Ancient variation of the AvrPm17 gene in powdery mildew limits the effectiveness of the introgressed rye Pm17 resistance gene in wheat

Introgressions of chromosomal segments from related species into wheat are important sources of resistance against fungal diseases. The durability and effectiveness of introgressed resistance genes upon agricultural deployment is highly variable-a phenomenon that remains poorly understood, as the corresponding fungal avirulence genes are largely unknown. Until its breakdown, the Pm17 resistance gene introgressed from rye to wheat provided broad resistance against powdery mildew (Blumeria graminis). Here, we used quantitative trait locus (QTL) mapping to identify the corresponding wheat mildew avirulence effector AvrPm17. It is encoded by two paralogous genes that exhibit signatures of reoccurring gene conversion events and are members of a mildew sublineage specific effector cluster. Extensive haplovariant mining in wheat mildew and related sublineages identified several ancient virulent AvrPm17 variants that were present as standing genetic variation in wheat powdery mildew prior to the Pm17 introgression, thereby paving the way for the rapid breakdown of the Pm17 resistance. QTL mapping in mildew identified a second genetic component likely corresponding to an additional resistance gene present on the 1AL.1RS translocation carrying Pm17. This gene remained previously undetected due to suppressed recombination within the introgressed rye chromosomal segment. We conclude that the initial effectiveness of 1AL.1RS was based on simultaneous introgression of two genetically linked resistance genes. Our results demonstrate the relevance of pathogen-based genetic approaches to disentangling complex resistance loci in wheat. We propose that identification and monitoring of avirulence gene diversity in pathogen populations become an integral part of introgression breeding to ensure effective and durable resistance in wheat

A qPCR-based, population dynamics approach for the development of a bacteriophage-based biopesticide

Bacteriophages are viruses that target specific bacteria and kill them through their own replicative life cycle. As more countries ban the use of antibiotics for the control of fire blight and antibiotic resistant strains of Erwinia amylovora become more widespread, the use of phages as biological control agents is rapidly gaining interest. In the multinational Horizon 2020 Project PhageFire, several academic and industry partners have teamed up to develop a phage-based product for the control of fire blight. To design an effective and affordable phage formulation, the choice of phages in the cocktail is critical. The ultimate goal is to maximize synergistic interactions and minimize antagonistic interactions between the different phages while using the fewest number of phages possible to reduce production costs. To achieve this goal, we used a quantitative real-time PCR (qPCR) approach to study different combinations of a collection of phages against a combined library of E. amylovora strains representative of the pathogen diversity in Europe. With qPCR, the populations of the phages and E. amylovora can be measured individually over time in liquid cultures. This allows us to determine which phages synergize best together, while eliminating those that get outcompeted and add little overall value to the cocktail. With this work, in conjunction with additional product formulation, regulatory efforts, and field trials we aim to develop an effective, affordable, phage-based biopesticide for the control of fire blight

PhageFire : formulation of a bacteriophage-based biopesticide against Erwinia amylovora

Many plant protection agents traditionally used to combat fire blight are subjected to restrictions in an increasing number of countries. The emergence of streptomycin-resistant bacteria has called for antibiotic-free alternatives, while the use of aluminum- and copper-based products has raised environmental concerns. In this scope, there is a high demand for alternative products with lower risk profiles, for example antagonistic bacteria, yeasts, or bacteriophages (phages). Phages are considered safe for both the environment and human health, and they are highly specific for their target bacterium. Some phage-based agents have already been approved for use in plant protection and food safety. However, diverse environmental factors can impair the phages’ stability. UV-light, for example, which is damaging to DNA, can inactivate phages in the field. In the European Horizon 2020 project PhageFire, the goal of all involved partners is to develop such a phage-based biopesticide against fire blight. Here, we tested different UV-B absorbing substances and surfactants to develop an effective formulation to protect the bacteriophages from UV-B light and to ensure an even foliage coverage and adherence of the phages to the plant surface. Under artificial UV-B illumination, the phages’ survival could be increased by the addition of UV-B absorbents. We could also show that many commercially available surfactants are compatible with phages and do not affect their stability. With these contributions, complemented by phage characterization, field trials, and regulatory aspects, we aim to develop an effective and safe biopesticide against fire blight