Semester of Graduation

Spring 2025

Degree

Master of Science (MS)

Department

Plant Pathology and Crop Physiology

Document Type

Thesis

Abstract

Frogeye leaf spot (FLS), caused by Cercospora sojina, is a significant foliar disease of soybean (Glycine max) and is responsible for substantial yield losses worldwide. While management strategies rely on host resistance and fungicide applications, the emergence of new virulent races and fungicide-resistant isolates necessitates a deeper understanding of C. sojina host interactions and genomic variability. Here, we employed comparative and functional genomic approaches to decipher the molecular mechanisms underlying the C. sojina-soybean interaction. A dual RNA sequencing approach was used to identify transcriptomic changes in G. max cultivars Blackhawk (susceptible) and Davis (resistant) across multiple infection stages (3, 9, and 14 days post-inoculation). Differential expression analyses and principal component analysis (PCA) revealed dynamic transcriptional changes associated with susceptibility and resistance. Davis exhibited an early activation of defense responses linked to its resistance to C. sojina, involving salicylic acid signaling (SA), naringenin production, and brassinosteroid regulation. On the other hand, Blackhawk showed a delayed immune response coinciding with the pathogen’s transition to necrotrophy. Infection stage-specific fungal effector gene expression was also characterized, which identified 16 effectors with distinct temporal expression patterns. To complement our transcriptomic findings, we performed a comparative genomics analysis of four C. sojina isolates: TN81 and TN209 from the United States, Race11 from Argentina, and Race15 from China, to focus on pangenome variation, virulence, and genome plasticity. The study uncovered substantial genome plasticity characterized by large-scale chromosomal rearrangements and transposable element expansions (24.52%-26.95% of the genome). Whole genome alignments identified eight major translocations in TN209, enriched in transposable elements, indicating their crucial role in genome evolution. Pangenome analysis classified 10,741 core genes, with effector orthogroups being enriched in accessory and singleton genes. In conclusion, this study explores host resistance mechanisms and pathogen adaptability to enhance potential molecular targets for breeding disease-resistant soybean varieties and improving C. sojina management strategies.

Date

4-23-2025

Committee Chair

Richards, Jonathan

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Available for download on Friday, April 03, 2026

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