Browsing by Author "McNish, Ian"
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Item The oat-crown rust pathosystem: an interaction of a plant, a pathogen, and time(2020-12) McNish, IanPlant diseases are often described as the interaction of a plant, a pathogen, and the environment. For a disease to develop, there must be a susceptible plant, a virulent pathogen, and an environment amenable to disease. This concept is useful to explain the presence or absence of a disease, but many important questions and ideas in plant pathology, plant genomics, plant phenomics, and plant cultivar development are also dependent on time. A pathogen population changes over time, by a process of selection, to defeat the resistances deployed in crop cultivars. The genetic architecture of disease resistance changes as a plant grows from a seedling to an adult plant, matures, and dies. The visual and spectral signature of plant stress and disease also changes as the plant grows and the disease develops. Finally, plant breeders attempt to limit the damage diseases cause by quickly improving plant populations and deploying disease resistant plant cultivars. The dimension of time has been well-explored in some areas of plant science such as gene expression, but time is often overlooked in plant breeding, quantitative genetics, and phenomics. Crown rust, caused by the fungal pathogen Puccinia coronata f. sp. avenae Erikss. (Pca), is a dynamic and devastating disease of cultivated oat (Avena sativa L.). In this research, I found that the North American Pca population has gained many virulences over the past thirty years and that the Pca isolates collected in recent years are capable of defeating a surprisingly high number of crown rust resistance genes. I found that the genetic architecture of crown rust resistance changed throughout the growing season. Many resistance loci were detected briefly, sometimes just for a couple of days, and few loci were detected at many points in time. I found that the spectral signature of disease and plant stress changed throughout the season and that the predictive value of the collected data was greatest for adult plants before senescence. Finally, I found that quantitative resistance to crown rust could be rapidly improved in an oat population, but the race-specificity of that resistance was difficult to determine. If plant breeders understand how time influences the composition of pathogen populations, the observations they make, the analyses they perform, and the technologies they develop, then they will be more capable of improving complex plant traits like disease resistance.Item Using R based image analysis to quantify rust on perennial ryegrass(2018-11) Heineck, Garett; Watkins, Eric; Jungers, Jacob; McNish, IanCrown and stem rust caused by Puccinia coronata f. sp. lolii and Puccinia graminis subsp. graminicola are major diseases of perennial ryegrass (Lolium perenne L.) when grown for turfgrass, forage, and seed. Plant breeders and pathologists often quantify rust severity in the field using the modified Cobb scale, but this method is subjective, labor intensive, and dependent on the skill and experience of the scorer. Our objective was to develop a novel, open-source system that couples both ImageJ and R to quantify rust severity on simple RGB images.