Adaptation to Partial Resistance to Powdery Mildew in the Hop Cultivar Cascade by Podosphaera macularis

Identification of quantitative trait loci associated with R1-mediated resistance to powdery mildew and sex determination in hop (Humulus lupulus L.)

KEY MESSAGE

Two QTL were identified using linkage mapping approaches, one on hop linkage group 3 (qHl_Chr3.PMR1) associated with powdery mildew resistance and a second on linkage group 10 (cqHl_ChrX.SDR1) associated with sex determination. Hop (Humulus lupulus L.) is a dioecious species cultivated for use in beer. Hop powdery mildew, caused by Podosphaera macularis, is a constraint in many growing regions. Thus, identifying markers associated with powdery mildew resistance and sex provides the opportunity to pyramid R-genes and select female plants as seedlings, respectively. Our objectives were to characterize the genetic basis of R1-mediated resistance in the cultivar Zenith which provides resistance to pathogen races in the US, identify quantitative trait loci (QTL) associated with R1 and sex, and develop markers for molecular breeding-based approaches. Phenotypic evaluation of the population indicated that R1-based resistance and sex are inherited monogenically. We constructed a genetic map using 1339 single nucleotide polymorphisms (SNPs) based upon genotype-by-sequencing of 128 F₁ progeny derived from a Zenith × USDA 21058M biparental population. SNPs were assigned to 10 linkage groups comprising a map length of 1204.97 cM with an average density of 0.94 cM/marker. Quantitative trait locus mapping identified qHl_Chr3.PMR1, associated with R1 on linkage group 3 (LOD = 23.57, R² = 57.2%), and cqHl_ChrX.SDR1, associated with sex on linkage group 10 (LOD = 5.42, R² = 25.0%). Kompetitive allele-specific PCR (KASP) assays were developed for both QTL and assessed against diverse germplasm. Our results indicate that KASP markers associated with R1 may be limited to materials that are pedigree-related to Zenith, whereas markers associated with sex may be transferable across populations. The high-density map, QTL, and associated KASP markers will enable selecting for sex and R1-mediated resistance in hop.

Temperature Influences on Powdery Mildew Susceptibility and Development in the Hop Cultivar Cascade

The hop cultivar 'Cascade' possesses partial resistance to powdery mildew (Podosphaera macularis) that can be overcome by recently emerged, virulent isolates of the fungus. Given that hop is a long-lived perennial and that brewers still demand Cascade, there is a need to better understand factors that influence the development of powdery mildew on this cultivar. Growth chamber experiments were conducted to quantify the effect of constant, transient, and fluctuating temperature on Cascade before, concurrent to, and after inoculation as contrasted with another powdery mildew-susceptible cultivar, 'Symphony'. Exposure of plants to supraoptimal temperature (26 and 32°C) before inoculation led to more rapid onset of ontogenic resistance in intermediately aged leaves in Cascade as compared with Symphony. Cascade was overall less susceptible to powdery mildew when exposed to constant temperature ranging from 18 to 32°C directly after inoculation. However, cultivar also interacted with temperature such that proportionately fewer and smaller colonies developed on Cascade than Symphony at supraoptimal yet permissive temperatures for disease. When plants were inoculated and then exposed to high temperature, colonies became progressively more tolerant to temperatures of 26 to 30°C with increasing time from inoculation to exposure, as moderated by cultivar, the specific temperature, and their interaction. Subjecting plants to simulated diurnal temperature regimes at the time of inoculation or 24 h later indicated Cascade and Symphony responded proportionately similarly on days predicted to be marginally unfavorable or marginally favorable for powdery mildew, although Cascade was quantitatively less susceptible than Symphony. In sum, this research indicates that Cascade is overall less susceptible to powdery mildew than Symphony, and supraoptimal temperature before, concurrent to, or after infection may interact differentially to moderate disease risk in Cascade. Therefore, cultivar-specific risk assessments for powdery mildew appear warranted.

Fungicide Physical Mode of Action: Impacts on Suppression of Hop Powdery Mildew

Understanding of the physical mode of action of fungicides allows more efficient and effective application and can increase disease control. Greenhouse and field studies were conducted to explore the preinfection and postinfection duration and translocative properties of fungicides commonly used to control hop powdery mildew, caused by Podosphaera macularis. In greenhouse studies, applications made 24 h before inoculation were almost 100% effective at suppressing powdery mildew, regardless of the fungicide evaluated. However, percentage control of powdery mildew based on the number of pathogen colonies per leaf varied significantly between fungicides with increasing time from inoculation to application, ranging from 50 to 100% disease control depending on the fungicide. Fluopyram or fluopyram + trifloxystrobin was particularly efficacious, suppressing nearly all powdery mildew development independent of application timing. In translocation studies, fluopyram and flutriafol were the most effective treatments in each of two separate experiments, resulting in zones of inhibition of 1,036 and 246.3 mm², respectively, on adaxial leaf surfaces when a single droplet of each fungicide was applied to the abaxial surface of leaves. In field experiments, all fungicide treatments provided nearly complete control of powdery mildew infection when applied before inoculation. Levels of disease control decreased with time depending on treatment, showing trends similar to those observed in greenhouse studies. In the 2017 field experiments, high levels of disease control (>75%) were observed at postinoculation time points for all treatments tested, whereas the same fungicides were more sensitive to application timing in a different year. Findings from this research indicate that differences in efficacy between fungicides are small when applications are made preventively, but postinfection activity and translaminar movement of certain fungicides may render some more effective depending on application coverage and preexisting infection.

Development of a Diagnostic Assay for Race Differentiation of Podosphaera macularis

Hop powdery mildew (caused by Podosphaera macularis) was confirmed in the Pacific Northwest in 1996. Before 2012, the most common race of P. macularis was able to infect plants that possessed powdery mildew resistance based on the R-genes Rb, R3, and R5. After 2012, two additional races of P. macularis were discovered that can overcome the resistance gene R6 and the partial resistance found in the cultivar Cascade. These three races now occur throughout the region, which can complicate management and research efforts because of uncertainty on which race(s) may be present in the region and able to infect susceptible hop genotypes. Current methods for determining the races of P. macularis are labor intensive, costly, and typically require more than 14 days to obtain results. We sought to develop a molecular assay to differentiate races of the fungus possessing virulence on plants with R6, referred to as V6-virulent, from other races. The transcriptomes of 46 isolates of P. macularis were sequenced to identify loci and variants unique to V6 isolates. Fourteen primer pairs were designed for 10 candidate loci that contained single nucleotide polymorphisms (SNP) and short insertion-deletion polymorphisms. Two differentially labeled locked nucleic acid probes were designed for a contig that contained a conserved SNP associated with V6-virulence. The resulting duplexed real-time PCR assay was validated against 46 V6 and 54 non-V6 P. macularis isolates collected from the United States and Europe. The assay had perfect discrimination of V6-virulence among isolates of P. macularis originating from the western U.S. but failed to predict V6-virulence in three isolates collected from Europe. The specificity of the assay was tested with different species of powdery mildew fungi and other microorganisms associated with hop. Weak nonspecific amplification occurred with powdery mildew fungi collected from Vitis vinifera, Fragaria sp., and Zinnia sp.; however, nonspecification amplification is not a concern when differentiating pathogen race from colonies on hop. The assay has practical applications in hop breeding, epidemiological studies, and other settings where rapid confirmation of pathogen race is needed.

A draft phased assembly of the diploid Cascade hop (Humulus lupulus) genome

Hop (Humulus lupulus L. var Lupulus) is a diploid, dioecious plant with a history of cultivation spanning more than one thousand years. Hop cones are valued for their use in brewing and contain compounds of therapeutic interest including xanthohumol. Efforts to determine how biochemical pathways responsible for desirable traits are regulated have been challenged by the large (2.8 Gb), repetitive, and heterozygous genome of hop. We present a draft haplotype-phased assembly of the Cascade cultivar genome. Our draft assembly and annotation of the Cascade genome is the most extensive representation of the hop genome to date. PacBio long-read sequences from hop were assembled with FALCON and partially phased with FALCON-Unzip. Comparative analysis of haplotype sequences provides insight into selective pressures that have driven evolution in hop. We discovered genes with greater sequence divergence enriched for stress-response, growth, and flowering functions in the draft phased assembly. With improved resolution of long terminal retrotransposons (LTRs) due to long-read sequencing, we found that hop is over 70% repetitive. We identified a homolog of cannabidiolic acid synthase (CBDAS) that is expressed in multiple tissues. The approaches we developed to analyze the draft phased assembly serve to deepen our understanding of the genomic landscape of hop and may have broader applicability to the study of other large, complex genomes.

Convergent Adaptation to Quantitative Host Resistance in a Major Plant Pathogen

Plant pathogens can adapt to quantitative resistance, eroding its effectiveness. The aim of this work was to reveal the genomic basis of adaptation to such a resistance in populations of the fungus Pseudocercospora fijiensis, a major devastating pathogen of banana, by studying convergent adaptation on different cultivars. Samples from P. fijiensis populations showing a local adaptation pattern on new banana hybrids with quantitative resistance were compared, based on a genome scan approach, with samples from traditional and more susceptible cultivars in Cuba and the Dominican Republic. Whole-genome sequencing of pools of P. fijiensis isolates (pool-seq) sampled from three locations per country was conducted according to a paired population design. The findings of different combined analyses highly supported the existence of convergent adaptation on the study cultivars between locations within but not between countries. Five to six genomic regions involved in this adaptation were detected in each country. An annotation analysis and available biological data supported the hypothesis that some genes within the detected genomic regions may play a role in quantitative pathogenicity, including gene regulation. The results suggested that the genetic basis of fungal adaptation to quantitative plant resistance is at least oligogenic, while highlighting the existence of specific host-pathogen interactions for this kind of resistance.IMPORTANCE Understanding the genetic basis of pathogen adaptation to quantitative resistance in plants has a key role to play in establishing durable strategies for resistance deployment. In this context, a population genomic approach was developed for a major plant pathogen (the fungus Pseudocercospora fijiensis causing black leaf streak disease of banana) whereby samples from new resistant banana hybrids were compared with samples from more susceptible conventional cultivars in two countries. A total of 11 genomic regions for which there was strong evidence of selection by quantitative resistance were detected. An annotation analysis and available biological data supported the hypothesis that some of the genes within these regions may play a role in quantitative pathogenicity. These results suggested a polygenic basis of quantitative pathogenicity in this fungal pathogen and complex molecular plant-pathogen interactions in quantitative disease development involving several genes on both sides.

Transcriptome-Derived Amplicon Sequencing Markers Elucidate the U.S. Podosphaera macularis Population Structure Across Feral and Commercial Plantings of Humulus lupulus

Obligately biotrophic plant pathogens pose challenges in population genetic studies due to their genomic complexities and elaborate culturing requirements with limited biomass. Hop powdery mildew (Podosphaera macularis) is an obligately biotrophic ascomycete that threatens sustainable hop production. P. macularis populations of the Pacific Northwest (PNW) United States differ from those of the Midwest and Northeastern United States, lacking one of two mating types needed for sexual recombination and harboring two strains that are differentially aggressive on the cultivar Cascade and able to overcome the Humulus lupulus R-gene R6 (V6), respectively. To develop a high-throughput marker platform for tracking the flow of genotypes across the United States and internationally, we used an existing transcriptome of diverse P. macularis isolates to design a multiplex of 54 amplicon sequencing markers, validated across a panel of 391 U.S. samples and 123 international samples. The results suggest that P. macularis from U.S. commercial hop yards form one population closely related to P. macularis of the United Kingdom, while P. macularis from U.S. feral hop locations grouped with P. macularis of Eastern Europe. Included in this multiplex was a marker that successfully tracked V6-virulence in 65 of 66 samples with a confirmed V6-phenotype. A new qPCR assay for high-throughput genotyping of P. macularis mating type generated the highest resolution distribution map of P. macularis mating type to date. Together, these genotyping strategies enable the high-throughput and inexpensive tracking of pathogen spread among geographical regions from single-colony samples and provide a roadmap to develop markers for other obligate biotrophs.

Population Diversity and Structure of Podosphaera macularis in the Pacific Northwestern United States and Other Populations

Powdery mildew, caused by Podosphaera macularis, is one of the most important diseases of hop. The disease was first reported in the Pacific Northwestern United States, the primary hop-growing region in this country, in the mid-1990s. More recently, the disease has reemerged in newly planted hopyards of the eastern United States, as hop production has expanded to meet demands of local craft brewers. The spread of strains virulent on previously resistant cultivars, the paucity of available fungicides, and the potential introduction of the MAT1-2 mating type to the western United States, all threaten sustainability of hop production. We sequenced the transcriptome of 104 isolates of P. macularis collected throughout the western United States, eastern United States, and Europe to quantify genetic diversity of pathogen populations and elucidate the possible origins of pathogen populations in the western United States. Discriminant analysis of principal components grouped isolates within three to five geographic populations, dependent on stringency of grouping criteria. Isolates from the western United States were phenotyped and categorized into one of three pathogenic races based on disease symptoms generated on differential cultivars. Western U.S. populations were clonal, irrespective of pathogenic race, and grouped with isolates originating from Europe. Isolates originating from wild hop plants in the eastern United States were genetically differentiated from all other populations, whereas isolates from cultivated hop plants in the eastern United States mostly grouped with isolates originating from the west, consistent with origins from nursery sources. Mating types of isolates originating from cultivated western and eastern U.S. hop plants were entirely MAT1-1. In contrast, a 1:1 ratio of MAT1-1 and MAT1-2 was observed with isolates sampled from wild plants or Europe. Within the western United States a set of highly differentiated loci were identified in P. macularis isolates associated with virulence to the powdery mildew R-gene R6. The weight of genetic and phenotypic evidence suggests a European origin of the P. macularis populations in the western United States, followed by spread of the pathogen from the western United States to re-emergent production regions in the eastern United States. Furthermore, R6 compatibility appears to have been selected from an extant isolate within the western United States. Greater emphasis on sanitation measures during propagation and quarantine policies should be considered to limit further spread of novel genotypes of the pathogen, both between and within production areas.

Pattern of local adaptation to quantitative host resistance in a major pathogen of a perennial crop

Understanding the mechanisms involved in pathogen adaptation to quantitative resistance in plants has a key role to play in establishing durable strategies for resistance deployment, especially in perennial crops. The erosion of quantitative resistance has been recently suspected in Cuba and the Dominican Republic for a major fungal pathogen of such a crop: Pseudocercospora fijiensis, causing black leaf streak disease on banana. This study set out to test whether such erosion has resulted from an adaptation of P. fijiensis populations, and to determine whether or not the adaptation is local. Almost 600 P. fijiensis isolates from Cuba and the Dominican Republic were sampled using a paired-population sampling design on resistant and susceptible banana varieties. A low genetic structure of the P. fijiensis populations was detected in each country using 16 microsatellite markers. Cross-inoculation experiments using isolates from susceptible and resistant cultivars were carried out, measuring a quantitative trait (the diseased leaf area) related to pathogen fitness on three varieties. A further analysis based on those data suggested the existence of a local pattern of adaptation to resistant cultivars in both of the study countries, due to the existence of specific (or genotype by genotype) host-pathogen interactions. However, neither cost nor benefit effects for adapted populations were found on the widely used "Cavendish" banana group. These results highlight the need to study specific host-pathogen interactions and pathogen adaptation on a wide range of quantitative resistance phenotypes in banana, in order to develop durable strategies for resistance deployment.

Cooperation and Coordination in Plant Disease Management

Scaling of management efforts beyond the boundaries of individual farms may require that individuals act collectively. Such approaches have been suggested several times in plant pathology contexts but rarely have been implemented, in part because the institutional structures that enable successful collective action are poorly understood. In this research, we conducted in-depth interviews with hop producers in Oregon and Washington State to identify their motivations for and barriers to collective action regarding communication of disease levels, coordination of management practices, and sharing of best management practices and other data for powdery mildew (caused by Podosphaera macularis). Growers were generally open to and engaged in communication with neighbors and others on disease status in their hop yards and some evidence of higher levels of information sharing on management practices was found. However, growers who had developed extensive knowledge and databases were reluctant to share information viewed as proprietary. Relationships, trust, and reciprocity were facilitating factors for communication and information sharing, whereas lack of these factors and social norms of independence and pride in portions of the grower community were identified as impediments. Given the heterogeneity of trust, lack of confidence in reciprocity, and weak shared norms, communication of disease risk and coordinated management may be most successful if directed at a smaller scale as a series of neighborhood-based partnerships of growers and their immediate neighbors. Developing a disease reporting system and coordinated disease management efforts with more producers and at larger spatial extents would require formalized structures and rules that would provide assurance that there is consistency in disease data collection and reporting, reciprocation, and sanctions for those who use the information for marketing purposes against other growers. Given the analyses presented here, we believe there is potential for collective action in disease management but with limitations on the scope and nature of the actions.

Prediction of Spread and Regional Development of Hop Powdery Mildew: A Network Analysis

Dispersal is a fundamental aspect of epidemic development at multiple spatial scales, including those that extend beyond the borders of individual fields and to the landscape level. In this research, we used the powdery mildew of the hop pathosystem (caused by Podosphaera macularis) to formulate a model of pathogen dispersal during spring (May to June) and early summer (June to July) at the intermediate scale between synoptic weather systems and microclimate (mesoscale) based on a census of commercial hop yards during 2014 to 2017 in a production region in western Oregon. This pathosystem is characterized by a low level of overwintering of the pathogen as a result of absence of the ascigerious stage of the fungus and consequent annual cycles of localized survival via bud perennation and pathogen spread by windborne dispersal. An individual hop yard was considered a node in the model, whose disease status in a given month was expressed as a nonlinear function of disease incidence in the preceding month, susceptibility to two races of the fungus, and disease spread from other nodes as influenced by their disease incidence, area, distance away, and wind run and direction in the preceding month. Parameters were estimated by maximum likelihood over all 4 years but were allowed to vary for time transition periods from May to June and from June to July. The model accounted for 34 to 90% of the observed variation in disease incidence at the field level, depending on the year and season. Network graphs and analyses suggest that dispersal was dominated by relatively localized dispersal events (<2 km) among the network of fields, being mostly restricted to the same or adjacent farms. When formed, predicted disease attributable to dispersal from other hop yards (edges) associated with longer distance dispersal was more frequent in the June to July time transition. Edges with a high probability of disease transmission were formed in instances where yards were in close proximity or where disease incidence was relatively high in large hop yards, as moderated by wind run. The modeling approach provides a flexible and generalizable framework for understanding and predicting pathogen dispersal at the regional level as well as the implications of network connectivity on epidemic development.

Risk Factors for Bud Perennation of Podosphaera macularis on Hop

The hop powdery mildew fungus Podosphaera macularis persists from season to season in the Pacific Northwestern United States through infection of crown buds because only one of the mating types needed to produce the ascigerous stage is presently found in this region. Bud infection and successful overwintering of the fungus leads to the emergence of heavily infected shoots in early spring (termed flag shoots). Historical data of flag shoot occurrence and incidence in Oregon and Washington State during 2000 to 2017 were analyzed to identify their association with the incidence of powdery mildew, growers' use of fungicides, autumn and winter temperature, and other production factors. During this period, flag shoots were found on 0.05% of plants evaluated in Oregon and 0.57% in Washington. In Oregon, the incidence of powdery mildew on leaves was most severe and the number of fungicide applications made by growers greatest in yards where flag shoots were found in spring. Similarly, the incidence of plants with powdery mildew in Washington was significantly associated with the number of flag shoots present in early spring, although the number of fungicide applications made was independent of flag shoot occurrence. The occurrence of flag shoots was associated with prior occurrence of flag shoots in a yard, the incidence of foliar powdery mildew in the previous year, grower pruning method, and, in Washington, winter temperature. A census of hop yards in the eastern extent of the Oregon production region during 2014 to 2017 found flag shoots in 27 of 489 yards evaluated. In yards without flag shoots, 338 yards (73.2%) were chemically pruning or not pruned, whereas the remaining 124 (26.8%) were mechanically pruned. Of the 27 yards with flag shoots, 22 were either chemically pruned or not pruned and 4 were mechanically pruned in mid-April, well after the initial emergence of flag shoots. The prevalence of yards with flag shoots also was related to thoroughness of pruning in spring (8.1% of yards with incomplete pruning versus 1.9% of yards with thorough pruning). A Bayesian logistic regression model was fit to the data from the intensively assessed yards in Oregon, with binary risk factors for occurrence of a flag shoot in the previous year, occurrence of foliar mildew in the previous year, and thoroughness of pruning in spring. The model indicated that the median and 95% highest posterior density interval of the probability of flag shoot occurrence was 0.0008 (0.0000 to 0.0053) when a yard had no risk factors but risk increased to 0.0065 (0.0000 to 0.0283) to 0.43 (0.175 to 0.709) when one to all three of the risk factors were present. The entirety of this research indicates that P. macularis appears to persist in a subset of chronically affected hop yards, particularly yards where spring pruning is conducted poorly. Targeted management of the disease in a subset of fields most at risk for producing flag shoots could potentially influence powdery mildew development regionwide.