Browsing by Author "Khodadadi, Fatemeh"

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    Fire blight resistance, irrigation and conducive wet weather improve Erwinia amylovora winter survival in cankers
    Santander, Ricardo D.; Khodadadi, Fatemeh; Meredith, Christopher L.; Radenovic, Zeljko; Clements, Jon; Aćimović, Srđan G. (Frontiers, 2022-10)
    Erwinia amylovora causes fire blight, a disease responsible for enormous economic losses in the pome fruit-producing areas where it is present. Despite the abundant research on fire blight, information about E. amylovora population dynamics and survival in fire blight cankers and the plant defense responses to this pathogen in the infected bark are limited. In our study, we obtained fire blight cankers in apple, pear, and Asian pear cultivars showing differing resistance to the disease by shoot inoculation with E. amylovora. We collected cankers from irrigated and non-irrigated trees every 3 months in two independent field experiments and analyzed samples by viability digital PCR. We also assessed the expression of pathogenicity-related (PR) genes in the bark of selected apple and Asian pear cultivars. A logistic regression analysis revealed the impact of environmental and host factors on E. amylovora detection rates in cankers. The chances of detecting live E. amylovora cells in cankers increased significantly in those collected from irrigated trees, in July, and/or during an experiment performed in a year with an expected average rainfall when compared to samples from non-irrigated trees, collected in January, and/or during an experiment performed under environmental conditions dominated by drought. We found a positive correlation between the pathogen detection rates in cankers and the host resistance to fire blight that might be explained by lower E. amylovora survival rates in more damaged tissues of susceptible hosts. The genes PR-1, PR-2, PR-5, and PR-8 were induced in the bark surrounding apple and Asian pear fire blight cankers. Our study, involving the analysis of more than 800 canker samples, provides new knowledge about the fire blight disease cycle and lays the foundation for improved fire blight management and eradication strategies in pome fruit orchards.
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    Genomic Resources of Four Colletotrichum Species (C. fioriniae, C. chrysophilum, C. noveboracense, and C. nupharicola) Threatening Commercial Apple Production in the Eastern United States
    Khodadadi, Fatemeh; Giroux, Emily; Bilodeau, Guillaume J.; Jurick, Wayne M. II; Aćimović, Srđan G. (American Phytopathological Society, 2023-03-07)
    The genus Colletotrichum includes nine major clades with 252 species and 15 major phylogenetic lineages, also known as species complexes. Colletotrichum spp. are one of the top fungal plant pathogens causing anthracnose and pre- and postharvest fruit rots worldwide. Apple orchards are imperiled by devastating losses from apple bitter rot, ranging from 24 to 98%, which is a serious disease caused by several Colletotrichum species. Bitter rot is also a major postharvest rot disease, with C. fioriniae causing from 2 to 14% of unmarketable fruit in commercial apple storages. Dominant species causing apple bitter rot in the Mid- Atlantic United States are C. fioriniae from the Colletotrichum acutatum species complex and C. chrysophilum and C. noveboracense from the C. gloeosporioides species complex (CGSC). C. fioriniae is the dominant species causing apple bitter rot in the Northeastern and Mid-Atlantic states. C. chrysophilum was first identified on banana and cashew but has been recently found as the second most dominant species causing apple bitter rot in the Mid-Atlantic. As the third most dominant pathogen, C. noveboracense MB 836581 was identified as a novel species in the CGSC, causing apple bitter rot in the Mid-Atlantic. C. nupharicola is a sister group to C. fructicola and C. noveboracense, also causing bitter rot on apple. We deliver the resources of 10 new genomes, including two isolates of C. fioriniae, three isolates of C. chrysophilum, three isolates of C. noveboracense, and two isolates of C. nupharicola collected from apple fruit, yellow waterlily, and Juglans nigra.
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    Multiplexed SSR marker analysis of Diplocarpon coronariae reveals clonality within samples from Middle Europe and genetic distance from Asian and North American isolates
    Oberhänsli, Thomas; Dalbosco, Anna; Leschenne, Virginie; Bohr, Anne; Buchleither, Sascha; Tamm, Lucius; Wille, Lukas; Aćimović, Srđan G.; Khodadadi, Fatemeh; Ryu, Young-Hyun; Studer, Bruno; Schärer, Hans-Jakob; Patocchi, Andrea (2021-05-29)
    Background Apple blotch (AB) caused by Diplocarpon coronariae (Dc) has been established in Europe since 2010. AB is a serious apple disease, mostly in low input orchards and in cider production areas in Northern Italy, Switzerland, Austria and Germany. However, the epidemiology and population genetic structure of this pathogen is unknown. Methods We developed twelve Dc-specific microsatellite markers and screened DNA of both pure fungal isolates and infected apple leaves. The marker data of 313 European samples of Dc were compared to Dc isolates from Asia (n = 7) and the USA (n = 3). Results We found 31 distinct multilocus genotypes (MLGs) in European samples, and seven additional MLGs in the Asian and USA samples. The European samples had the typical genetic signature of a recently introduced species including high clonality, a low number of private alleles and one dominant MLG across all the sampling sites. All European MLGs were genetically distant from those MLGs of Asian and USA origin. Based on the lack of linkage disequilibrium observed, there is evidence that Dc undergoes regular cycles of sexual recombination in the European population, although the sexual stage (apothecia) has not been observed in Europe. Conclusions The twelve newly developed SSR markers reported here provide a useful tool to characterize the population genetic diversity and structure of Dc in Europe. Our study supports the hypothesis that Dc is a recently introduced pathogen in Europe, but of currently unknown origin. Dc has a large effective population size during field epidemics, so we believe that the pathogen has substantial evolutionary potential. Application of the SSR markers to large-scale and diverse Dc samples will help to better understand the epidemiology of AB, which has become a global apple disease, and will help guide effective mitigation strategies based on disease management and resistance breeding.
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    Proof of Concept for Shoot Blight and Fire Blight Canker Management with Postinfection Spray Applications of Prohexadione-Calcium and Acibenzolar-S-Methyl in Apple
    Aćimović, Srđan G.; Meredith, Christopher L.; Santander, Ricardo Delgado; Khodadadi, Fatemeh (Scientific Societies, 2021-12-03)
    To reduce the severity of shoot blight and prevent the resulting development of cankers on perennial apple wood, we evaluated eight fire blight postinfection spray programs of prohexadione-calcium (PCA) alone or with acibenzolar-S-methyl (ASM) over 2 years. On mature trees of cultivar Royal Court, a single application of the high PCA rate (247 mg/liter) at 2 to 3 days after inoculation resulted in 89.5 and 69.5% reduction of shoot blight severity after inoculation. Two applications of PCA 247 mg/liter 12 or 14 days apart, with the first one applied 2 to 3 days after inoculation, resulted in 78.8 and 74.5% reduction of shoot blight severity in both years. A 100% control of canker incidence on perennial wood from infected shoots in both years was achieved with a single application of PCA (247 mg/liter) applied at 2 or 3 days after the inoculation, and three applications of PCA (125 mg/liter) + ASM (25 mg/liter) 12 to 16 days apart reduced canker incidence by 83.5 and 69% in the 2 years. The other programs with lower PCA rates and frequencies of application reduced shoot blight severity 50.8 and 51.8% (PCA) and 62.6 to 72% and 59.3% (PCA + ASM) over 2 years, respectively. Reduction of canker incidence on wood by the other programs was 66.5% and 69 to 90.4% in the two years, respectively. As fire blight cankers lead to death of dwarf apple trees and serve as primary sources of inoculum, our effective PCA and PCA + ASM programs could serve as viable postinfection management options. These treatments can reduce or prevent canker development and thus significantly abate tree losses in high-density apple orchards after fire blight epidemics occur.
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    Unveiling the Arsenal of Apple Bitter Rot Fungi: Comparative Genomics Identifies Candidate Effectors, CAZymes, and Biosynthetic Gene Clusters in Colletotrichum Species
    Khodadadi, Fatemeh; Luciano-Rosario, Dianiris; Gottschalk, Christopher; Jurick, Wayne M.; Aćimović, Srđan G. (MDPI, 2024-07-16)
    The bitter rot of apple is caused by Colletotrichum spp. and is a serious pre-harvest disease that can manifest in postharvest losses on harvested fruit. In this study, we obtained genome sequences from four different species, C. chrysophilum, C. noveboracense, C. nupharicola, and C. fioriniae, that infect apple and cause diseases on other fruits, vegetables, and flowers. Our genomic data were obtained from isolates/species that have not yet been sequenced and represent geographic-specific regions. Genome sequencing allowed for the construction of phylogenetic trees, which corroborated the overall concordance observed in prior MLST studies. Bioinformatic pipelines were used to discover CAZyme, effector, and secondary metabolic (SM) gene clusters in all nine Colletotrichum isolates. We found redundancy and a high level of similarity across species regarding CAZyme classes and predicted cytoplastic and apoplastic effectors. SM gene clusters displayed the most diversity in type and the most common cluster was one that encodes genes involved in the production of alternapyrone. Our study provides a solid platform to identify targets for functional studies that underpin pathogenicity, virulence, and/or quiescence that can be targeted for the development of new control strategies. With these new genomics resources, exploration via omics-based technologies using these isolates will help ascertain the biological underpinnings of their widespread success and observed geographic dominance in specific areas throughout the country.