Pathogen Aggressiveness Research Articles

Evaluation of Pathogenic Variability Based on Leaf Blotch Disease Development Components of Bipolaris sorokiniana in Triticum aestivum and Agroclimatic Origin.

Leaf blotch of wheat caused by Bipolaris sorokiniana is a major constraint to wheat production, causing significant yield reduction resulting in severe economic impact. The present study characterizes to determine and compare pathogenic variability exist/not based on components of leaf blotch disease development and level of aggressiveness due to agroclimatic condition of B. sorokiniana in wheat. A total of 169 virulent isolates of B. sorokiniana isolated from spot blotch infected leaf from different wheat growing agroclimate of Bangladesh. Pathogenic variability was investigated on a susceptible wheat variety ‘kanchan’ now in Bangladesh. A clear evidence of positive relationship among the components was recorded. From hierarchical cluster analysis five groups were originating among the isolates. It resolved that a large amount of pathogenic diversity exists in Bipolaris sorokiniana. Variation in aggressiveness was found among the isolates from different wheat growing areas. Most virulent isolates BS 24 and BS 33 belonging to High Ganges River Flood Plain agro-climatic zones considered by rice-wheat cropping pattern, hot and humid weather, high land and low organic matter content in soil. Positive relationship was found between pathogenic variability and aggressiveness with agro-climatic condition.

Pantoea ananatis Genetic Diversity Analysis Reveals Limited Genomic Diversity as Well as Accessory Genes Correlated with Onion Pathogenicity.

Pantoea ananatis is a member of the family Enterobacteriaceae and an enigmatic plant pathogen with a broad host range. Although P. ananatis strains can be aggressive on onion causing foliar necrosis and onion center rot, previous genomic analysis has shown that P. ananatis lacks the primary virulence secretion systems associated with other plant pathogens. We assessed a collection of fifty P. ananatis strains collected from Georgia over three decades to determine genetic factors that correlated with onion pathogenic potential. Previous genetic analysis studies have compared strains isolated from different hosts with varying diseases potential and isolation sources. Strains varied greatly in their pathogenic potential and aggressiveness on different cultivated Allium species like onion, leek, shallot, and chive. Using multi-locus sequence analysis (MLSA) and repetitive extragenic palindrome repeat (rep)-PCR techniques, we did not observe any correlation between onion pathogenic potential and genetic diversity among strains. Whole genome sequencing and pan-genomic analysis of a sub-set of 10 strains aided in the identification of a novel series of genetic regions, likely plasmid borne, and correlating with onion pathogenicity observed on single contigs of the genetic assemblies. We named these loci Onion Virulence Regions (OVR) A-D. The OVR loci contain genes involved in redox regulation as well as pectate lyase and rhamnogalacturonase genes. Previous studies have not identified distinct genetic loci or plasmids correlating with onion foliar pathogenicity or pathogenicity on a single host pathosystem. The lack of focus on a single host system for this phytopathgenic disease necessitates the pan-genomic analysis performed in this study.

Candidate Genes for Aggressiveness in a Natural Fusarium culmorum Population Greatly Differ between Wheat and Rye Head Blight.

Fusarium culmorum is one of the species causing Fusarium head blight (FHB) in cereals in Europe. We aimed to investigate the association between the nucleotide diversity of ten F. culmorum candidate genes and field ratings of aggressiveness in winter rye. A total of 100 F. culmorum isolates collected from natural infections were phenotyped for FHB at two locations and two years. Variance components for aggressiveness showed significant isolate and isolate-by-environment variance, as expected for quantitative host-pathogen interactions. Further analysis of the isolate-by-environment interaction revealed the dominant role of the isolate-by-year over isolate-by-location interaction. One single-nucleotide polymorphism (SNP) in the cutinase (CUT) gene was found to be significantly (p < 0.001) associated with aggressiveness and explained 16.05% of the genotypic variance of this trait in rye. The SNP was located 60 base pairs before the start codon, which suggests a role in transcriptional regulation. Compared to a previous study in winter wheat with the same nucleotide sequences, a larger variation of pathogen aggressiveness on rye was found and a different candidate gene was associated with pathogen aggressiveness. This is the first report on the association of field aggressiveness and a host-specific candidate gene codifying for a protein that belongs to the secretome in F. culmorum.

Reaction of brazilian cotton genotypes to white mold depends on pathogen aggressiveness and incubation conditions

Reaction of brazilian cotton genotypes to white mold depends on pathogen aggressiveness and incubation conditions

Effects of Temperature Stresses on the Resistance of Chickpea Genotypes and Aggressiveness of Didymella rabiei Isolates.

Chickpea (Cicer arietinum L.) is an important food and rotation crop in many parts of the world. Cold (freezing and chilling temperatures) and Ascochyta blight (Didymella rabiei) are the major constraints in chickpea production. The effects of temperature stresses on chickpea susceptibility and pathogen aggressiveness are not well documented in the Cicer-Didymella pathosystem. Two experiments were conducted under controlled conditions using chickpea genotypes and pathogen isolates in 2011 and 2012. In Experiment 1, four isolates of D. rabiei (AR-01, AR-02, AR-03 and AR-04), six chickpea genotypes (Ghab-1, Ghab-2, Ghab-3, Ghab-4, Ghab-5 and ICC-12004) and four temperature regimes (10, 15, 20, and 25°C) were studied using 10 day-old seedlings. In Experiment 2, three chickpea genotypes (Ghab-1, Ghab-2, and ICC-12004) were exposed to 5 and 10 days of chilling temperature exposure at 5°C and non-exposed seedlings were used as controls. Seedlings of the three chickpea genotypes were inoculated with the four pathogen isolates used in Experiment 1. Three disease parameters (incubation period, latent period and disease severity) were measured to evaluate treatment effects. In Experiment 1, highly significant interactions between genotypes and isolates; genotypes and temperature; and isolate and temperature were observed for incubation and latent periods. Genotype x isolate and temperature x isolate interactions also significantly affected disease severity. The resistant genotype ICC-12004 showed long incubation and latent periods and low disease severity at all temperatures. The highly aggressive isolate AR-04 caused symptoms, produced pycnidia in short duration as well as high disease severity across temperature regimes, which indicated it is adapted to a wide range of temperatures. Short incubation and latent periods and high disease severity were observed on genotypes exposed to chilling temperature. Our findings showed that the significant interactions of genotypes and isolates with temperature did not cause changes in the rank orders of the resistance of chickpea genotypes and aggressiveness of pathogen isolates. Moreover, chilling temperature predisposed chickpea genotypes to D. rabiei infection; developing multiple stress resistance is thus a pre-requisite for the expansion of winter-sown chickpea in West Asia and North Africa.

Host resistance and pathogen aggressiveness are key determinants of coinfection in the wild.

Coinfection, whereby the same host is infected by more than one pathogen strain, may favor faster host exploitation rates as strains compete for the same limited resources. Hence, coinfection is expected to have major consequences for pathogen evolution, virulence, and epidemiology. Theory predicts genetic variation in host resistance and pathogen infectivity to play a key role in how coinfections are formed. The limited number of studies available has demonstrated coinfection to be a common phenomenon, but little is known about how coinfection varies in space, and what its determinants are. Our aim is to understand how variation in host resistance and pathogen infectivity and aggressiveness contribute to how coinfections are formed in the interaction between fungal pathogen Podosphaera plantaginis and Plantago lanceolata. Our phenotyping study reveals that more aggressive strains are more likely to form coinfections than less aggressive strains in the natural populations. In the natural populations most of the variation in coinfection is found at the individual plant level, and results from a common garden study confirm the prevalence of coinfection to vary significantly among host genotypes. These results show that genetic variation in both the host and pathogen populations are key determinants of coinfection in the wild.

Study of Fitness, Virulence, and Fungicide Sensitivity of Lambertella corni-maris Causing Yellow Rot on Apple.

Very little is known about the biology, epidemiology, and best practices to manage Lambertella rot, a newly identified postharvest disease caused by Lambertella corni-maris on apples in the United States. In this study, we investigated the prevalence of L. corni-maris in 92 grower lots throughout Washington State in 2016, evaluated the effect of nutrient availability on L. corni-maris growth, and L. corni-maris sensitivity to pH, osmotic stress, and fungicides in vitro. We assessed pathogen aggressiveness on major apple cultivars and the efficacy of pre- and postharvest fungicides to control L. corni-maris on detached fruit. L. corni-maris was widespread and was found in 40% of the growers lots surveyed at frequencies ranging from 2 to 40% of the total decay. The fungus grew faster on acidic media such as apple juice agar and V8 agar media and was able to grow equally at pH values ranging from 3 to 7. L. corni-maris isolates showed relatively low sensitivity to osmotic stress and grew evenly at 1M KCl. All nine apple cultivars tested were susceptible to L. corni-maris, but the disease severity was significantly higher on some cultivars such as Honeycrisp, Piñata, and Gala. The baseline sensitivity of 100 L. corni-maris isolates was determined based on the effective concentration necessary to inhibit 50% mycelial growth (EC50) for fludioxonil, boscalid, pyraclostrobin + SHAM, pyrimethanil, and thiabendazole. The respective mean EC50 values were 0.07, 0.84, 1.32, 2.45, and 3.68 µg/ml. Fludioxonil and pyrimethanil applied at label rates were the only fungicides able to control L. corni-maris effectively on detached apple fruit. This study is a first step toward understanding the eco-physiological requirements for L. corni-maris to survive and cause decay on apple, assessing potential shifts in fungicide sensitivity, and enhancing Lambertella rot management. We suggest "yellow rot" as the new common name for Lambertella rot.

Linear Correlation Analysis of Zymoseptoria tritici Aggressiveness with In Vitro Growth Rate.

Zymoseptoria tritici is a globally distributed plant-pathogenic fungus causing Septoria tritici blotch of wheat. In this study, the in vitro growth rates and aggressiveness of 141 genetically distinct isolates sampled from four wheat fields on three continents were assessed to determine the association of these two ecological parameters. Aggressiveness was assessed on two spring wheat cultivars ('Toronit' and 'Greina') in a greenhouse using percentages of leaf area covered by lesions and pycnidia. We found a positive correlation between aggressiveness of pathogen strains on the two cultivars, consistent with a quantitative and host-nonspecific interaction in this pathosystem. We also found a positive correlation between aggressiveness and average growth rate at two temperatures, suggesting that in vitro pathogen growth rate may make a significant contribution to pathogen aggressiveness.

Slow erosion of a quantitative apple resistance to Venturia inaequalis based on an isolate-specific Quantitative Trait Locus

Quantitative plant resistance affects the aggressiveness of pathogens and is usually considered more durable than qualitative resistance. However, the efficiency of a quantitative resistance based on an isolate-specific Quantitative Trait Locus (QTL) is expected to decrease over time due to the selection of isolates with a high level of aggressiveness on resistant plants. To test this hypothesis, we surveyed scab incidence over an eight-year period in an orchard planted with susceptible and quantitatively resistant apple genotypes. We sampled 79 Venturia inaequalis isolates from this orchard at three dates and we tested their level of aggressiveness under controlled conditions. Isolates sampled on resistant genotypes triggered higher lesion density and exhibited a higher sporulation rate on apple carrying the resistance allele of the QTL T1 compared to isolates sampled on susceptible genotypes. Due to this ability to select aggressive isolates, we expected the QTL T1 to be non-durable. However, our results showed that the quantitative resistance based on the QTL T1 remained efficient in orchard over an eight-year period, with only a slow decrease in efficiency and no detectable increase of the aggressiveness of fungal isolates over time. We conclude that knowledge on the specificity of a QTL is not sufficient to evaluate its durability. Deciphering molecular mechanisms associated with resistance QTLs, genetic determinants of aggressiveness and putative trade-offs within pathogen populations is needed to help in understanding the erosion processes.

Changes in the Aggressiveness and Fecundity of Hot Pepper Anthracnose Pathogen (Colletotricum acutatum) under Elevated CO2 and Temperature over 100 Infection Cycles.

We observed the changes in aggressiveness and fecundity of the anthracnose pathogen Colletotrichum acutatum on hot pepper, under the ambient and the twice-ambient treatments. Artificial infection was repeated over 100 cycles for ambient (25°C/400 ppm CO2) and twice-ambient (30°C/700 ppm CO2) growth chamber conditions, over 3 years. During repeated infection cycles (ICs) on green-pepper fruits, the aggressiveness (incidence [% of diseased fruits among 20 inoculated fruits] and severity [lesion length in mm] of infection) and fecundity (the average number of spores per five lesions) of the pathogen were measured in each cycle and compared between the ambient and twice-ambient treatments, and also between the early (ICs 31–50) and late (ICs 81–100) generations. In summary, the pathogen’s aggressiveness and fecundity were significantly lower in the late generation. It is likely that aggressiveness and fecundity of C. acutatum may be reduced as global CO2 and temperatures increase.

The Temperature Response and Aggressiveness of Peyronellaea pinodes Isolates Originating from Wild and Domesticated Pisum sp. in Israel.

Domesticated pea fields are grown in relatively close proximity to wild pea species in Israel. Despite the major role attributed to ascochyta blight in causing yield losses in domesticated pea, very limited information is available on the pathogens prevailing in natural ecosystems. The objectives of this study were (i) to identify the species causing ascochyta blight symptoms on leaves, stems, and petioles of domesticated pea and wild Pisum plants in Israel, and (ii) to quantify the temperature response(s) and aggressiveness of such pathogens originating from Pisum plants growing in sympatric and allopatric contexts. Eighteen fungal isolates were examined and identified; three of them were sampled from Pisum sativum, 11 from Pisum fulvum, and four from Pisum elatius. All isolates were identified as Peyronellaea pinodes. Spore germination and mycelial growth took place over a wide range of temperatures, the lower and upper cardinal temperatures being 2 to 9 and 33 to 38°C, respectively; the optimal temperatures ranged from 22 to 26°C. At an optimal temperature, disease severity was significantly higher for plants maintained under moist conditions for 24 h postinoculation than for those exposed to humidity for 5 or 10 h. Analyses of the data revealed that temperature responses, spore germination rates, and aggressiveness of isolates sampled from domesticated pea plants did not differ from those of isolates sampled from adjacent or distant wild populations. Host specificity was not observed. These observations suggest that Israel may be inhabited by a single metapopulation of P. pinodes.

Weeds, as ancillary hosts, pose disproportionate risk for virulent pathogen transfer to crops

BackgroundThe outcome of the arms race between hosts and pathogens depends heavily on the interactions between their genetic diversity, population size and transmission ability. Theory predicts that genetically diverse hosts will select for higher virulence and more diverse pathogens than hosts with low genetic diversity. Cultivated hosts typically have lower genetic diversity and thus small effective population sizes, but can potentially harbour large pathogen population sizes. On the other hand, hosts, such as weeds, which are genetically more diverse and thus have larger effective population sizes, usually harbour smaller pathogen population sizes. Large pathogen population sizes may lead to more opportunities for mutation and hence more diverse pathogens. Here we test the predictions that pathogen neutral genetic diversity will increase with large pathogen population sizes and host diversity, whereas diversity under selection will increase with host diversity. We assessed and compared the diversity of a fungal pathogen, Rhynchosporium commune, on weedy barley grass (which have a large effective population size) and cultivated barley (low genetic diversity) using microsatellites, effector locus nip1 diversity and pathogen aggressiveness in order to assess the importance of weeds in the evolution of the neutral and selected diversity of pathogens.ResultsThe findings indicated that the large barley acreage and low host diversity maintains higher pathogen neutral genetic diversity and lower linkage disequilibrium, while the weed maintains more pathotypes and higher virulence diversity at nip1. Strong evidence for more pathogen migration from barley grass to barley suggests transmission of virulence from barley grass to barley is common.ConclusionsPathogen census population size is a better predictor for neutral genetic diversity than host diversity. Despite maintaining a smaller pathogen census population size, barley grass acts as an important ancillary host to R. commune, harbouring highly virulent pathogen types capable of transmission to barley. Management of disease on crops must therefore include management of weedy ancillary hosts, which may harbour disproportionate supplies of virulent pathogen strains.Electronic supplementary materialThe online version of this article (doi:10.1186/s12862-016-0680-6) contains supplementary material, which is available to authorized users.

Evaluation of Spray and Point Inoculation Methods for the Phenotyping of Puccinia striiformis on Wheat

The fungus Puccinia striiformis causes yellow (stripe) rust on wheat worldwide. In the present article, new methods utilizing an engineered fluid (Novec 7100) as a carrier of urediniospores were compared with commonly used inoculation methods. In general, Novec 7100 facilitated a faster and more flexible application procedure for spray inoculation and it gave highly reproducible results for virulence phenotyping. Six point inoculation methods were compared to find the most suitable for assessment of pathogen aggressiveness. The use of Novec 7100 and dry dilution with Lycopodium spores gave an inoculation success rate of 100% in two independent trials, which was significantly higher and more consistent than for spore suspension in Soltrol 170, water, water + Tween 20, and Noble agar + Tween 20. Both Soltrol 170 and Novec 7100 allowed precise quantification of inoculum, which is important for the assessment of quantitative epidemiological parameters. New protocols for spray and point inoculation of P. striiformis on wheat are presented, along with the prospect for applying these in rust research and resistance breeding activities.

Comparative Validation of Conventional and RNA-Seq Data-Derived Reference Genes for qPCR Expression Studies of Colletotrichum kahawae.

Colletotrichum kahawae is an emergent fungal pathogen causing severe epidemics of Coffee Berry Disease on Arabica coffee crops in Africa. Currently, the molecular mechanisms underlying the Coffea arabica—C. kahawae interaction are still poorly understood, as well as the differences in pathogen aggressiveness, which makes the development of functional studies for this pathosystem a crucial step. Quantitative real time PCR (qPCR) has been one of the most promising approaches to perform gene expression analyses. However, proper data normalization with suitable reference genes is an absolute requirement. In this study, a set of 8 candidate reference genes were selected based on two different approaches (literature and Illumina RNA-seq datasets) to assess the best normalization factor for qPCR expression analysis of C. kahawae samples. The gene expression stability of candidate reference genes was evaluated for four isolates of C. kahawae bearing different aggressiveness patterns (Ang29, Ang67, Zim12 and Que2), at different stages of fungal development and key time points of the plant-fungus interaction process. Gene expression stability was assessed using the pairwise method incorporated in geNorm and the model-based method used by NormFinder software. For C. arabica—C. kahawae interaction samples, the best normalization factor included the combination of PP1, Act and ck34620 genes, while for C. kahawae samples the combination of PP1, Act and ck20430 revealed to be the most appropriate choice. These results suggest that RNA-seq analyses can provide alternative sources of reference genes in addition to classical reference genes. The analysis of expression profiles of bifunctional catalase-peroxidase (cat2) and trihydroxynaphthalene reductase (thr1) genes further enabled the validation of the selected reference genes. This study provides, for the first time, the tools required to conduct accurate qPCR studies in C. kahawae considering its aggressiveness pattern, developmental stage and host interaction.

The interface between abiotic and biotic stress responses.

The interface between abiotic and biotic stress responses.

Resistance of soybean genotypes to Sclerotinia sclerotiorum isolates in different incubation environments.

Sclerotinia sclerotiorum is an important soybean pathogen. The objectives of this study were to evaluate levels of resistance of soybean genotypes to the fungus, and to determine the effects of different incubation environments on host resistance and pathogen aggressiveness. Two experiments were conducted using 103 genotypes from the seed collection of Laboratório de Desenvolvimento de Germoplasma, Universidade Federal de Uberlândia (LAGER-UFU). The first experiment was conducted in a greenhouse, and the second in a growth chamber. Inoculations were performed by the straw test method using two Brazilian isolates of the fungus, one from Uberaba, Minas Gerais, and the other from Jataí, Goiás. The average stem-lesion length (cm) at 5 days post-inoculation was used to determine levels of resistance. Overall, the most resistant genotype was EMGOPA-316, and the most susceptible genotype was LAGER-29. Incubation in a growth chamber and use of the Jataí isolate generated the most reliable data, and multivariate analysis indicated that the genotypes were divergent under the growth chamber conditions. Therefore, when studying host resistance of soybean genotypes to S. sclerotiorum, it is important to use environmental conditions favorable to the fungus and aggressive isolates.

Cytogenomic characterization of Colletotrichum kahawae, the causal agent of coffee berry disease, reveals diversity in minichromosome profiles and genome size expansion

Colletotrichum kahawae is an emerging fungal pathogen, which has recently undergone a speciation process from a generalistic ‘C. gloeosporioides species complex' background by acquiring the unique capacity to infect green coffee berries, thus causing coffee berry disease. This is a severe and widespread disease in Africa and an imminent threat to Arabica coffee cultivation in Asia and America, if the pathogen enters those continents. Genetic diversity within C. kahawae is low but notorious differences in pathogen aggressiveness have been described. This work characterized two cytogenomic traits (genome size and minichromosome profiles) of a collection of C. kahawae isolates, representing the breadth of its genetic diversity and distinct aggressiveness classes, along with closely related taxa. The results obtained constitute the first flow cytometry‐based genome size estimation in the genus Colletotrichum and show a c. 8 Mb genome size expansion between C. kahawae (79·5 Mb on average) and its closest relatives (71·3 Mb), corroborating evidence indicating that C. kahawae (i.e. the coffee berry disease pathogens) should remain as a distinct species. Results have also shown the presence of two to five minichromosomes in C. kahawae, suggesting a positive relationship between the number of minichromosomes and the level of aggressiveness of the different isolates analysed, while no correlation could be established between aggressiveness and whole genome size. Overall, these results may be the basis for the identification of pathogenicity/aggressiveness‐related factors in such minichromosomes, and may provide clues to the characterization of specific markers for aggressiveness classes.

Response of selected winter wheat cultivars to inoculation with different Mycosphaerella graminicola isolates

Sip V., Chrpova J., Palicova J. (2015): Response of selected winter wheat cultivars to inoculation with different Mycosphaerella graminicola isolates. Czech J. Genet. Plant Breed., 51: 86–95. Five winter wheat cultivars, differing in resistance to Septoria tritici blotch (STB), were spray inoculated under field conditions for two years and at two locations with nine Mycosphaerella graminicola isolates and a mixture of isolates that were obtained from different regions of the Czech Republic. Main aims of this study were (i) to compare isolate, host cultivar and environmental effects on five traits indicative of STB severity and (ii) to analyse pathogen aggressiveness and host-pathogen relations for improving evaluation of cultivar resistance. ANOVA showed in all traits, except the reduction in 1000 grain weight, significant isolate effects. However, the effects of isolate and genotype by isolate interactions were much lower (2.3–4%) than cultivar (19.1–53.7%) and environmental (11.9–58.6%) effects. Cultivar resistance to the disease limited much the loss in grain weight per spike to a halve, from 34.7% in the susceptible Bakfis to 17.3% in the resistant Arina. Visual scoring of symptoms in the middle and at the end of disease development (performed on the 1–9 scale), reflecting the disease progress and infected leaf area, showed the highest cultivar effect (54%) and could be recommended for evaluation of cultivar resistance in breeding practice. All examined traits were significantly interrelated, but significant differences between all the five cultivars were only detected after examination of the % coverage of flag leaves with lesions bearing pycnidia. Resistance in the cultivar Arina was detected by all isolates and the isolate mixture. In spite of significant differences in classification of resistances in the cultivars Bohemia and Mulan after inoculation with one isolate (1081), specific interactions between cultivars and isolates collected in this Central European region are rare. The study leads to a conclusion that investigation into stability of STB resistance across a wide range of environments is more valuable for breeding purposes than the study of cultivar response to different isolates. Combination of important isolate properties in a mixture of isolates is stressed as well

How can research on pathogen population biology suggest disease management strategies? The example of barley scald (Rhynchosporium commune)

Barley scald fungus, Rhynchosporium commune, belongs to a host‐specialized species complex infecting grasses. Coalescent analyses of several genes indicate that R. commune originated c. 2500 years ago, after the domestication of barley. Phylogeographical analyses identified a diversity hotspot in Scandinavia, indicating an origin in northern Europe. After its emergence, R. commune became distributed globally on infected seeds, eventually invading the Fertile Crescent and infecting wild barley progenitors. Analyses of gene flow identified historical routes of migration out of Scandinavia and indicate a high degree of modern gene flow among South Africa, Australia and New Zealand. About 76% of global species diversity is found within barley fields, with all field populations showing a genetic structure consistent with sexual recombination. High levels of regional gene flow suggest wind‐dispersed ascospores and movement of infected seed. Quantitative traits, including pathogen aggressiveness, thermal sensitivity and fungicide resistance, showed high heritability and high levels of diversity within nine globally representative populations. Field experiments provided evidence for a fitness cost associated with complex virulence and a trade‐off between pathogenic and saprophytic fitness. All findings indicate that global R. commune populations have significant potential to evolve rapidly in response to environmental changes, including deployment of resistant cultivars, fungicide applications and global warming. Specific recommendations to improve management of barley scald include: (i) focus resistance breeding efforts in northern Europe, which offers the best location to screen germplasm and may provide useful sources of scald resistance; (ii) improve seed treatment, certification and quarantine programmes to limit long distance pathogen movement; (iii) manage barley stubble to decrease pathogen population size, limit production of sexual inoculum and reduce the pathogen's evolutionary potential.

Elucidating the molecular responses of apple rootstock resistant to ARD pathogens: challenges and opportunities for development of genomics-assisted breeding tools.

Apple replant disease (ARD) is a major limitation to the establishment of economically viable orchards on replant sites due to the buildup and long-term survival of pathogen inoculum. Several soilborne necrotrophic fungi and oomycetes are primarily responsible for ARD, and symptoms range from serious inhibition of growth to the death of young trees. Chemical fumigation has been the primary method used for control of ARD, and manipulating soil microbial ecology to reduce pathogen density and aggressiveness is being investigated. To date, innate resistance of apple rootstocks as a means to control this disease has not been carefully explored, partly due to the complex etiology and the difficulty in phenotyping the disease resistance. Molecular defense responses of plant roots to soilborne necrotrophic pathogens are largely elusive, although considerable progress has been achieved using foliar disease systems. Plant defense responses to necrotrophic pathogens consist of several interacting modules and operate as a network. Upon pathogen detection by plants, cellular signals such as the oscillation of Ca2+ concentration, reactive oxygen species (ROS) burst and protein kinase activity, lead to plant hormone biosynthesis and signaling. Jasmonic acid (JA) and ethylene (ET) are known to be fundamental to the induction and regulation of defense mechanisms toward invading necrotrophic pathogens. Complicated hormone crosstalk modulates the fine-tuning of transcriptional reprogramming and metabolic redirection, resulting in production of antimicrobial metabolites, enzyme inhibitors and cell wall refortification to restrict further pathogenesis. Transcriptome profiling of apple roots in response to inoculation with Pythium ultimum demonstrated that there is a high degree of conservation regarding the molecular framework of defense responses compared with those observed with foliar tissues. It is conceivable that the timing and intensity of genotype-specific defense responses may lead to different outcomes between rootstocks in response to invasion by necrotrophic pathogens. Elucidation of host defense mechanisms is critical in developing molecular tools for genomics-assisted breeding of resistant apple rootstocks. Due to their perennial nature, use of resistant rootstocks as a component for disease management might offer a durable and cost-effective benefit to tree performance than the standard practice of soil fumigation for control of ARD.