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The Gy14 cucumber (Cucumis sativus) is resistant to oomyceteous downy mildew (DM), bacterial angular leaf spot (ALS) and fungal anthracnose (AR) pathogens, but the underlying molecular mechanisms are unknown. Quantitative trait locus (QTL) mapping for the disease resistances in Gy14 and further map-based cloning identified a candidate gene for the resistant loci, which was validated and functionally characterized by spatial-temporal gene expression profiling, allelic diversity and phylogenetic analysis, as well as local association studies. We showed that the triple-disease resistances in Gy14 were controlled by the cucumber STAYGREEN (CsSGR) gene. A single nucleotide polymorphism (SNP) in the coding region resulted in a nonsynonymous amino acid substitution in the CsSGR protein, and thus disease resistance. Genes in the chlorophyll degradation pathway showed differential expression between resistant and susceptible lines in response to pathogen inoculation. The causal SNP was significantly associated with disease resistances in natural and breeding populations. The resistance allele has undergone selection in cucumber breeding. The durable, broad-spectrum disease resistance is caused by a loss-of-susceptibility mutation of CsSGR. Probably, this is achieved through the inhibition of reactive oxygen species over-accumulation and phytotoxic catabolite over-buildup in the chlorophyll degradation pathway. The CsSGR-mediated host resistance represents a novel function of this highly conserved gene in plants.

Tree species world-wide are under increasing threat from diseases and insects, many of which are non-native. The integrity of our natural, urban and plantation forest ecosystems, and the services they provide are seriously imperiled. Breeding programs that harness the natural genetic resistance within tree species can provide a durable solution to these threats. In many cases, genetic resistance offers the key to restoration of forests and may even prevent extinction of some tree species. The potential use of genetic resistance is often widely discussed, but the development of applied programs and use of resistant seed has only taken place in a relatively few species. The reflections here from some of the most advanced applied resistance programs, as well as some of the unknowns and limitations of implementing a resistance program will provide a guide to managers considering this approach. In any such program, there is a research component, a tree improvement component and a restoration and reforestation component. These three components, along with sustained management and public support, need to be linked for any genetic resistance program to be fully successful in facilitating the recovery of healthy forests. Other management activities and newly developing technologies may serve to complement genetic resistance or to expedite its development, but premature, over-emphasis on some of these may slow the operational program. An understanding of the level, frequency, durability and stability of resistance and its limitations are necessary to management planning.

Extending the durability of plant resistance genes towards fungal pathogens is a major challenge. We identified and investigated the relationship between two avirulence genes of Leptosphaeria maculans, AvrLm3 and AvrLm4‐7. When an isolate possesses both genes, the Rlm3‐mediated resistance of oilseed rape (Brassica napus) is not expressed due to the presence of AvrLm4‐7 but virulent isolates toward Rlm7 recover the AvrLm3 phenotype.Combining genetic and genomic approaches (genetic mapping, RNA‐seq, BAC (bacterial artificial chromosome) clone sequencing and de novo assembly) we cloned AvrLm3, a telomeric avirulence gene of L. maculans. AvrLm3 is located in a gap of the L. maculans reference genome assembly, is surrounded by repeated elements, encodes for a small secreted cysteine‐rich protein and is highly expressed at early infection stages.Complementation and silencing assays validated the masking effect of AvrLm4‐7 on AvrLm3 recognition by Rlm3 and we showed that the presence of AvrLm4‐7 does not impede AvrLm3 expression in planta. Y2H assays suggest the absence of physical interaction between the two avirulence proteins.This unusual interaction is the basis for field experiments aiming to evaluate strategies that increase Rlm7 durability.

Once deployed uniformly in the field, genetically controlled plant resistance is often quickly overcome by pathogens, resulting in dramatic losses. Several strategies have been proposed to constrain the evolutionary potential of pathogens and thus increase resistance durability. These strategies can be classified into four categories, depending on whether resistance sources are varied across time (rotations) or combined in space in the same cultivar (pyramiding), in different cultivars within a field (cultivar mixtures) or among fields (mosaics). Despite their potential to differentially affect both pathogen epidemiology and evolution, to date the four categories of deployment strategies have never been directly compared together within a single theoretical or experimental framework, with regard to efficiency (ability to reduce disease impact) and durability (ability to limit pathogen evolution and delay resistance breakdown). Here, we used a spatially explicit stochastic demogenetic model, implemented in the R package landsepi, to assess the epidemiological and evolutionary outcomes of these deployment strategies when two major resistance genes are present. We varied parameters related to pathogen evolutionary potential (mutation probability and associated fitness costs) and landscape organization (mostly the relative proportion of each cultivar in the landscape and levels of spatial or temporal aggregation). Our results, broadly focused on qualitative resistance to rust fungi of cereal crops, show that evolutionary and epidemiological control are not necessarily correlated and that no deployment strategy is universally optimal. Pyramiding two major genes offered the highest durability, but at high mutation probabilities, mosaics, mixtures and rotations can perform better in delaying the establishment of a universally infective superpathogen. All strategies offered the same short‐term epidemiological control, whereas rotations provided the best long‐term option, after all sources of resistance had broken down. This study also highlights the significant impact of landscape organization and pathogen evolutionary ability in considering the optimal design of a deployment strategy.

The wheat-rust pathosystem has been well-studied among host–pathogen interactions since last century due to its economic importance. Intensified efforts toward cloning of wheat rust resistance genes commenced in the late 1990s with the first successful isolation published in 2003. Currently, a total of 24 genes have been cloned from wheat that provides resistance to stem rust, leaf rust, and stripe rust. Among them, more than half (15) were cloned over the last 4 years. This rapid cloning of resistance genes from wheat can be largely credited to the development of approaches for reducing the genome complexity as 10 out of the 15 genes cloned recently were achieved by approaches that are summarized as TEnSeq (Target-sequence Enrichment and Sequencing) pipelines in this review. The growing repertoire of cloned rust resistance genes provides new tools to support deployment strategies aimed at achieving durable resistance. This will be supported by the identification of genetic variation in corresponding Avr genes from rust pathogens, which has recently begun. Although developed with wheat resistance genes as the primary targets, TEnSeq approaches are also applicable to other classes of genes as well as for other crops with complex genomes.

Eastern filbert blight (EFB), caused by Anisogramma anomala , is the primary limiting factor for hazelnut ( Corylus sp.) production in the United States. In this study, 82 cultivars and selections shown to be resistant or tolerant to EFB in Oregon were field planted in New Jersey in 2017 and 2019 and evaluated for their EFB response under high disease pressure. The trees carry known single resistance (R) genes with most mapped to their respective linkage groups (LG), including LG2, LG6, and LG7, or they express quantitative resistance (QR, horizontal resistance). Disease incidence and severity was documented, stem cankers counted and measured, and the proportion of diseased wood calculated. The EFB disease response of some cultivars/selections varied considerably between New Jersey and Oregon while others were consistent. Trends were observed in relation to resistance source origin and LGs, which provide insight into durability and usefulness of resistance. In striking contrast to Oregon, nearly all selections with R-genes mapped to LG6, including those carrying the ‘Gasaway’ resistance allele, exhibited severe EFB infections (232 of 266 [87%]). This finding is of consequence since the U.S. hazelnut industry currently relies solely on LG6 resistance for EFB resistance. Further, for the first time, EFB was observed on several selections carrying LG7 resistance, specifically offspring of ‘Ratoli’ from Spain. Interestingly, selections carrying LG7 resistance from origins other than ‘Ratoli’ remained free of EFB, with one exception, all selections carrying LG2 (n=9) resistance also remained free from EFB. Interestingly, the EFB responses of selections expressing QR (n=26) more closely resembled the disease phenotypes they exhibited in Oregon. Overall, the divergence in EFB response between Oregon and New Jersey, where pathogen populations differ, supports the presence of pathogenic variation in A. anomala and highlights potential limitations of using single R-genes to manage the disease. Results also suggest trees expressing QR may be more stable across pathogenic populations.

Long-lived tree species face a myriad of biotic and abiotic threats over their lifetime, some of the most serious being the presence of non-native diseases or pests capable of killing greater than 95% of trees that are exposed to them. Fortunately, the genetic diversity in many of the affected species also includes some individuals and populations with genetic resistance. Over the last 50 years, applied resistance programs have been undertaken in a range of tree species in the U.S. and resistant parent trees have been selected, tested in seedling inoculation trials and in field trials, selections placed into seed orchards, and the resulting seed used for reforestation and restoration. Both major gene resistance (MGR) and quantitative resistance (QR) have been documented in these resistance programs. However, for each resistance program the question arises whether the resistance will be durable, permitting the species to be used in managed plantations, urban plantings or in native forest restoration over the long-term. Field plantings to-date indicate that in some cases virulence to MGR can arise relatively quickly and QR appears to offer the best opportunity for durability. Ultimately, more time and plantings will be needed to discern if resistance is durable in affected tree species. Changes in climate may alter dynamics that could influence durability of resistance. However, even in the case of virulence to MGR, the pathogen or pest may not spread throughout the range of plantings, and genetic resistance will likely continue to be an invaluable tool for species affected by diseases and pests.

Late blight has been the most devastating potato disease worldwide. The causal agent, , is notorious for its capability to rapidly overcome host resistance. Changes in the expression pattern and the encoded protein sequences of effector genes in the pathogen are responsible for the loss of host resistance. Among numerous effector genes, the class of RXLR effector genes is well-known in mediating host genotype-specific resistance. We therefore performed deep sequencing of five genetically diverse strains using materials infected with zoospores (12 h post inoculation) and focused on the identification of RXLR effector genes that are conserved in coding sequences, are highly expressed in early stages of plant infection, and have defense suppression activities. In all, 245 RXLR effector genes were expressed in five transcriptomes, with 108 being co-expressed in all five strains, 47 of them comparatively highly expressed. Taking sequence polymorphism into consideration, 18 candidate core RXLR effectors that were conserved in sequence and with higher expression levels were selected for further study. -mediated transient expression of the selected effector genes in and potato demonstrated their potential virulence function, as shown by suppression of PAMP-triggered immunity (PTI) or/and effector-triggered immunity (ETI). The identified collection of core RXLR effectors will be useful in the search for potential durable late blight resistance genes. Analysis of 10 known RXLR genes revealed that the resistance genes , - , - , - , and - may be effective in potato cultivars. Analysis of 8 (Suppressor of early Flg22-induced Immune response) RXLR effector genes showed that , and were highly expressed in all examined strains, suggesting their potentially important function in early stages of pathogen infection.

For over a century, breeders have worked to develop tomato (Solanum lycopersicum) cultivars with resistance to Fusarium wilt (Fol) caused by the soilborne fungus Fusarium oxysporum f. sp. lycopersici. Host resistance is the most effective strategy for the management of this disease. For each of the three Fol races, resistance has been introgressed from wild tomato species, predominately in the form of R genes. The I, I-2, I-3, and I-7 R genes have each been identified, as well as the corresponding Avr effectors in the fungus with the exception of Avr7. The mechanisms by which the R gene protein products recognize these effectors, however, has not been elucidated. Extensive genetic mapping, gene cloning, and genome sequencing efforts support the development of tightly-linked molecular markers, which greatly expedite tomato breeding and the development of elite, Fol resistant cultivars. These resources also provide important tools for pyramiding resistance genes and should support the durability of host resistance.

Functional stacking of broad spectrum resistance (R) genes could potentially be an effective strategy for more durable disease resistance, for example, to potato late blight caused by Phytophthora infestans (Pi). For this reason, three broad spectrum potato R genes (Rpi), Rpi-sto1 (Solanum stoloniferum), Rpi-vnt1.1 (S. venturii) and Rpi-blb3 (S. bulbocastanum) were selected, combined into a single binary vector pBINPLUS and transformed into the susceptible cultivar Desiree. Among the 550 kanamycin resistant regenerants, 28 were further investigated by gene specific PCRs. All regenerants were positive for the nptII gene and 23 of them contained the three Rpi genes, referred to as triple Rpi gene transformants. Detached leaf assay and agro-infiltration of avirulence (Avr) genes showed that the 23 triple Rpi gene transformants were resistant to the selected isolates and showed HR with the three Avr effectors indicating functional stacking of all the three Rpi genes. It is concluded that Avr genes, corresponding to the R genes to be stacked, must be available in order to assay for functionality of each stack component. No indications were found for silencing or any other negative effects affecting the function of the inserted Rpi genes. The resistance spectrum of these 23 triple Rpi gene transformants was, as expected, a sum of the spectra from the three individual Rpi genes. This is the first example of a one-step approach for the simultaneous domestication of three natural R genes against a single disease by genetic transformation.