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Previous studies have highlighted the role of three quantitative trait loci (QTL, i.e. 'qT1', 'qF11' and 'qF17') in partial resistance to apple scab. Underlying molecular mechanisms of these loci are yet unknown. Exploring differential gene expression between apple genotypes carrying contrasting combinations of these QTLs could depict original candidate genes and pathways implicated. We therefore carried out RNA sequencing just before and five days after inoculation of the pathogenic fungi Venturia inaequalis, in sixteen genotypes from a pseudo-F1 progeny segregating for resistant or susceptible alleles of the three QTLs. The current dataset includes i) transcriptomic profile description, ii) analysis of differentially expressed genes related to none or combined QTLs, infected or not with Venturia inaequalis and iii) disease phenotyping of the same genetic materials. The raw data files have been deposited in the Gene Expression Omnibus (GEO) repository with the accession number GSE250309. These outputs represent the first step towards elucidating the genetic basis of quantitative apple scab resistance. In the long term, this data set will improve apple breeding strategies on how to combine qualitative (used so far) and quantitative resistances to apple scab, with the aim of diversifying selective pressures on the pathogen.

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Phosphonate-based products have demonstrated diverse abilities to protect crops against pests, with various modes of action proposed. In this article, we specifically investigated potassium phosphonate (KHP) on apple crops. Its performance to control three major apple bioagressors (Venturia inaequalis, Erwinia amylovora, and Dysaphis plantaginea) was evaluated under semicontrolled conditions. The product was able to confer significant protection rates (40 to 75% for apple scab, 40% for fire blight, and 30% for rosy aphid), which can be explained by its more or less efficient biocidal activity against the three pests, and by its ability to induce apple immunity (pathogenesis-related proteins and secondary metabolites genes). A cumulative effect of treatments as well as the systemic behavior of the product was demonstrated. Fields trials against apple scab and the postharvest disease bull's eyes rot (Neofabraea vagabunda) were performed on different apple varieties by applying KHP combined with light pest management programs either reducing (dessert orchards) or suppressing (cider orchards) fungicide applications. KHP was able to reduce apple scab by 70 to 90% on shoots and young and harvested fruit, and bull's eyes rot by 70 to 90% on harvested fruit. Overall, our results indicate that KHP is useful for the protection of apple trees against its major pests by direct effect and by triggering the host defense system.

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Pathenogenesis-related (PR) proteins are extensively used as molecular markers to dissect the signaling cascades leading to plant defense responses. However, studies focusing on the biochemical or biological properties of these proteins remain rare. Here, we identify and characterize a class of apple (Malus domestica) PR proteins, named M. domestica AGGLUTININS (MdAGGs), belonging to the amaranthin-like lectin family. By combining molecular and biochemical approaches, we show that abundant production of MdAGGs in leaf tissues corresponds with enhanced resistance to the bacterium Erwinia amylovora, the causal agent of the disease fire blight. We also show that E. amylovora represses the expression of MdAGG genes by injecting the type 3 effector DspA/E into host cells and by secreting bacterial exopolysaccharides. Using a purified recombinant MdAGG, we show that the protein agglutinates E. amylovora cells in vitro and binds bacterial lipopolysaccharides at low pH, conditions reminiscent of the intercellular pH occurring in planta upon E. amylovora infection. We finally provide evidence that negatively charged polysaccharides, such as the free exopolysaccharide amylovoran progressively released by the bacteria, act as decoys relying on charge-charge interaction with the MdAGG to inhibit agglutination. Overall, our results suggest that the production of this particular class of PR proteins may contribute to apple innate immunity mechanisms active against E. amylovora.

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Acibenzolar-S-methyl (ASM) is a chemical compound, which is able to induce resistance in several model and non-model plants, but the end-players of this induced defense remain ill-defined. Here, we test the hypothesis that treatment with ASM can protect apple (Malus × domestica) against the rosy apple aphid (Dysaphis plantaginea) and investigate the defense molecules potentially involved in resistance. We measured aphid life traits and performed behavioral assays to study the effect of ASM on plant resistance against the aphid, and then combined transcriptomic, bioinformatics, metabolic and biochemical analyses to identify the plant compounds involved in resistance. Plants treated with ASM negatively affected several life traits of the aphid and modified its feeding and host seeking behaviors. ASM treatment elicited up-regulation of terpene synthase genes in apple and led to the emission of (E,E)-α-farnesene, a sesquiterpene that was repellent to the aphid. Several genes encoding amaranthin-like lectins were also strongly up-regulated upon treatment and the corresponding proteins accumulated in leaves, petioles and stems. Our results link the production of specific apple proteins and metabolites to the antibiosis and antixenosis effects observed against Dysaphis plantaginea, providing insight into the mechanisms underlying ASM-induced herbivore resistance.

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Plant resistance inducers, also called elicitors, could be useful to reduce the use of pesticides. However, their performance in controlling diseases in the field remains unsatisfactory due to lack of specific knowledge of how they can integrate crop protection practices. In this work, we focused on apple crop and acibenzolar-S-methyl (ASM), a well-known SAR (systemic acquired resistance) inducer of numerous plant species. We provide a protocol for orchard-effective control of apple scab due to the ascomycete fungus Venturia inaequalis, by applying ASM in combination with a light integrated pest management program. Besides we pave the way for future optimization levers by demonstrating in controlled conditions (i) the high influence of apple genotypes, (ii) the ability of ASM to prime defenses in newly formed leaves, (iii) the positive effect of repeated elicitor applications, (iv) the additive effect of a thinning fruit agent.