Date of Graduation


Document Type


Degree Name

Master of Science in Plant Pathology (MS)

Degree Level



Plant Pathology


Burton H. Bluhm

Committee Member

John Rupe

Second Committee Member

Ainong Shi


Fixation Index, FLS, Frogeye Leaf Spot, Pool-sequencing, Resistance, Soybean


Frogeye leaf spot (FLS), caused by Cercospora sojina, is an important and recurrent disease of soybean in many production regions. Genetic resistance is potentially one of the most cost-effective and sustainable strategies to control FLS. However, C. sojina has already demonstrated the ability to overcome resistance conveyed by single R-genes (resistance genes) of soybeans, followed by the emergence of new physiological races. Although understanding population genomics and the virulence gene inventories in fungal plant pathogens is extremely important to improve disease control measures, studies regarding host specificity and pathogenesis in C. sojina are very limited. Therefore, the overarching goal of this study was to elucidate the genetic and molecular basis of race specificity, and pathogenesis in general, in C. sojina. To this end, a bulk-sequencing analysis was performed on two subcollections of C. sojina classified by differential infection responses (virulence or avirulence) on cultivars Blackhawk and Hood followed by mapping to the recently assembled C. sojina strain 2.2.3 reference genome. From the 18004 SNPs identified among the two subcollections, 75 SNPs showed an Fst> 0.2 and were localized within three distinct loci of the C. sojina genome, which harbored genes implicated in oxidative stress and pathogenesis. Unusual genomic architectures were also observed in these regions, possibly resulting from InDels or duplications in the C. sojina genome. Further SNP annotation analysis also identified candidate effector genes under positive selection pressure (dN/dS > 1.0), including two genes potentially restricted to the Cercospora genus. Intriguingly, C. cf. flagellaris isolates causing FLS-like lesions and C. sojina isolates virulent on cultivar Davis were also identified within the collection of fungal isolates, which underscores the importance of better understanding host specificity in the C. sojina and Cercospora spp. general. Altogether, this study provided key resources to unravel the genetics and genomics of race specificity and pathogenesis in C. sojina, and augmented long-term efforts to improve FLS resistance in soybeans through breeding and genetic engineering approaches.