Unravelling the genetic mechanisms for target spot resistance in soybean

Abstract

Soybean production has grown over the years and has become one of the main crops in the world. Biotic stress is an obstacle to soybean production, and developing resistant varieties is one of the major focuses of soybean breeders. Target spot of soybean is caused by foliar pathogen Corynespora cassiicola, a devastating disease in tropical and subtropical areas. The development of highly humid conditions and warm temperatures in the Mid-south and southeastern United States facilitated the spread of disease and reduced the potential crop yield. The overall objective of this dissertation was to identify germplasm resistant to the target spot and understand the underlying genetic mechanism of resistance. The first chapter reviewed the literature on C. cassiicola infection in soybean, pathogen characteristics, target spot management, soybean genomics, and the use of available resources and techniques. Chapter two focused on using a consistent and reproducible procedure for screening soybean varieties against multiple C. cassiicola isolates to identify horizontal resistance to the target spot. Herein, we also investigated the genetic diversity of C. cassiicola isolates by performing phylogenetic analysis based on four loci and cassiicolin-encoding genes. The third chapter indicated the first molecular mechanisms of soybean resistance to C. cassiicola infection by conducting comparative RNA sequencing (RNA-Seq) study. This study revealed several genes encoding leucine-rich repeat (LRR) domain, dirigent proteins (DIRs), and Cysteine (C)-rich receptor-like kinases (CRKs), flavonoids, jasmonic, salicylic, and brassinosteroids acid were upregulated in resistant genotypes after C. cassiicola infection. The fourth chapter revealed the first Genome-wide Association Study (GWAS) for target spot resistance in soybean. The GWAS and RNA-Seq study helped narrow down candidate target spot defense-associated genes. Additionally, we identified genomic regions that might be co-localized for resistance to several biotic and abiotic stress. These findings provided germplasm and insight into the complex genetic architecture of target spot resistance in soybean and would promote marker-assisted selection in soybean breeding.