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Field apple scab susceptibility of a diverse Malus germplasm collection identifies potential sources of resistance for apple breeding



Breeding for resistance to apple scab (caused by Venturia inaequalis), the most devastating fungal disease of apples, relies on genetic resources maintained in germplasm collections.


To identify new sources of scab resistance, we evaluated 177 Malus accessions, including 27 primary and 13 hybrid Malus species from diverse geographical origins, in an orchard at Geneva, New York. We also screened a differential host set for 2 years to monitor for changes in the effectiveness of ten known scab resistance genes, which allowed us to confirm the presence of virulent pathogen races in the orchard.


We found that ~ 37% of the wild Malus accessions and domesticated cultivars were resistant to apple scab in the field. Several of these accessions were unrelated to sources of previously known resistance genes and are promising for apple scab genetic research and resistance breeding. Cultivars carrying the Rvi6 (Vf) gene from Malus floribunda clone 821, e.g. ‘Liberty’ or ‘Florina’, remained resistant despite the breakdown of Rvi6. ‘Demir’, a Malus hybrid from Turkey, and ‘Chisel Jersey’, a traditional English hard cider cultivar, showed fewer symptoms than the Rvi6 resistant cultivar ‘Prima’. Races 1 to 7 and 9 of V. inaequalis were present in the orchard, but no scab was observed on the indicator host accessions for races 11 and 12.


Detailed and systematic screening of Malus germplasm identified resistant and moderately resistant donor accessions based on resistance reaction types. These accessions are promising for use in future genetic studies to identify novel sources of scab resistance alleles for apple breeding to develop cultivars with durable apple scab resistance.


Disease susceptibility of commercial apple cultivars (Malus domestica Borkh.), and the continual emergence of new pathogenic races that overcome resistance genes, are major threats to the apple industry worldwide. Apple scab (causal agent: Venturia inaequalis Cke./Wint.) is the most devastating fungal disease of apples in humid areas throughout the world where apple is grown (González-Domínguez et al. 2017). The majority of apple cultivars grown commercially in the USA are susceptible to apple scab. Apple scab lesions on fruit mainly impact their cosmetic appearance, severely limiting their marketability. Growers must apply approximately 12–18 fungicide sprays per growing season to limit quality and yield loss due to apple scab (Peck et al. 2010; MacHardy et al. 2001). Frequent use of fungicides contributes significantly to production costs, and to negative human health and environmental impacts. Apple cultivars resistant to scab require fewer fungicide applications, saving on costs and reducing the environmental impact of disease control (Papp et al. 2019; Brown and Maloney 2008; MacHardy et al. 2001). Malus accessions and land races maintained in the US national germplasm repository are sources of diverse functional alleles that can be used to breed apple cultivars with enhanced and durable resistance (Byrne et al. 2018). In fact, large-scale screening of germplasm repositories is a common strategy to identify valuable traits for use in breeding for many major crop species (Girichev et al. 2018; Liang et al. 2015; Vasudevan et al. 2014). Conventional commercial apple production is driven mainly by desirable fruit quality traits including taste and shelf life, but development of new apple scab resistant, or tolerant, cultivars might allow reduction of disease management costs, fungicide resistance development, as well as reduce negative environmental and health impacts, and is especially critical for organic and low input production (Koutis et al. 2018; Kellerhals et al. 2004). Unfortunately, the introgression of disease resistance alleles from wild sources into apple cultivars with good fruit quality is a slow and challenging process and so the proportion of scab-resistant cultivars in commercial production remains low (Brown and Maloney 2013).

Genetic resistance to scab in apple is primarily guided by major resistance genes, in a classical gene-for-gene relationship with the Avr genes of the pathogen. To date, 20 resistance genes (Rvi genes) have been described in V. inaequalis, most of which were identified in wild Malus accessions and landraces (Bus et al. 2011; Khajuria et al. 2018). Only two of the Rvi genes, Rvi6 (receptor kinase gene) and Rvi15 (TIR-NBS-LRR gene) have been characterized and their functionally validated (Schouten et al. 2014; Jansch et al. 2014). Unfortunately, many of the resistance genes, including the well-characterized Rvi6 gene, have been overcome by novel virulent races of the scab pathogen (Papp et al. 2019; Parisi et al. 1993, 2004; Xu et al. 2008). A successful apple scab resistance breeding program in the USA between the Universities of Purdue, Rutgers and Illinois (the PRI initiative), used resistance genes from four sources, M. floribunda Sieb. ex Van Houtte clone 821 (Rvi6 and Rvi7) (Japanese crabapple), M. micromalus Makino (Rvi5) (Midget crabapple or Kaido crabapple), M. domestica sel. R12740-7A (Rvi2 and Rvi4), and the common apple ‘Antonovka’ (Rvi10, Rvi17, polygenic), to develop commercial scab-resistant cultivars and pre-breeding materials. These four genotypes became the foundation for later breeding work worldwide (Crosby et al. 1992). However, most modern scab resistant cultivars carry Rvi6 resistance from M. floribunda 821 (Brown and Maloney 2013).

Monitoring the virulence of pathogen races, as well as understanding the evolutionary and genetic mechanisms responsible for loss of host resistance, are essential both for managing disease resistance and developing durable resistance (Patocchi et al. 2020). In the USA, races 1 to 5 and 9 of V. inaequalis have been previously reported to overcome Rvi1, Rvi5 and Rvi9, respectively (Beckerman et al. 2009; Durham et al. 1999; Hagan et al. 2000; Shay and Williams 1956; Williams and Kuc 1969), but there is no information regarding races of V. inaequalis with an ability to cause disease on apple genotypes with Rvi11 and Rvi12 resistance genes (derived from M. baccata (L.) Borkh. ‘jackii’ and ‘Hansens baccata #2’). The presence of races 6 and 7, which can infect M. floribunda 821, was suggested by Beckerman et al. (2009), but was only recently confirmed by characterization of monosporic isolates of V. inaequalis collected from M. floribunda 821 (Papp et al. 2019). According to the most recent update from monitoring scab resistance of differential indicator cultivars and accessions in 14 countries, the most promising R genes, exhibiting consistent resistance across locations to date, are Rvi5, Rvi11, Rvi12, Rvi14 and Rvi15 (Patocchi et al. 2020).

Screening the existing apple germplasm collections for scab resistance can contribute to the identification of additional scab resistance gene resources, and if utilized, eventually to the development of new resistant cultivars with good fruit quality (Papp et al. 2019). The national Malus collection at the USDA (United States Department of Agriculture) Plant Genetic Resources Unit (PGRU) is the world’s largest apple germplasm repository, with 5004 unique Malus accessions growing in the field and 1603 seedlots representing M. domestica, 33 Malus species, and 15 hybrid species from around the world (Volk et al. 2015a). Approximately 2500 accessions in the collection have been evaluated for a 28-trait descriptor set (Volk et al. 2015a). The collection exhibits broad diversity for a large range of morphological descriptors (e.g., leaf, shoot, flower and bark characteristics), economically important horticultural traits (e.g., tree vigor, shoot traits, ploidy, flowering, fruiting characteristics), disease and pest resistance, and fruit quality traits (Forsline and Aldwinckle 2001, 2003; Harshman et al. 2017; Hokanson et al. 2001; Jurick et al. 2011; Khan and Chao 2017; Luby et al. 1996, 2002; Momol et al. 1999; Myers et al. 2008; Norelli et al. 2013;

Comprehensive genetic characterization of the entire USDA-PGRU apple collection for disease resistance is laborious and logistically challenging, especially for disease evaluation in the field. Some wild Malus accessions of the USDA-PGRU collection, particularly M. sieversii (Ledeb.) M.Roem. (Aldwinckle et al. 1997; Hokanson et al. 1997; Volk et al. 2005) and M. orientalis Uglitzk. ex Juz. (Volk et al. 2008), have been screened for apple scab resistance, and a considerable number of the accessions showed resistance to V. inaequalis in those studies. In general, and with the exception of a few specifically bred cultivars, M. domestica cultivars show a low level of scab resistance (Aldwinckle et al. 1997; Brown and Maloney 2008, 2013). Development of core collections, representing maximum genetic and trait diversity in the genepool of various crop species, has been widely adopted to lower the maintenance costs and evaluation of crop germplasm (Escribano et al. 2008; Liang et al. 2015; Schoen and Brown 1995). To this end, a core collection of 258 individual Malus accessions, representing genetic diversity of the whole collection, was established at five field locations in the U.S.A. to assess disease resistance, fruit quality, and horticultural traits (Luby et al. 1996; Potts et al. 2012). With regard to disease resistance, the Malus core collection has been evaluated for fire blight resistance in the greenhouse (Khan et al. 2013), but no extensive evaluation has yet been initiated to screen the 258 Malus accessions for resistance to apple scab.

Screening accessions in the field is the most direct method to assess scab resistance relevant to production systems. However, for successful infection with the pathogen, not only are a virulent race of V. inaequalis and a susceptible host required, but a favorable environment is also needed, so as to satisfy the host/pathogen/environment interactions (Francl 2001). Particularly humid years are conducive to spore germination (Machardy and Gadoury 1989) and offer an excellent opportunity to identify scab resistance in the field; indeed, the identification of Vf resistance occurred in such a season (Crosby et al. 1992). The growing season was wet in 2019, and the resulting favorable weather conditions for development of epidemics of scab may have contributed to the development and occurrence of new races of V. inaequalis with the ability to infect the previously resistant M. floribunda 821 (Papp et al. 2019).

In this study, firstly, we evaluated the scab resistance of 177 diverse Malus accessions in the field, including wild species, cultivars, and hybrid selections to identify new sources of scab resistance. Secondly, we assessed scab on a differential host set of ten apple genotypes to monitor the breakdown of resistance for each of the ten known scab resistance genes, and also to monitor the presence of virulent pathogen races in the orchard.

Materials and methods

Plant material

The apple scab resistance reaction types of 177 accessions of the Malus core collection were evaluated in the research orchard at Cornell AgriTech, Geneva, New York (42° 52′ 38″ N, 77° 03′ 08″ W). The orchard comprises four replicated blocks of the core collection. The core collection is derived from the USA national Malus germplasm repository and includes 27 primary wild Malus species and 13 interspecific hybrid species, 61 domestic apple cultivars/landraces and 36 unspecified hybrid selections (Table 1). Most of the hybrid selections were developed by the PRI Initiative and other breeding programs, or are crabapples of unknown parentage. The 177 accessions represent the major part of a core collection of 258 individual Malus accessions that was established at five field locations in the U.S.A. to evaluate disease resistance, fruit quality, and horticultural traits (Khan et al. 2013; Luby et al. 1996; Potts et al. 2012). Some trees were lost over time at some orchard locations and were not replaced. The unique Plant Introduction (PI) number of each accession used in this study (Table 1) was obtained from the USDA Germplasm Resources Information Network (GRIN) database (, and can be used to compare accessions evaluated in different studies. In addition, the research orchard includes ten differential host accessions with known apple scab resistance genes to identify previously characterized races of V. inaequalis. If a differential host was not available as proposed by Bus et al. (2011), alternative hosts (some with more than one R gene) present in the core collection were evaluated as surrogates for that resistance reaction type (Table 2). Information on Malus taxonomy for each species was obtained from the GRIN database, which adheres to the Malus systematics of Rehder (1915) and Langenfeld (1970).

Table 1 Apple scab resistance of accessions from a Malus core collection in a research orchard at Geneva, New York
Table 2 Severity of apple scab at two timepoints in 2019 on a scab differential host set in the research orchard at Geneva, New York

Orchard maintenance and weather data

Malus accessions in the core collection are grafted on ‘M9’ rootstocks and are planted in 12 consecutive rows. The 12 rows are divided into 4 blocks (replications) with each replication arranged in 3 rows of trees. Accessions within each replicated block are planted using a randomized block design; in each block there is only one replicate of any accession (i.e., a single tree of each accession per block). Trees have 1.8 m in-row spacing and 3.9 m between-row spacing with a four-wire training system. Trees are approximately 15–20 years old. No pesticides (i.e., insecticides, fungicides, and antibiotics) have been applied in the orchard since 2017 to avoid any possible pathogen, host and pesticide interactions and to observe pathogen isolates and host resistance responses under natural epidemic and selection environments. Trees were occasionally pruned, and a regular mowing schedule was maintained for laneways. The orchard was not fertilized or irrigated during the study period.

A Hobo RX3000 weather station equipped with temperature (Temp) and relative humidity (RH) sensors (Onset Computer Corporation, Bourne, MA) was located approximately 800 m east of the core collection research orchard and was used to collect weather data in 2018 and 2019. Temp and RH readings were collected at 5-min intervals and transmitted in real-time to the HOBO RX3000 base station, which uploaded data at 15-min intervals to HOBOlink. Datasets were generated in HOBOlink for download, with hourly summarizations and subsequent analysis. Wet periods (RH > 90%) represented infection risk and were used to calculate Mills periods, based on the Temp and wet period duration according to MacHardy and Gadoury (1989).

Assessment of apple scab symptoms

Symptoms of apple scab on the 177 Malus accessions and the 10 differential apple host genotypes were evaluated three times a year in June, July, and August in 2018 and 2019. Evaluations consisted of a careful examination of the visible leaves in the tree canopy of each of the 177 trees and 10 differentials, in each of the 4 replicated blocks. The scab evaluations were used to ascertain the resistance response types of each of the accessions in the orchard, using a previously developed rank ordering of scab symptoms (Chevalier et al. 1991). The classes of the ordinal scale are as follows:

0—no symptoms; 1—pin point pits; 2—chlorotic lesions; 3a—necrotic and some chlorotic lesions, very weak sporulation; 3b—clearly sporulating chlorotic and necrotic lesions; and 4—abundantly sporulating lesions covering most of the leaf area. Based on the symptom classes we distinguished four response categories: 1—Resistant (symptom class: 0, 1, 2), 2—moderately resistant (3a), 3—Moderately susceptible (3b), 4—susceptible (4).

In addition, the 10 differential host accessions in the four replicated orchard blocks were evaluated for scab severity in early July and August of 2019. The most severely infected tree of each host accession in the four replicated blocks was used to represent the accession. The scab severity within the tree canopy was visually evaluated using a 9 point ordinal scale described by Lateur and Populer (1994) and adapted by Patocchi et al. (2009): 0—no observation (missing plant); 1—no visible scab lesions; 2—one or very few scab lesions detectable on close scrutiny of the tree (0–1%); 3—Immediately apparent scab lesions, generally clustered in a few parts of the tree (1–5%); 4—intermediate; 5—numerous scab lesions widespread over a large proportion of the tree (± 25%); 6—intermediate; 7—severe symptoms of scab with half of the leaves severely scabbed exhibiting multiple lesions (± 50%); 8—intermediate (± 75%); or 9—foliage of tree completely affected with (nearly) all the leaves severely diseased by multiple scab lesions (> 90%).

Data analyses and visualization

Statistical analyses were performed to evaluate the difference between the weather conditions of the 2 years, and to test differences in scab resistance of the accessions. The scab resistance reaction type data collected at three time points in 2018 and 2019 were used to assess scab susceptibility of each of the accessions. Scab resistance reaction type and severity data collected over 2 years for the differential hosts with ten known scab resistance genes were used to assess whether any local races of V. inaequalis were able to overcome the genetic resistance in hitherto resistant differentials and to identify novel sources of apple scab resistance. Results of daily RH and Temp data from April to October and scab resistance responses of accessions/Malus taxonomy groups for each species were visualized in R version 3.6.2 (R Core Team 2020) using the inbuilt functions and the ggplot2 package (Wickham 2016). The effect of different genotypes and different time points within and across years on the disease severity inferred from the scab resistance reactions was explored using an ordinal logistic regression model in IBM SPSS Statistics v.25.0 (Arkmonk, NY). Furthermore, the total number of plants in each of the four categories of resistance response symptom classes for each month (June, July and August) in 2018 and 2019 and the corresponding weather variables were used to perform principal component analysis (PCA) analysis to study the effect of weather variables on disease susceptibility. The PCA results were explored graphically using biplots with the packages FactoMineR (Husson et al. 2020) and factoextra (Kassambara and Mundt 2017) in R version 3.6.2. Weather variables used included: average RH (RHave), minimum RH (RHmin), maximum RH (RHmax), average temperature (Tave), minimum temperature (Tmin), and maximum temperature (Tmax) for June, July and August 2018 and 2019. Pearson’s correlation analysis among these variables was performed in R version 3.6.2. A chi-square test was performed to evaluate relationship among Malus taxonomic groups and scab severity.


Impact of weather conditions on apple scab severity

In 2019, a higher proportion of the Malus core collection trees were infected with scab, which reached a plateau of approximately 50% of all the trees in the orchard, in contrast to 25% in 2018 (Figs. 1 and 2). The ordinal logistic model showed significant (P < 0.0001) difference among the genotypes and the six timepoints in apple scab susceptibility. According to the dispersion of Mills periods across the two study years, 2019 experienced conditions favorable to infection by apple scab 2 weeks earlier (data not shown). During the early vegetative phase of growth, both average Temp and RH (%) were higher in 2019 compared to in 2018 (Fig. 3). Later in the season, the relative difference in temperature between the 2 years shifted, but was close to the 16 to 23.9 ºC optimum for scab development. The high Temp peaks in June and July of 2018 were > 32 ºC, higher than the more consistent daily temperatures experienced in 2019. The average monthly RH was higher in April, May, and July in 2019, and RH was > 90% more often throughout the whole season in 2019, providing more suitable conditions for spore germination of V. inaequalis.

Fig. 1
figure 1

Proportion of resistance reaction type classes observed on each of six evaluation dates during the growing seasons of 2018 and 2019 in the Malus germplasm core collection in the research orchard at Geneva, New York. Resistance categories were assessed as proposed by Chevalier et al. (1991). The orchard was not sprayed with pesticides

Fig. 2
figure 2

Severe apple scab symptoms on ‘Calville Blanc’ apples (a) leaves and (b) fruit in the Malus core collection in the research orchard at Geneva, New York

Fig. 3
figure 3

Daily dispersion of (a) temperature (ºC) and (b) relative humidity (%) from April to August in 2018–2019, at the same location as the Malus germplasm core collection at Geneva, New York. Different colors indicate different months. The red line shows (a) the mean temperature, and (b) the mean relative humidity for each of the months

The PCA biplot showed a strong positive association among RHave, RHmin and Tmin, and negative association between RHmax and Tmax (Fig. 4). The variables RHave and RHmin, RHave and Tmin, and RHmin and Tmin showed positive correlations (r) of 0.96, 0.86 and 0.93, respectively, whereas RHmax and Tmax showed a negative correlation (r) of − 0.61. The first two PCs (principal components) explained 86.6% of the variation; PC1 and PC2 explained 53.6% and 33% of the variation, respectively. Apple scab susceptibility was found to be influenced by RHmax, RHave, RHmin and Tmin, whereas apple scab resistance was found to be influenced by Tmax as depicted by the location of RHmax in relation to the moderately susceptible accessions, RHave, RHmin, Tmin, and the susceptible accessions, and Tmax and the resistant accessions in the same quadrant of the PCA biplot i.e. quadrant II, I and IV of the PCA biplot, respectively. The presence of RHmax and susceptible accessions, and Tmax and resistant accessions in close proximity to each other in the PCA biplot shows strong association of RHmax and scab symptom development, and Tmax and disease resistance respectively (Fig. 4).

Fig. 4
figure 4

PCA biplot showing PC1 and PC2 to depict the relationship between different weather parameters and apple scab severity (resistance reaction type) for the six dates when scab was evaluated. The number of plants in the Malus germplasm core collection in each of four categories of symptom classes: Resistant, Moderately resistant, Moderately susceptible, and Susceptible were counted in June, July and August of 2018 and 2019, and used to perform principal component analysis (PCA) using the package FactoMineR (Husson et al. 2020) and factoextra (Kassambara and Mundt 2017) in R version 3.6.2 (R Core Team 2020). Weather variables are: average relative humidity (RHave), minimum relative humidity (RHmin), maximum relative humidity (RHmax), average temperature (Tave), minimum temperature (Tmin), and maximum temperature (Tmax)

Scab severity on the differential set

The indicator accessions with ten known scab resistance genes were used to monitor the severity of scab infection in relation to races of V. inaequalis present in the orchard (Table 2). ‘Gala’ showed heavy scab infection in both years. Scab severity on ‘Golden Delicious’, carrying Rvi1, was even higher (class 7) compared to severity on the susceptible control. Differential hosts 2 (TSR34t15), 3 (M. × ‘Geneva’), 4 (TSR33t239), 5 (OR45T132) and 9 (M. × ‘Dolgo’) were all severely diseased with scab, indicating the presence of races 1 to 5 and race 9. Scab severity was as high as class 4, except for host differential indicator for race 4, which was rated in scab severity class 5 by the end of the season. M. baccata ‘Jackii’ (indicator for race 11) and ‘Hansens baccata #2’ (indicator for race 12) were free of scab. Severe scab was observed on M. floribunda 821, the source of Rvi6 and Rvi7 resistance, as reported earlier by Papp et al. (2019), but ‘Priscilla’ (Rvi6) was free of scab symptoms. Overall, resistance response types were consistent over the period of assessment, with only slight differences in severity.

Sources of novel scab genetic resistance in the core collection

Of the 177 Malus accessions evaluated for apple scab symptom, a total of 49, 17, 32, and 79 accessions were free of scab or resistant (ordinal scale classes 0, 1, 2), had weak sporulation (3a), had well-developed sporulating lesions (3b), or were completely susceptible (4), respectively (Table 1; Additional file 1: Table S1). The 49 resistant accessions are mostly primary Malus species (46.9%), hybrids from breeding programs (22.4%), secondary Malus sp. (14.3%), and Rvi6 resistant cultivars (12.2%); there were two apple ‘Antonovka’ landraces (4%). In contrast to the large number of resistant accessions among the primary apple species, no modern domestic cultivar lacking a known major resistance gene was found to be completely free of scab. In the most susceptible category (n = 79), 51.8% were domestic cultivars. Out of 61 M. domestica accessions included in the study, 8 were resistant to apple scab (‘Antonovka 172670-B’, ‘Antonovka 43470 lb’, ‘Britegold’, ‘Dayton’, ‘Florina’, ‘Jonafree’, ‘Liberty’, and ‘Redfree’). Most of these accessions with scab resistant phenotypes can be traced back to PRI breeding materials and are considered to have Rvi6 resistance from M. floribunda 821. Sporulation of scab lesions was noticed on Rvi6 cultivars ‘Prima’ and ‘Nova Easygro’ and has been reported previously (Papp et al. 2019). In addition, PRI cultivars ‘Murray’ (Rvi5), ‘Trent’ (Rvi6) and ‘Viking’ were found to show scab symptoms. Only 5 of the 19 hybrid selections listed by their PRI codes did not show symptoms during the 2 years. The selections PRI 333-9 (syn. OR45T132, Rvi5) and PRI 384-1 (syn. TSR34T15, Rvi2) were both severely scabbed. Besides the PRI derivates, two cultivars: ‘Demir’ and ‘Chisel Jersey’, were evaluated as moderately resistant to scab. Traditional heritage cultivars including ‘Gravenstein Washington Red’ and ‘Irish Peach’, or ‘Burgundy’ had less severe symptoms compared to ‘McIntosh’, ‘Granny Smith’, ‘Gala’, or ‘Golden Delicious’.

The highest number of scab infected accessions are in the Malus section. In August 2019, scab severity was the highest in the Malus section at all time points; approximately 81% of the genotypes in the Malus section showed scab susceptibility (Additional file 1: Table S1). The percentage of scabbed genotypes for the interspecific hybrids was approximately 41%, and for the sections Chloromeles, Gymnomeles, and Sorbomalus was 35%, 28%, and 18% of trees, respectively (Fig. 5). No completely susceptible accession was identified in the sections Sorbomalus and Dyconiopsis. However, the section Dyconiopsis, comprised only one accession with 3 samples, which showed moderate susceptibility in 2018, but not in 2019. Scab resistance differed significantly among six taxonomic groups (χ2(d.f. 4) = 40.365, p < 0.001). Although the proportion of trees with apple scab increased from 2018 to 2019, this did not affect the relative differences between the scab susceptibilities of the taxonomic groups.

Fig. 5
figure 5

Proportion of infected trees of each accession according to their taxonomic affiliation (obtained from the USDA GRIN) at six timepoints during 2018 and 2019 in the Malus germplasm core collection in the research orchard at Geneva, New York. Symptom classes (resistance response types) were assessed as proposed by Chevalier et al. (1991). Numbers provided in parenthesis refers to the number of trees in the section


Detailed and systematic screening of diverse Malus germplasm can identify donor accessions for sources of novel and durable apple scab resistance. We have identified potential new sources of scab resistance among M. domestica cultivars and crabapples. Resistant and moderately resistant accessions are promising for use in future genetic studies to identify novel sources of scab resistant alleles for apple breeding (Patocchi et al. 2020; Papp et al. 2019). Domestic cultivars ‘Demir’ and ‘Chisel Jersey’ were moderately resistant. Although occasional weak sporulation was observed on some of the trees, the sporulation was slight and the severity low enough to preclude posing any economic threat to production. In addition, we noticed that both ‘Demir’ and ‘Chisel Jersey’ are late season and there is the possibility that they escaped a high-risk infection period. ‘Demir’ is a Turkish fresh eating cultivar, while ‘Chisel Jersey’ is a cider cultivar from the United Kingdom (UK). Many of the crabapples with unknown resistance were free of scab, including accessions of unknown hybrid species, breeding materials and Malus species. The majority of R genes are derived from small-fruited crabapples: Rvi2 and Rvi4 from M. pumila R12740-7A, Rvi5 from M. × atrosanguinea Schneid. sel. 804 and M. micromalus 245–38, Rvi6 and Rvi7 from M. floribunda 821, Rvi8 from M. sieversii GMAL4302-X8, Rvi11 from M. baccata ‘jackii’, Rvi12 from M. baccata ‘Hansen’s 2#’ and Rvi9 from M. × ‘Dolgo’, possibly a clone of M. baccata or M. prunifolia (Willd.) Borkh. (Bus et al. 2011). We lack molecular and genomic data to characterize the genetic basis of the resistance of many of these promising accessions, although it is possible that these resistances were due to already-described major genes or by polygenic quantitative resistance. Novel single gene-based resistance can be easier to characterize and provide new opportunities for apple breeding. At the same time new technologies including biotechnology, genomics, marker assisted selection and novel breeding methods might make polygenic resistance sources more accessible and reliable for apple breeding in the future.

We observed the breakdown of major resistance genes Rvi1 to Rvi7 and Rvi9 in the research orchard. The V. inaequalis races 1, 7 and 9 have all been reported previously from the U.S.A. (Beckerman et al. 2009; Durham et al. 1999; Papp et al. 2019; Shay and Williams 1956; Williams and Kuc 1969). No scab was observed on the differentials of race 11 and 12, although of these, only host 11 (alongside the host for race 15, which was not included in the study) were assigned as ‘not overcome’ by a recent update on worldwide race distributions (Patocchi et al. 2020). In the case of hosts for races 2 (PRI 384-1) and 5 (PRI 333-9, ‘Murray’, Malus sp. ‘Prairie Fire’), all other genotypes screened that possessed known R genes have confirmed breakdown; in the case of Rvi6, many cultivars remained resistant (e.g. ‘Liberty’, ‘Florina’). It should be noted that the only apple cultivars with good fruit quality, and that have scab resistance are those with the Rvi6 gene. We do not yet know why Rvi6 cultivars retain their resistance when the original host source of the Rvi6 resistance can be infected by V. inaequalis. Investigating the reason why infection of Malus floribunda 821, the source of Rvi6 resistance, is possible, but infection of descendant cultivars is not will be of value for informed development of scab resistant cultivars in the future.

In our study, we have identified a clear relationship between the taxonomic affiliation and the scab susceptibility of Malus germplasm. The relationship might reflect host frequency-based selection on the pathogen, hypothesizing that scab susceptibility of wild species is directly related to their genetic proximity to the domesticated apple. The domestication of apples started in Central Asia, where the primary progenitor, M. sieversii exists in large natural populations. Congruent with this host distribution, V. inaequalis populations infecting domesticated apples originated from Central Asia and coevolved with M. sieversii during the domestication process (Gladieux et al. 2008, 2010). Populations of the pathogen tend to show distinct genetic structure related to their original Malus host species, and the breakdown of resistance genes derived from wild Malus species might be caused by divergent pathogen populations emerging from wild apple reservoirs, as has been demonstrated in the case of Rvi6 resistance (Gladieux et al. 2010; Lemaire et al. 2016; Leroy et al. 2016; Michalecka et al. 2018). M. sieversii accessions (including the accession of M. kirghisorum syn. M. sieverii var. kirghisorum) were susceptible to apple scab in our study. There is substantial genetic evidence that the European wild apple M. sylvestris, M. orientalis with gene centers to the west of Central Asia, as well as M. baccata with gene centers in East Asia, have hybridized with domestic apple during the domestication process (Cornille et al. 2012, 2014; Duan et al. 2017; Volk et al. 2015b). Overall, accessions of M. domestica and M. sieversii, two closely related species, had considerably more severe scab compared to the accessions of the other wild Malus species. Despite this finding, the inoculum of V. inaequalis from the Malus core collection research orchard might simply not be diverse enough to reflect larger scale trends and might represent races specialized to domestic cultivars. Larger-scale genetic studies and genome-based analysis of local isolates will contribute to understanding the pathogen in relation to host specificity patterns in the Malus-Venturia pathosystem.

A consequence of modern production systems with large acreage of monocultures could facilitate specialization of pathogen strains on particular cultivars, the build-up of large populations on uniform host populations with rapid dissemination of the new strain (McDonald and Stukenbrock 2016). The sexual and asexual phases of V. inaequalis can allow it to evolve rapidly and in the context of modern high-density apple orchards, it has the ability to quickly overcome genetic resistance in apples. Therefore, it is critical to continue to identify and characterize new sources of both qualitative and quantitative scab resistance and pyramid multiple resistance sources in order to develop apple cultivars with durable scab resistance. The scab resistance screening data from this study can be combined with previous assessments for fire blight resistance, fruit quality, and horticultural traits (Khan et al. 2013; Luby et al. 1996; Potts et al. 2012) available for the majority of the accessions in the Malus core collection to identify potential sources for introgression of multiple traits for cultivar development. At the same time, it is also important to understand the relationship between the evolutionary potential of V. inaequalis and current disease management practices for enhancing the durability of the resistance genes. Disease management practices to decrease population sizes of the pathogen, limiting production of sexual inoculum, may also contribute to reducing the pathogen's evolutionary potential (McDonald 2015).

Availability of data and materials

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This research was supported by the New York Apple Research and Development Program (ARDP). David Papp is supported by the Miklos Faust scholarship in fruit science.

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AK designed the experiment, supervised the research and revised the manuscript. DP and LG collected the apple scab data in 2018 and 2019 respectively. DP analyzed the data and wrote the manuscript, RT helped with statistical analysis, DO supported weather data collection. All authors read and approved the manuscript.

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Correspondence to Awais Khan.

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Additional file 1: Table S1.

Apple scab resistance response type of 177 Malus accessions in four blocks (replications) across six sampling dates in 2018 and 2019. Resistance response type was evaluated in a research orchard at Geneva, New York by visually assessing scab severity on single leaves throughout the visible tree canopy of single trees/accessions in each replicated block. Plant Introduction (PI) number of each accession is provided according to the USDA Germplasm Resources Information Network (GRIN).

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Papp, D., Gao, L., Thapa, R. et al. Field apple scab susceptibility of a diverse Malus germplasm collection identifies potential sources of resistance for apple breeding. CABI Agric Biosci 1, 16 (2020).

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