Genome evolution of a pandemic clonal lineage of the wheat blast fungus
Lead Research Organisation:
UNIVERSITY COLLEGE LONDON
Department Name: Genetics Evolution and Environment
Abstract
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Technical Summary
Our team was commissioned by CIMMYT to investigate the genetic identity of the African wheat blast pathogen that was first reported in September 2020. We rapidly processed samples from Zambia and released them to the community as open science resources through the OpenWheatBlast initiative (samples received on 21 January 2021; first dataset published on 15 March 2021). Analyses of the genetic data by our teams and others linked the pathogen populations in South America, South East Asia and Zambia to a single pandemic clone of the fungus Magnaporthe oryzae, we called B71. All the samples from Zambia collected from 2018 to 2020 were the same clone indicating that there was probably only a single introduction to the country.
The aim of this project is to map the genome evolution of the pandemic B71 clonal lineage of the wheat blast fungus and determine the evolutionary potential of newly emerged variants. Our approach combines genomics surveillance of field isolates with laboratory experiments that will test specific hypotheses about the impact of sequence and structural variation on the fungus biology and pathology. The central hypothesis of the proposed research, based on preliminary data, is that the B71 clonal lineage of the wheat blast fungus undergoes genetic changes that impact its capacity to cause disease and resist chemical control. We hypothesize that novel mutations and structural variants will impact virulence and other important traits that are relevant to disease management.
We aim to introduce the concept of Variants of Concern (VOC), popularised during the COVID19 pandemic, to plant pathology. At the completion of this study, we will have determined the extent to which VOC carry mutations that impact virulence and response to chemical control, and therefore affect disease epidemiology. We will generate a model on the evolutionary potential of the pathogen that should prove useful for guiding disease management and plant breeding strategie
The aim of this project is to map the genome evolution of the pandemic B71 clonal lineage of the wheat blast fungus and determine the evolutionary potential of newly emerged variants. Our approach combines genomics surveillance of field isolates with laboratory experiments that will test specific hypotheses about the impact of sequence and structural variation on the fungus biology and pathology. The central hypothesis of the proposed research, based on preliminary data, is that the B71 clonal lineage of the wheat blast fungus undergoes genetic changes that impact its capacity to cause disease and resist chemical control. We hypothesize that novel mutations and structural variants will impact virulence and other important traits that are relevant to disease management.
We aim to introduce the concept of Variants of Concern (VOC), popularised during the COVID19 pandemic, to plant pathology. At the completion of this study, we will have determined the extent to which VOC carry mutations that impact virulence and response to chemical control, and therefore affect disease epidemiology. We will generate a model on the evolutionary potential of the pathogen that should prove useful for guiding disease management and plant breeding strategie
Organisations
People |
ORCID iD |
| Hernan Andres Burbano Roa (Principal Investigator) |
Publications
Barragan AC
(2024)
Multiple Horizontal Mini-chromosome Transfers Drive Genome Evolution of Clonal Blast Fungus Lineages.
in Molecular biology and evolution
Latorre S
(2023)
Genomic surveillance uncovers a pandemic clonal lineage of the wheat blast fungus
in PLOS Biology
Latorre S
(2022)
A pandemic clonal lineage of the wheat blast fungus
| Description | Wheat, a vital food crop for billions of people, is under threat from a disease known as wheat blast. This disease originated in Brazil in 1985 and first appeared in Bangladesh in 2016 and Zambia in 2018. By analyzing the genomes of dozens of wheat blast isolates, we discovered that a specific strain of the wheat blast fungus recently spread from South America to Asia (Bangladesh) and Africa (Zambia) through two separate introductions. Our research demonstrated that genomics-informed disease management is possible. By analyzing the fungus's genetic makeup and conducting laboratory tests, we found that the current outbreak can be controlled using a wheat gene called Rmg8, which provides resistance to the disease. Additionally, we discovered that the strain is vulnerable to a common class of antifungal chemicals known as strobilurin fungicides. Our findings suggest that wheat varieties carrying resistance genes can be deployed in high-risk areas to act as a firewall, preventing the spread of the disease. However, our study warns that the fungus could evolve to resist these treatments and may even mix genetically with local strains in Africa, potentially creating new, harder-to-control variants. This highlights the urgent need for continued genomic surveillance-closely monitoring the fungus's genetic changes-to prevent further spread and to help develop wheat varieties that are resistant to the wheat blast disease. To facilitate the genomic surveillance of wheat blast, our research provides a computational framework to rapidly analyze newly sequenced wheat blast isolates within the context of previously identified genetic diversity. Furthermore, we have implemented the early release of data and analyses as pre-prints through the OpenWheatBlast Zenodo Community, enabling easy and rapid access to wheat blast-related genomic and other resources. Our publications have helped raise awareness of the threat wheat blast poses to global food security. As a result, members of our team have participated in training sessions in Zambia to build research capacity and increase awareness within the local and international community, especially in at-risk countries. |
| Exploitation Route | The outcomes of this research can be further utilized by breeders to develop wheat varieties resistant to wheat blast and by policymakers at the national level to implement containment and management measures if wheat blast emerges in their countries. Moreover, our research is both basic and applied in the study of disease resistance genes, as recent papers have shown that the same gene conferring resistance to wheat blast is also involved in resistance to wheat powdery mildew. |
| Sectors | Agriculture Food and Drink |
| Description | Our research contributes to one of the world's largest crop pathogen surveillance systems as part of an impressive international collaboration constituting 23 institutes. This effort is coordinated by CIMMYT (International Maize and Wheat Improvement Center), which has announced that the initiative is set to expand its analytic and knowledge systems capacity to protect wheat productivity in food-vulnerable areas of East Africa and South Asia. |
| First Year Of Impact | 2023 |
| Sector | Agriculture, Food and Drink |
| Impact Types | Policy & public services |
| Title | Git repository: Genomic surveillance uncovers a pandemic clonal lineage of the wheat blast fungus |
| Description | Git repository: Genomic surveillance uncovers a pandemic clonal lineage of the wheat blast fungus |
| Type Of Material | Computer model/algorithm |
| Year Produced | 2023 |
| Provided To Others? | Yes |
| Impact | Transparent sharing of code and analysis pipelines according to modern standards of open science. |
| URL | https://zenodo.org/records/7590238 |
| Description | Interview for Nature News |
| Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Public/other audiences |
| Results and Impact | On the occasion of the publication of our PLoS Biology paper (https://doi.org/10.1371/journal.pbio.3002052) on the Wheat Blast Pandemic, I was interviewed for Nature News by Ewen Callaway. The interview resulted in an article in Nature News. |
| Year(s) Of Engagement Activity | 2023 |
| URL | https://www.nature.com/articles/d41586-023-01043-8 |
| Description | Press briefing at the Science Media Centre, London, UK |
| Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Media (as a channel to the public) |
| Results and Impact | To further disseminate this paper, my collaborators and I participated in a press briefing for UK journalists organized by the Science Media Centre, a charity that promotes more informed science in the media, and provides a service to journalists, providing background briefings on current scientific issues and facilitating interviews with scientists. This interaction shows my engagement with national organizations outside of academia to accurately disseminate scientific research to science journalists. |
| Year(s) Of Engagement Activity | 2023 |
| URL | https://www.sciencemediacentre.org/is-the-world-prepared-for-a-new-global-plant-pandemic/ |