Date of Graduation


Document Type


Degree Name

Doctor of Philosophy in Plant Science (PhD)

Degree Level



Plant Pathology


John C. Rupe

Committee Member

Craig Rothrock

Second Committee Member

Douglas Karcher

Third Committee Member

Pengyin Chen

Fourth Committee Member

Ron Sayler

Fifth Committee Member

Burt Bluhm


Biological sciences, Community amplicon sequencing, Phomopsis lonhicolla, Seed, Seed pathology, Seed storage, Soybean


High seed vigor (SV), or the ability of seed to germinate and grow in a stressful environment is important, as many field emergence conditions are stressful for germination. Soybean SV can be affected by cultivar, seed storage environment conditions, the growing environment during seed development, crop management practices such as foliar fungicide applications, pathogens, and other factors. To assess the effects of some of these factors on soybean, the objectives of this work were to determine 1. the effect of cultivar and foliar azoxystrobin application on soybean yield, germination, vigor, microflora, and their relationships under harvest delay conditions; 2. if amplicon sequence community analysis using next generation sequencing characterized more fungi and bacteria than culture dependent methods; and 3. changes in seed quality and performance of high and low quality soybean seed stored in a commercial warehouse and under controlled conditions during the summer season as measured by SG, vigor, and field emergence.

Cultivar had a significant impact on yield and soybean SV, which were at least partly due to differences in seedborne pathogen infection. Differences in pathogen incidence among cultivars appeared to be influenced by genes for disease resistance. Foliar azoxystrobin application affected SV and seedborne pathogen incidence inconsistently, particularly Phomopsis longicolla. Seed infection by fungi and bacteria significantly reduced SV.

Seedborne pathogens are problematic in all soybean growing areas. Culture dependent methods, the current standard, may only detect a small portion of the microorganisms in a seed lot. Next generation amplicon sequencing of fungal and bacterial DNA revealed over two dozen seedborne microorganisms. Five fungi and bacteria were found using culture methods from the same seed lot.

During storage seed are best maintained by cool and low humidity conditions, which are not always available in seed warehouses. In this study, seed stored in high temperatures and relative humidity had greater reductions of field emergence and SV to a lesser degree than controls. Overall, soybean SV was affected by cultivar, environmental conditions at harvest, and appeared to be affected by conditions of storage, which affected SV through changes in seed physiology and infection by fungal and bacterial pathogens.