UC Davis

Worldwide, 20-25% of all fruit and vegetables are lost in the field and throughout the postharvest supply chain to rotting caused by fungal pathogens. This issue is particularly exacerbated in fleshy fruit, which become more susceptible to fungal pathogens as they ripen. Fungal pathogens with necrotrophic lifestyles are among the most devastating postharvest pathogens, as they actively kill the host tissues, resulting in extensive rotting. Plant defense responses to necrotrophs are complex and multi-layered, and a better understanding of the mechanisms behind the establishment of a compatible interaction between necrotrophs and fruit hosts is required for developing novel and effective management strategies. The overarching goal of my Ph.D. dissertation was to understand the biology of the interactions between fruit and necrotrophic fungal pathogens to identify: 1) infection mechanisms deployed by fungal pathogens when interacting with fruit (Chapter 1); 2) constitutive, preformed, and induced plant defense mechanisms contributing to resistance to fungal pathogens in fruit (Chapter 2); and 3) features of early fungal pathogen-fruit interactions that can aid the timely detection of disease (Chapter 3). In Chapter 1, I employed a genomic and transcriptomic approach to characterize the infection strategies of the impactful postharvest pathogen Rhizopus stolonifer, causal agent of soft rot, when infecting four fruit commodities of relevance to California agriculture (tomato, grape, strawberry, and plum). With collaborators, we developed publicly available, novel genomic resources that will further advance our understanding on how R. stolonifer interacts with its fruit hosts. I also performed a transcriptomics analysis that revealed that R. stolonifer possesses a necrotrophic core infection toolbox consisting of cell wall degrading enzymes, proteases, and oxidoreductases, that allow the fungus to macerate tissue and quickly colonize multiple hosts, and which have the potential to be targets for pathogen control. The knowledge generated in this study will aid the development of better integrated pest management approaches to minimize losses due to soft rot. In Chapter 2, I characterized the mechanisms underlying the resistance to anthracnose disease, caused by Colletotrichum spp., displayed by a pre-commercial papaya variety. With collaborators, we observed fruit surface and cuticular properties using confocal and scanning electron microscopy and analyzed fruit physicochemical properties. These analyses revealed the resistant variety has a thicker cuticular layer, lower stomatal density, greater firmness, and lower total soluble sugars, characteristics that can be considered preformed barriers or correlate with reduced susceptibility factors. I also performed differential gene expression and weighted gene co-expression network analyses to gain insight into induced defenses upon pathogen infection. The resistant variety seemed to respond earlier to fungal presence by synthesizing elements contributing to cuticular and cell wall integrity. On the other hand, the susceptible variety had a stronger immune response, but a higher presence of susceptibility factors and a delayed response to the pathogen that rendered it unable to control the disease. These results highlight the need to comprehensively characterize preformed and induced defenses, as well as susceptibility factors, to better understand fruit-pathogen interactions and inform breeding programs with strong targets for developing resistant varieties. In Chapter 3, I utilized multispectral imaging (MSI) and volatile organic compound (VOC) profiling approaches to study biomarkers of early interactions between the necrotrophic fungus Botrytis cinerea, causal agent of gray mold, and strawberry fruit. With collaborators, I compared the spectral and VOC profiles of B. cinerea-inoculated and mock-inoculated fruit from 0 to 48 hours post inoculation (hpi). Reflectance profiles of B. cinerea-inoculated fruit differed from mock-inoculated ones as early as 12 hpi, and infected samples displayed distinct VOC profiles as early as 9 hpi, as well as emitted VOCs with antifungal activity. Lastly, I performed a transcriptomic study of strawberries mock- and B. cinerea-inoculated at early time points (3, 6, 12, and 24 hpi), which revealed differentially expressed genes involved in secondary metabolic pathways and redox processes that could explain the features revealed by the MSI and VOC analyses, pointing to an early coordinated host response to B. cinerea. This research highlights the potential of complementary, non-destructive approaches for early detection of gray mold disease. Taken together, the results of this thesis improve our understanding of the interactions between fruit and plant pathogenic fungi at a molecular level. Insights into the pathogen infection toolbox, the role of preformed and induced defenses and abundance of susceptibility factors, as well as how to leverage the molecular understanding of fruit-pathogen interactions for disease detection, are key for the development of novel and more efficient disease management strategies to minimize postharvest food losses.