will anchor research to the local research and development uptake pathways. The BecA-ILRI hub in Kenya will support regional up-and-outscaling of the project outputs, including the repository, disease management strategies arising, and newly developed rice cultivars. The project associate partners will include stakeholders not primarily involved in the research, but necessary for product development and uptake. These will include national level farmer organizations, extension agencies, and the Association for Strengthening Agricultural Research in Eastern and Central Africa (ASARECA) The programme will disseminate information through a communications strategy that provides access to knowledge and technology via publication, bulletins, and extension agencies. In the median to long-term, the output of this project will reach the farming community through engagement of national institutions with their associate partners.
 
Description To conduct a regional population analysis of the rice blast pathogen to underpin variety development and deployment in sub-Saharan Africa - We have extended our collections throughout Sub-Saharan Africa using the uniformly agreed methodology and storage procedures developed in Year 1. We have genotyped 144 isolates so far, originating from Kenya (94), Burkina Faso (39), Tanzania (6), and Uganda (4). These have been classified at Exeter by ITS sequencing. An example strain from each ITS clade has been genome sequenced. Vegetative compatibility testing has been carred out at Arkansas and GBS genotyping carried out at OSU. Currently, two field officers and graduate student David Mwongera Thuranira are collecting blast isolates in the field throughout Kenya and will bring strains to Exeter in December 2014. These are all GPS-tagged. We are also collecting infected blast material for potential targeted effector-RNA-seq analysis. We aim to collect more than 1000 infected rice plant samples in this round of collections. The two sets of IRRI differentials underwent field seed increases in Arkansas in the 2013 and 2014 growing seasons for distribution of seed across the consortium.

To develop a rice blast-resistance gene profile in locally-adapted rice cultivars from sub-
Saharan Africa and a repository system for management of rice blast disease screening - We have screened 40 selected African isolates using the IRRI differentials targeting 24 known Resistance genes. This has been carried out in parallel blind tests in Arkansas and Exeter. We aim to identify putative effectors corresponding to Avr proteins that trigger effector-triggered immunity in response to major Resistance genes in rice. We are also testing isolates against the most commonly grown Kenyan rice cultivars, including widely grown NERICA lines. All isolates are being stored at the ILRI-becA Bio-bank in Nairobi where the rice blast repository will be established.

To utilize marker-assisted breeding to develop durably resistance rice blast cultivars for
deployment in Sub-Saharan Africa - This work is well underway, co-ordinated from OSU and Arkansas. We are adopting two main approaches. selection marker. Firstly, at OSU we have developed transformation procedures for two popular Africa rice cultivars, NERICA 4 and 7, to generate Pi9 marker-free cisgenic lines. Transgenic plants are currently being tested for the presence of the Pi9 gene and absence of the hygromycin selection marker. More rice transformation will be performed in order to obtain over 10 Pi9 marker-free cisgenic lines. We then aim to make transgenic lines carrying a single cassette containing the Pi-zt, Pi-ta and Pi-b resistance genes to see if this excludes the majority of African rice blast isolates from our collections. Meanwhile we are carrying out an analysis to identify sources of resistance within NERICA lines of rice. In Arkansas, we have generated an F2 population of 300 individuals from a cross between M204 (susceptible to US isolate 49D) to NERICA 12 (resistant to isolate 49D) which has been phenotyped, yielding 275 Resistant and 25 Susceptible individuals. Tissue fromm the 300 plants has been collected for DNA isolation and SNP analysis. We have also carried out a large-scale genome wide association study (GWAS) in OSU. Inoculation experiments of 163 rice cultivars of the Rice Diversity Panel with three African isolates (UG-05, KE-037 and TZ-01) has been performed. GWAS showed 13 QTLs (LOD scores >4.0) are highly associated with the resistance to all the three isolates. We are now testing all 163 lines with eight African isolates (two from each of Kenya, Tanzania, Uganda and Burkina Fuso) to validate these QTLs. More QTLs that are effective to African isolates will be identified in this way. We have also inoculated 235 Africa rice cultivars with six blast isolates from Kenya, Uganda, Burkina Faso and Tanzania. About 70% of the cultivars were highly susceptible to these isolates. Interestingly, 10 cultivars conferred high levels of resistance to all six isolates. These cultivars are candidates for genetic mapping of novel blast resistance genes.
When considered together, we are in a position where we will shortly be testing the efficacy of three known rice blast resistance genes (Pi-zt, Pi-ta and Pi-b) to the control of blast in sub-Saharan Africa using a transgenic approach and also be conventional introgression. We are also identifying known R- genes with broad spectrum control potential of African rice blast populations and, finally, we are identifying both mono-genic resistance and QTL associated with increased disease tolerance in NERICA lines and traditional African rice varieties. We aim to apply these in the next 24 months to a cross section of the African rice blast population.
Exploitation Route The principal outputs so far from the project have been uniform methodologies for collection, genotype analysis and curation of rice blast isolates collected throughout sub-Saharan Africa. These are now being stored at Arkansas, OSU, Exeter and in the Rice Blast Repository in becA-ILRI in Kenya. IN addition, we have developed procedures for The whole consortium met at the International Rice Blast Conference on Jeju Island in South Korea in August 2013 and a further meeting of the US contingent took place in Arkansas in January 2014. Jagger Harvey also visited Exeter in April 2014. In addition, regular Skype meetings have taken place on a monthly basis between project partners in addition to frequent email contact and a regular Newsletter. Two PhD students have now been hired, David Mwongera Thuranina and Vincent Were, who will commence their studies in Exeter in Autumn 2013. Their work will study the evolutionary biology of the rice blast fungus and in particular how this has emerged within the populations of sub-Saharan Africa. They will analyse both the diversification and proliferation of the fungus and particularly different race types within sub-Saharan Africa with a view to establishing the repertoire of effectors and, in particular, the number of distinct avirulence genes present within the African population. Isolate collection and repository establishment have been carried out as part of the Capacity Building element of the grant.
 
Description The aim of this project is to use a combination of next generation DNA sequencing and genome wide association studies to carry out genotypic and phenotypic diversity studies of the rice blast pathogen, Magnaporthe oryzae, in Africa. This information will be used to identify novel sources of rice blast resistance that will be deployed through marker-assisted rice breeding programmes to produce high yielding, locally-adapted rice cultivars with durable disease resistance. Specifically, the target countries will include Kenya, Uganda, and Burkina Faso where rice blast remains a major disease constraint that significantly impacts grain yields. The overall goal of this project is to develop a strategic and efficient method to breed for improved disease resistance based on pathogen diversity and availability of host resistance genes. The project will bring together leading international scientists from the rice blast research community with complementary expertise in pathogen biology and genomics (Talbot, Mitchell), rice blast resistance genetics and breeding (Correll, Wang) and local expertise in rice blast resistance deployment and rice breeding (Wasilwa, Okori, Harvey, Ibrahima). This international team is well-equipped to carry out the fundamental science proposed, but also to translate the findings into durable resistance that will impact directly on farmers' ability to grow rice successfully in resource-poor regions of Africa. The overall objective of the project is to gain a thorough understanding of the phenotypic and genotypic diversity of the regional rice blast pathogen population in order to guide introgression of multiple sources of resistance into New Rice for Africa (NERICA) rice lines and other high performance rice cultivars using marker assisted breeding. The principal outputs so far from the project have been uniform methodologies for collection, genotype analysis and curation of rice blast isolates collected throughout sub-Saharan Africa. We have also generated standard operating procedures for the repository in terms of storage of isolates and ther tracking via our relational database. This is one of the key outputs of the project. The major breakthrough in this reporting period was the meeting in Naivasha in Kenya on June 4th-7th 2015. We invited the whole consortium, as well as new project partners at IRRI, represented by Dr Bo Zhou, and Africa Rice, represented by Dr. Moussa Sie. This was highly productive and we formulated rice breeding strategies for rice blast exclusion in West Africa and East Africa. We agreed a schedule for breeding programmes and a mirroring exercise to be carried out at IRRI. This is a huge advance and we have followed this up by moving the relevant germplasm to each site and starting the breeding programmes. We have also established the repository, which is a key capacity building outcome of the project. A further meeting took place between the consortium at the International Rice Research Institute (IRRI) in The Philippines in October 2017 to plan marker-assisted breeding and this was followed by the end of project meeting in Arusha, Tanzania in July 2017 at which we planned further resistance gene pyramiding to be undertaken at IRRI, Inera, Burkina Faso, and KALRO in Kenya. Field trials of the rice lines developed so far in the project are also planned to take place during 2018-20 in 24 sites across 7 countries in sub-Saharan Africa. This is now being supported by a BBSRC SASSA programme grant that was awarded in August 2018 and which has transferred with the Principal Applicant to The Sainsbury Laboratory. The work is now underway and further breeding work is also underway, so that multiple forms of disease resistance, linked to the pathogen population level diversity, will be tested in locally grown cultivars.
First Year Of Impact 2017
Sector Agriculture, Food and Drink
Impact Types Societal

 
Description Durable Rice Blast Resistance for Sub-Saharan Africa
Amount £1,501,700 (GBP)
Funding ID BB/R020698/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 09/2018 
End 08/2021
 
Description Farmer Engagement Activities 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact During 2016-17, the BBSRC-SCPRID project trained 24 Plant Doctors in 14 Counties and 30 Sub-Counties of Kenya. This was carried out in collaboration with the CABI Plant Clinic process. These professionals have knowledge of disease diagnosis, agronomy and crop protection. They are also able to discuss the disease surveillance programme and how farmers can contribute to this. A total of 49 Plant Clinics has been held so far in Kenya. In Tanzania, we have carried out 86 Plant Clinics using the same model. Led by Dr. Lusike Wasilwa, KALRO and BecA team has developed 66 factsheets on rice production. These factsheets will be used in training of plant doctors and farmers on the appropriate rice production methods, and how to control key constraints in rice production. The factsheets will be available electronically (on tablets) and as hard copies. This effort is aimed at ensuring that farmers have enough access to information about rice production constraints, and how to mitigate them, hence enhancing increased rice production and food security in the region. The effort will include establishment of plant clinics, which will be located at strategic points within the rice growing area. Farm visits for training and evaluation of rice blast disease.
Year(s) Of Engagement Activity 2016,2017,2018