Identifying genes for breeding disease resistance in vulnerable crops
Plant health is vital for food security, but up to 30 % of our most important staple food crops are lost to disease. Crop tissue can be chemically treated above ground, but root systems are more complicated to protect. Most efforts involve selectively breeding plants resistant against specific pathogens or through genetic modification. “But pathogens eventually overcome or evade disease resistance genes,” explains Sebastian Schornack, coordinator of the ACHILLES-HEEL project, which was funded by the European Research Council. ACHILLES-HEEL has identified essential plant processes that pathogens rely on to enter and establish themselves in a plant. “We thought of this dependence as their Achilles heel. If we can eliminate these processes, we weaken the pathogen’s ability to cause disease,” adds Schornack from the University of Cambridge, project host. As similar pathogens would likely require similar plant processes for infection, this approach offers the possibly of a broad-ranging solution. ACHILLES-HEEL has identified genes that can confer on plants more resilience to root infection, after partial or full function manipulation.
Finding the test pathogen
The team’s first challenge was that pathogens reliant on co-opting a plant’s processes – as opposed to simply killing the host – have usually adapted to specific hosts, making any infection-enabling processes identified relevant to that pathogen only. Examples include maize smuts, pea rusts and barley powdery mildews. “We needed a pathogen that infects a broad range of unrelated plants, while keeping tissue alive. This highlights the common plant mechanisms the pathogen uses and which should be deactivated,” explains Schornack. Phytophthora palmivora fitted the bill, as it colonises the roots and leaves of legumes, barley, wheat and, as discovered by the team, liverworts. After developing data analysis software, the team conducted root and leaf pathogen infection tests resulting in the identification of two genes in a legume (Medicago truncatula), capable of manipulating the plant processes used by the pathogen. One, RAD1, is not suitable as it disrupts beneficial fungal colonisation, but the other, API, is currently being tested in barley. “Barley has three such genes. We are inactivating them all individually to see if the plants become more resistant to Phytophthora root infection. First results look promising, but we still have to test effects on beneficial fungi,” says Schornack. To do this, the team are using an artificial intelligence-based tool of their own design called AMFinder which detects fungal structures inside roots. A surprising discovery has been that plants with resistant roots could still be susceptible in their shoots and vice versa. “Colonisation by filamentous microbes is organ-specific, and inactivating a gene across the plant might not have the same impact everywhere,” remarks Schornack.
Growing potential
Traditionally, breeding resistant plants involves introducing immune receptor genes called NLRs. But this is time-consuming and usually confers resistance to a specific pathogen only, while faster transgenic approaches face legal barriers in many EU countries. If proven effective, the genes identified in ACHILLES-HEEL could be used by plant breeders of staple crops to help ensure food supplies, with potential for other cash crops typically grown in the developing world and attacked by Phytophthora palmivora, such as oil palm, cocoa, coconut, rubber trees and papaya. “Given the similarity of Phytophthora’s infection strategy to other pathogens, this will likely be relevant for other pathogens such as Pythium, rust fungi and Fusarium,” concludes Schornack. The project’s published resources will help researchers detect and characterise Phytophthora palmivora, and include a description of its life cycle and an annotated root infection transcriptome.
Keywords
ACHILLES-HEEL, crops, pathogen, disease, infection, gene, resistance, breeding, fungi, API, plant, roots, tissue
