Multiple species of Colletotrichum can cause bitter rot disease of apple, but the identities and relative representation of the species causing the disease in Kentucky are unknown. A total of 475 Colletotrichum isolates were collected from diseased apples in 25 counties and characterized both morphologically and by using various molecular approaches. Four morphotypes corresponded to reported descriptions of bitter rot species. Morphotype 1, distinguished by the production of a pink color on potato dextrose agar (PDA), orange conidial masses, and fusiform spores, was consistent with C. acutatum. Morphotype 2, which produced gray or white mycelial colonies with orange conidial masses and fusiform spores, was also similar to C. acutatum. Morphotype 3 had abundant gray mycelium and rounded spores and was identical to C. gloeosporioides. Morphotype 4 produced ascospores and resembled Glomerella cingulata. Species-specific polymerase chain reaction (PCR) indicated that both Morphotype 1 and Morphotype 2 belonged to the C. acutatum species complex, whereas Morphotype 3 and Morphotype 4 corresponded to the C. gloeosporioides complex. Multigene sequence analyses revealed that sample isolates belonged to several newly erected species within these species complexes. Morphotype 1 was identified as C. fioriniae, which resides within the C. acutatum species complex. Morphotype 2 was identified as C. nymphaeae, which is also a species within the C. acutatum species complex. Some isolates of Morphotype 3 were identified as C. siamense and some as C. theobromicola; both species are grouped within the C. gloeosporioides species complex. Morphotype 4 was identified as C. fructicola, which is also placed within the C. gloeosporioides species complex. C. fioriniae was the most common species causing bitter rot in Kentucky, comprising more than 70% of the isolates. Molecular fingerprinting using random amplified polymorphic DNA (RAPD) suggested that isolates within C. fioriniae belonged to a relatively homogeneous population, while isolates within C. siamense, C. theobromicola and C. fructicola were more diverse. Infectivity tests on detached fruit showed that C. gloeosporioides species-complex isolates were more aggressive than isolates in the C. acutatum species complex. However, isolates within the C. acutatum species complex produced more spores on lesions compared to isolates within the C. gloeosporioides species complex. Aggressiveness varied among individual species within a species complex. C. siamense was the most aggressive species identified in this study. Within the C. acutatum species complex, C. fioriniae was more aggressive than C. nymphaeae, causing larger, deeper lesions. Apple cultivar did not have significant effect on lesion development. However, Colletotrichum species produced more spores on Red Stayman Winesap than on Golden Delicious. Fungicide sensitivity tests revealed that the C. acutatum species complex was more tolerant to thiophanate-methyl, myclobutanil, trifloxystrobin, and captan compared to the C. gloeosporioides species complex. The study also revealed that mycelial growth of C. siamense was more sensitive to tested fungicides compared to C. fructicola and C. theobromicola. These research findings emphasize the importance of accurate identification of Colletotrichum species within each species complex, since they exhibit differences in pathogenicity and fungicide sensitivity.

In the realm of tree fruit cultivation, the management of various diseases affecting pome fruits like apples and pears is crucial for sustaining production. This study amalgamates findings from three distinct disease investigations to propose an integrated approach to their management. Firstly, in pursuit of mitigating shoot blight severity caused by Erwinia amylovora and preventing fire blight cankers on pear trees, a two-year evaluation was conducted. The study assessed the efficacy of preventive treatments, including foliar spray and trunk injection applications of Giant Knotweed Extract (RSE) alongside antibiotics. Results highlighted the effectiveness of RSE in controlling both shoot blight severity and canker incidence, offering a sustainable alternative to antibiotics. Secondly, in addressing the bitter rot of apples caused by Colletotrichum spp., eighteen fungicide treatments were evaluated over two years, focusing on newer fungicide options to mitigate fungicide resistance development. Fungicides such as Omega, Aprovia, Ferbam, Captan, Ziram, and Cabrio were proven reliable management tools, complementing the existing effective fungicides that growers heavily depend on. Lastly, the emergence of European canker (Neonectria ditissima) on cider apple cultivars was investigated. Molecular analysis confirmed the presence of N. ditissima as the causal agent, posing a significant threat to cider apple production. Koch's postulates were fulfilled through various tests, proving the pathogenicity of N. ditissima. Further research avenues, including genome sequencing were conducted to enhance understanding and control of a devastating pathogen like N. ditissima. Integrating findings from these studies proposes a comprehensive management strategy incorporating preventive spray programs, alternative fungicides, and pathogen identification to combat these diseases effectively, ensuring sustainable production of apples and pears in orchards. This holistic approach offers growers a multifaceted toolkit to manage diseases effectively, safeguarding apple and pear orchards' productivity and economic viability. / Master of Science in Life Sciences / In the world of growing apples and pears, keeping diseases under control is crucial for keeping orchards thriving and productive. We conducted studies on three endemic and emerging diseases aiming to create a well-rounded approach to managing them. First, we looked into ways to reduce the impact of shoot blight and fire blight cankers on pear trees caused by a devastating bacterium Erwinia amylovora. We tested the efficacy of preventive spray applications of plant extract of giant knotweed alongside antibiotics and found more sustainable alternatives to antibiotics that effectively control this disease. Next, we studied bitter rot disease in apples caused by many different species of fungi in Colletotrichum genus. We determined the efficacy of eighteen different biorational and synthetic fungicide spray programs over two years to find new options that can help prevent fungicide resistance development against currently available fungicides in the market. Several fungicides showed promise in managing this disease including Omega, Aprovia, Ferbam, Captan, Ziram and Cabrio, adding to the effective materials that growers already rely on. Lastly, we investigated the emergence of European canker on cider apple trees. This disease, caused by a fungus Neonectria ditissima, poses a serious threat to cider production. We confirmed the pathogen's identity and its capability of causing the disease in controlled experiments. We propose a comprehensive strategy for managing these diseases by including preventive spray applications of alternative materials and classic fungicides, combined with accurately identifying the pathogens. Our holistic approach provides growers with a range of tools to effectively protect their orchards, ensuring sustainable production of both apples and pears.