Scab resistance in ‘Geneva’ apple is conditioned by a resistance gene cluster with complex genetic control

Apple scab, caused by the fungal pathogen Venturia inaequalis, is one of the most severe diseases of apple worldwide. It is the most studied plant–pathogen interaction involving a woody species using modern genetic, genomic, proteomic and bioinformatic approaches in both species. Although ‘Geneva’ apple was recognized long ago as a potential source of resistance to scab, this resistance has not been characterized previously. Differential interactions between various monoconidial isolates of V. inaequalis and six segregating F1 and F2 populations indicate the presence of at least five loci governing the resistance in ‘Geneva’. The 17 chromosomes of apple were screened using genotyping‐by‐sequencing, as well as single marker mapping, to position loci controlling the V. inaequalis resistance on linkage group 4. Next, we fine mapped a 5‐cM region containing five loci conferring both dominant and recessive scab resistance to the distal end of the linkage group. This region corresponds to 2.2 Mbp (from 20.3 to 22.5 Mbp) on the physical map of ‘Golden Delicious’ containing nine candidate nucleotide‐binding site leucine‐rich repeat (NBS‐LRR) resistance genes. This study increases our understanding of the complex genetic basis of apple scab resistance conferred by ‘Geneva’, as well as the gene‐for‐gene (GfG) relationships between the effector genes in the pathogen and resistance genes in the host.     

Virulence Pattern of Venturia inaequalis Field Isolates and Corresponding Differential Resistance in Malus x domestica

All commercially important apple cultivars are susceptible in the field to scab caused by Venturia inaequalis. The scope of this study was to investigate variation in virulence in Venturia inaequalis populations towards commercial apple cultivars. For this purpose, primary lesions were sampled in orchards with different varietal compositions and diversities. The virulence pattern of monosporic isolates, obtained by isolation of single conidia, was assessed by cross inoculations of the cv. Ananas Reinette, Boskoop, Glockenapfel, Golden Delicious, Gravenstein, James Grieve, Jonathan, Maigold, Reinette de Champagne, Spartan and Yellow Transparent. All cultivars were susceptible to some isolates and resistant to others. No cultivar behaved the same way, which suggests the presence of differential resistance in each cultivar and corresponding virulence in some isolates. Isolates from a monoculture of Golden Delicious consisted mainly of a pathotype that was virulent to Golden Delicious but not to other cultivars. In the samples from cultivar mixtures, virulence pattern variation was considerable. The results give further evidence of the existence of a large pool of differential and ephemeral resistances in Malus, which were overcome by the local scab populations during co‐evolution.     

Molecular characterization of cisgenic lines of apple ‘Gala’ carrying the Rvi6 scab resistance gene

Using resistance genes from a crossable donor to obtain cultivars resistant to diseases and the use of such cultivars in production appears an economically and environmentally advantageous approach. In apple, introgression of resistance genes by classical breeding results in new cultivars, while introducing cisgenes by biotechnological methods maintains the original cultivar characteristics. Recently, plants of the popular apple ‘Gala’ were genetically modified by inserting the apple scab resistance gene Rvi6 (formerly HcrVf2) under control of its own regulatory sequences. This gene is derived from the scab‐resistant apple ‘Florina’ (originally from the wild apple accession Malus floribunda 821). The vector used for genetic modification allowed a postselection marker gene elimination to achieve cisgenesis. In this work, three cisgenic lines were analysed to assess copy number, integration site, expression level and resistance to apple scab. For two of these lines, a single insertion was observed and, despite a very low expression of 0.07‐ and 0.002‐fold compared with the natural expression of ‘Florina’, this was sufficient to induce plant reaction and reduce fungal growth by 80% compared with the scab‐susceptible ‘Gala’. Similar results for resistance and expression analysis were obtained also for the third line, although it was impossible to determine the copy number and TDNA integration site–such molecular characterization is requested by the (EC) Regulation No. 1829/2003, but may become unnecessary if cisgenic crops become exempt from GMO regulation.     

O‐Methyltransferases involved in biphenyl and dibenzofuran biosynthesis

Biphenyls and dibenzofurans are the phytoalexins of the Malinae involving apple and pear. Biosynthesis of the defence compounds includes two O‐methylation reactions. cDNAs encoding the O‐methyltransferase (OMT) enzymes were isolated from rowan (Sorbus aucuparia) cell cultures after treatment with an elicitor preparation from the scab‐causing fungus, Venturia inaequalis. The preferred substrate for SaOMT1 was 3,5‐dihydroxybiphenyl, supplied by the first pathway‐specific enzyme, biphenyl synthase (BIS). 3,5‐Dihydroxybiphenyl underwent a single methylation reaction in the presence of S‐adenosyl‐l ‐methionine (SAM). The second enzyme, SaOMT2, exhibited its highest affinity for noraucuparin, however the turnover rate was greater with 5‐hydroxyferulic acid. Both substrates were only methylated at the meta‐positioned hydroxyl group. The substrate specificities of the OMTs and the regiospecificities of their reactions were rationalized by homology modeling and substrate docking. Interaction of the substrates with SAM also took place at a position other than the sulfur group. Expression of SaOMT1, SaOMT2 and SaBIS3 was transiently induced in rowan cell cultures by the addition of the fungal elicitor. While the immediate SaOMT1 products were not detectable in elicitor‐treated cell cultures, noraucuparin and noreriobofuran accumulated transiently, followed by increasing levels of the SaOMT2 products aucuparin and eriobofuran. SaOMT1, SaOMT2 and SaBIS3 were N‐ and C‐terminally fused with the super cyan fluorescent protein and a modified yellow fluorescent protein, respectively. All the fluorescent reporter fusions were localized to the cytoplasm of Nicotiana benthamiana leaf epidermis cells. A revised biosynthetic pathway of biphenyls and dibenzofurans in the Malinae is presented.     

Formation of biphenyl and dibenzofuran phytoalexins in the transition zones of fire blight-infected stems of Malus domestica cv. ‘Holsteiner Cox’ and Pyrus communis cv. ‘Conference’

In the rosaceous subtribe Pyrinae (formerly subfamily Maloideae), pathogen attack leads to formation of biphenyls and dibenzofurans. Accumulation of these phytoalexins was studied in greenhouse-grown grafted shoots of Malus domestica cv. ‘Holsteiner Cox’ and Pyrus communis cv. ‘Conference’ after inoculation with the fire blight bacterium, Erwinia amylovora. No phytoalexins were found in leaves. However, both classes of defence compounds were detected in the transition zone of stems. The flanking stem segments above and below this zone, which were necrotic and healthy, respectively, were devoid of detectable phytoalexins. The transition zone of apple stems contained the biphenyls 3-hydroxy-5-methoxyaucuparin, aucuparin, noraucuparin and 2′-hydroxyaucuparin and the dibenzofurans eriobofuran and noreriobofuran. In pear, aucuparin, 2′-hydroxyaucuparin, noreriobofuran and in addition 3,4,5-trimethoxybiphenyl were detected. The total phytoalexin content in the transition zone of pear was 25 times lower than that in apple. Leaves and stems of mock-inoculated apple and pear shoots lacked phytoalexins. A number of biphenyls and dibenzofurans were tested for their in vitro antibacterial activity against some Erwinia amylovora strains. The most efficient compound was 3,5-dihydroxybiphenyl (MIC = 115 μg/ml), the immediate product of biphenyl synthase which initiates phytoalexin biosynthesis.     

Quantification of polyphenolic compounds and relative gene expression studies of phenylpropanoid pathway in apple (Malus domestica Borkh) in response to Venturia inaequalis infection

Apple (Malus domestica Borkh) is rich in phenolic compounds, which may enhance resistance to scab disease caused by Venturia inaequalis. In present study, apple cv. Golden Delicious was used for estimation of total phenols, flavonoids and quantification of six individual phenolic compounds. between control vs inoculated samples at different inoculation stages. The relative gene expression of phenylalanine ammonia lyase, chalcone synthase and flavanone 3 hydroxylase increased and polyphenolic compounds were constitutively upregulated at different post-inoculation stages. Data suggest that synthesis and accumulation of polyphenols is closely related with disease resistance against Venturia inaequalis. This study may play a vital role in understanding and finding out the governing mechanisms of scab resistance.     

Efficacy of Boric Acid,Monopotassium Phosphate and Sodium Metabisulfite on the Control of Apple Scab

In vitro experiments indicated that boric acid, monopotassium phosphate, sodium metabisulfite and synthetic fungicide fluopyram + tebuconazole were effective in inhibiting conidia germination and germ‐tube elongation of Venturia inaequalis. Monopotassium phosphate even at the highest concentration used in the study reduced conidia germination and germ‐tube elongation of V. inaequalis by 22.1% and 28.8%, respectively; however, the difference between two compounds at lower concentrations except 0.05% (for conidia germination) and 0.1% (for germ‐tube elongation) of boric acid was statistically significant (P ≤ 0.05). Complete inhibition was achieved by 0.01% sodium metabisulfite, 0.035% fluopyram + tebuconazole and 0.2% boric acid. Two orchard trials were conducted on the highly susceptible cv. Mutsu to apple scab to ascertain the efficacy of 0.2% boric acid, 0.5% monopotassium phosphate, 0.5% sodium metabisulfite and 0.035% fluopyram + tebuconazole for the control of apple scab. In both 2013 and 2014, except for the applications of monopotassium phosphate and sodium metabisulfite, the applications of boric acid and fluopyram + tebuconazole to trees at 10‐day intervals significantly reduced disease incidence and severity on leaves and fruit compared to the water‐treated control. In both years, the efficacy of boric acid and fluopyram + tebuconazole treatments was similar in reducing both disease incidence and severity on leaves and fruit in all monthly assessments from July to September. All treatments were neither phytotoxic to leaves and fruit nor did they adversely affect quality parameters of harvested fruit. These results show that boric acid treatment may be applied as an alternative chemical for the control of apple scab.     

Enzyme activity of the phenylpropanoid pathway as a response to apple scab infection

The study was performed on apple trees, ‘Golden Delicious' cv., which is a scab-susceptible cultivar. The phenolic content of apple fruit was determined in different parts of the peel. The phenolic compounds were analysed in the scab spot, in the tissue around the spot and in the healthy tissue. We determined the concentration of various phenolic compounds and related enzyme activities. Infection with the Venturia inaequalis fungus enhanced the metabolism of phenolic compounds at the scab spot, around the spot and in healthy peel. Compared with the healthy tissue and the tissue around the spot, the scab spot showed higher enzyme activity for all tested enzymes, except for dihydrochalcone 2′-O-glucosyltransferase, which had lower activity in the scab spot. In comparison to the healthy peel, the scab spot showed up to 3.4 times more hydroxycinnamic acids, up to 1.1 times more dihydrochalcones and up to 1.4 times more flavan-3-ols. In contrast, the healthy peel showed up to 1.6 times more flavonols than the scab spot.     

A new enzymatic activity from elicitor‐treated pear cell cultures converting trans‐cinnamic acid to benzaldehyde

Cell cultures of Asian pear (Pyrus pyrifolia) are known to produce benzoate‐derived biphenyl phytoalexins upon elicitor treatment. Although the downstream pathway for biphenyl phytoalexin biosynthesis is almost known, the upstream route of benzoic acid biosynthesis in pear has not been completely elucidated. In the present work, we report benzaldehyde synthase (BS) activity from yeast extract‐treated cell suspension cultures of P. pyrifolia. BS catalyzes the in vitro conversion of trans‐cinnamic acid to benzaldehyde using a non‐oxidative C₂‐side chain cleavage mechanism. The enzyme activity was strictly dependent on the presence of a reducing agent, dithiothreitol being preferred. C₂‐side chain shortening of the cinnamic acid backbone resembled the mechanisms catalyzed by 4‐hydroxybenzaldehyde synthase (HBS) activity in Vanilla planifolia and salicylaldehyde synthase (SAS) activity in tobacco and apple cell cultures. A basal BS activity was also observed in the non‐elicited cell cultures. Upon yeast extract‐treatment, a 13‐fold increase in BS activity was observed when compared to the non‐treated control cells. Moreover, feeding of the cell cultures with trans‐cinnamic acid, the substrate for BS, resulted in an enhanced level of noraucuparin, a biphenyl phytoalexin. Comparable accumulation of noraucuparin was observed upon feeding of benzaldehyde, the BS product. The preferred substrate for BS was found to be trans‐cinnamic acid, for which the apparent K_m and V_max values were 0.5 mM and 50.7 pkat mg^?1 protein, respectively. Our observations indicate the contribution of BS to benzoic acid biosynthesis in Asian pear via the CoA‐independent and non‐β‐oxidative route.     

Evaluation of the Use of Ammonium Bicarbonate and Oregano (Origanum vulgare ssp. hirtum) Extract on the Control of Apple Scab

In vitro experiments showed that ammonium bicarbonate and aqueous extracts of oregano were effective in inhibiting conidia germination and germ‐tube elongation of Venturia inaequalis. Complete inhibition was achieved by 1% ammonium bicarbonate, 2% oregano extract and 0.01% synthetic fungicide difenoconazole. Two orchard experiments were conducted on the highly susceptible cv. Mutsu to apple scab to investigate the efficacy of ammonium bicarbonate alone or in combination with an aqueous extract of oregano for the control of apple scab. In 2008 and 2009, except for the applications of 1% aqueous extract of oregano, the applications of ammonium bicarbonate (0.5 and 1%) and difenoconazole (0.01%) to trees at 10‐day intervals significantly reduced disease incidence and severity on leaves and fruit compared to the water‐treated control. In both years, the efficacy of 0.5 and 1% ammonium bicarbonate in inhibiting both disease incidence and severity on leaves and fruit was equally effective in all monthly assessments from June to September. Combining 0.5 and 1% ammonium bicarbonate with 1% aqueous extract of oregano did not significantly improve the efficacy of stand‐alone applications of treatments in the final assessment in 2008 and 2009. All treatments were neither phytotoxic to leaves and fruit nor did they adversely affect quality parameters of fruit including physiological disorders and taste both at harvest and after storage. These results indicate that ammonium bicarbonate treatment may be applied as an alternative chemical for the control of apple scab.     

Isolation of 21 new polymorphic microsatellite loci in the phytopathogenic fungus Venturia inaequalis

Twenty‐one new polymorphic microsatellite markers were isolated in the phytopathogenic fungus Venturia inaequalis, the causal agent of apple scab. An enrichment protocol was used to isolate microsatellite loci and the level of polymorphism was assessed on 44 European isolates. All loci were polymorphic with an average of 9.1 alleles per locus (range 2–24). Tests of cross‐species amplifications suggest that at least some of these microsatellites could be used in different species, mainly Spilocaea pyracanthae and S. eriobotryae.     

Infection and Stroma Formation by Venturia inaequalis on Apple Leaves with Different Degrees of Susceptibility to Scab

Conidia of Venturia inaequalis germinated and formed appressoria on all leaves independently of age and origin within the first 15 hours after inoculation. On the youngest expanded leaves of the apple variety Golden Delicious 80% of the conidia developed stromata within the first 24 hours, sporulation occurred after 8 days. On the second leaf (counted from the top of the twig) stroma formation was slowed down compared to the first and sporulation occurred after 10 days only. On the third leaf the fungus rarely formed stromata and never sporulated. The fourth leaf already showed complete ontogenetic resistance. In the diploid variety Priscilla the gene Vf, which confers resistance against scab to apple leaves, was expressed as reduced stroma formation without sporulation, as in the case of ontogenetic resistance. In the triploid variety Sir Prize with the gene Vf, stroma formation was retarded and colonization and sporulation occurred later on the first leaf, similarly to the reaction of the second leaf of variety Golden Delicious.     

Phenolic compounds in apple leaves after infection with apple scab

Leaves of the scab-susceptible apple (Malus domestica) cultivar Golden Delicious were harvested from May to August 2008 and 2009. Some leaves were healthy and some infected with fungus Venturia inaequalis. The phenolic compounds were analysed in healthy leaves, infected leaves and in the scab spot tissue. In comparison to healthy leaves, the infected leaves showed higher contents of hydroxycinnamic acid, flavanols and phloridzin, while lower contents on procyanidins, quercetins and phloretin. The total amount of phenolic compounds in the infected tissue was 10 to 20 % higher than in the healthy leaves. Accumulation of phenolic compounds is a post-infection response, and probably their further transformation is a prerequisite for plant resistance.     

Phenotypic Reaction and Genetic Analysis Using AFLP-derived SCARs for Resistance to Apple Scab

Six sequence‐characterized amplified region (SCAR) markers linked to the apple scab resistance gene Vf were evaluated for their utility in marker‐assisted selection (MAS) in apple breeding. Of the six SCARs used in this study, ACS‐6 was located left of the Vf gene, ACS‐7 and ACS‐9 co‐segregated with Vf, and ACS‐8, ACS‐4, ACS‐5 were located right of the Vf gene. Three families derived from crosses between scab‐resistant and scab‐susceptible cultivars, including ‘Liberty’ × ‘Deljub’, ‘Liberty’ × ‘Delcorf’, and ‘Florina’ בDelcorf’, previously screened for scab resistance following greenhouse inoculation with the fungal pathogen Venturia inaequalis, were genotyped and compared with phenotypic reactions to scab infection in the field. For each family, a subset progeny of 30 seedlings (propagated onto Malling 9 rootstock and of 7 years old) was selected based on fungal sporulation according to the following scheme. Ten seedlings with no visible scab sporulation on leaves were given phenotypic scores of 0 (deemed resistant); 10 seedlings with moderate scab sporulation were given phenotypic scores of 1.0 (deemed moderately resistant); and 10 seedlings with heavy sporulation were given phenotypic scores of 2.0 (deemed susceptible). DNA was isolated from leaf tissue collected from all 90 seedlings, parents and Malus floribunda 821, the original source of the Vf gene, and screened with all six SCARs. All six SCARs were present in the two scab‐resistant parents, ‘Liberty’ and ‘Florina’, and M. floribunda 821; while, the two scab‐susceptible parents, ‘Deljub’ and ‘Delcorf’, lacked all SCARs. All SCARs were either present or absent in varying numbers of seedlings in each progeny with phenotypic ratings of either 0 (resistant) or 1.0 (moderately resistant); while all seedlings with phenotypic ratings of 2.0 (susceptible) lacked all SCARs. The inconsistencies between phenotypic scab ratings and SCAR marker data are discussed.     

Susceptibility of selected apple cultivars to the Mediterranean fruit fly

Ceratitis capitata (Wiedemann), the Mediterranean fruit fly, is one of the key pest species affecting deciduous fruit orchards along the Mediterranean coasts. Because of global warming, C. capitata is gradually spreading north and is becoming a major pest of apples. Determining the susceptibility of the main apple varieties grown in the region will serve as a cornerstone to the management of this pest. In this study, we show the results of a field and laboratory no‐choice test conducted to determine the Medfly preferences on different apple cultivars. The seven main varieties of apples (Gala, Red Delicious, Golden Delicious, Granny Smith, Kanzi, Morgen Dallago and Fuji) were tested. The results demonstrate that C. capitata lays eggs on all apple cultivars in both field and laboratory conditions. The Granny Smith, Red Delicious and Morgen Dallago varieties showed the lowest susceptibility in laboratory conditions, (0.75, 1.55, 2 oviposition punctures/fruit, respectively), with significant differences in oviposition compared to the Golden Delicious, Kanzi and Fuji (3.27, 3.31, 3.1 oviposition punctures/fruit, respectively) varieties, which were shown to be the most susceptible to Medfly attack in laboratory conditions. On the other hand, only slight and not statistically significant differences emerged from the field trials. In relation to the physico‐chemical characteristics, the apple cultivars showing the lowest susceptibility (Granny Smith, Red Delicious and Morgen Dallago) had harder peels and pulps and lower sugar contents than the most susceptible cultivars (Golden Delicious, Fuji and Kanzi). These results were also confirmed through evaluation of larval development on different varieties. In fact, Granny Smith, Red Delicious and Morgen Dallago were the three varieties that did not allow adequate larval and adult development and reduced the possibility of the emergence of a new generation.     

Engineering fire blight resistance into the apple cultivar ‘Gala’ using the FB_MR5 CC‐NBS‐LRR resistance gene of Malus × robusta 5

The fire blight susceptible apple cultivar Malus × domestica Borkh. cv. ‘Gala’ was transformed with the candidate fire blight resistance gene FB_MR5 originating from the crab apple accession Malus × robusta 5 (Mr5). A total of five different transgenic lines were obtained. All transgenic lines were shown to be stably transformed and originate from different transgenic events. The transgenic lines express the FB_MR5 either driven by the constitutive CaMV 35S promoter and the ocs terminator or by its native promoter and terminator sequences. Phenotyping experiments were performed with Mr5‐virulent and Mr5‐avirulent strains of Erwinia amylovora, the causal agent of fire blight. Significantly less disease symptoms were detected on transgenic lines after inoculation with two different Mr5‐avirulent E. amylovora strains, while significantly more shoot necrosis was observed after inoculation with the Mr5‐virulent mutant strain ZYRKD3_1. The results of these experiments demonstrated the ability of a single gene isolated from the native gene pool of apple to protect a susceptible cultivar from fire blight. Furthermore, this gene is confirmed to be the resistance determinant of Mr5 as the transformed lines undergo the same gene‐for‐gene interaction in the host–pathogen relationship Mr5–E. amylovora.     

Expression profiling in HcrVf2-transformed apple plants in response to Venturia inaequalis

Apple scab resistance is one of the most well-characterized plant–pathogen interactions in a woody plant species. While the HcrVf2 gene from the wild apple Malus floribunda 821 has proved capable of conferring scab resistance to the susceptible cv. Gala after genetic transformation, its identification represents only the first step in understanding the molecular mechanisms and, hence, the network of genes underlying the defence response. We used a PCR-based suppression subtractive hybridization to identify apple genes that are differentially expressed after Venturia inaequalis inoculation. Subtractive hybridization was performed between cDNA from challenged leaves of HcrVf2-resistant transgenic Gala and susceptible cv. Gala plants. A library of 523 unigenes was constructed and characterized by assigning a putative function via comparison with public databases. This set of pathogen-modulated apple genes includes many defence-related genes and is therefore an important source of information for understanding the molecular basis of the Malus–V. inaequalis interaction. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Genetic control of α‐farnesene production in apple fruit and its role in fungal pathogenesis

Terpenes are important compounds in plant trophic interactions. A meta‐analysis of GC‐MS data from a diverse range of apple (Malus × domestica) genotypes revealed that apple fruit produces a range of terpene volatiles, with the predominant terpene being the acyclic branched sesquiterpene (E,E)‐α‐farnesene. Four quantitative trait loci (QTLs) for α‐farnesene production in ripe fruit were identified in a segregating ‘Royal Gala’ (RG) × ‘Granny Smith’ (GS) population with one major QTL on linkage group 10 co‐locating with the MdAFS1 (α‐farnesene synthase‐1) gene. Three of the four QTLs were derived from the GS parent, which was consistent with GC‐MS analysis of headspace and solvent‐extracted terpenes showing that cold‐treated GS apples produced higher levels of (E,E)‐α‐farnesene than RG. Transgenic RG fruit downregulated for MdAFS1 expression produced significantly lower levels of (E,E)‐α‐farnesene. To evaluate the role of (E,E)‐α‐farnesene in fungal pathogenesis, MdAFS1 RNA interference transgenic fruit and RG controls were inoculated with three important apple post‐harvest pathogens [Colletotrichum acutatum, Penicillium expansum and Neofabraea alba (synonym Phlyctema vagabunda)]. From results obtained over four seasons, we demonstrate that reduced (E,E)‐α‐farnesene is associated with decreased disease initiation rates of all three pathogens. In each case, the infection rate was significantly reduced 7 days post‐inoculation, although the size of successful lesions was comparable with infections on control fruit. These results indicate that (E,E)‐α‐farnesene production is likely to be an important factor involved in fungal pathogenesis in apple fruit.