Taxonomic and Genetic Diversity, and Pathogenicity of Diaporthe Species Associated with Soybean

Diaporthe species (anamorph: Phomopsis) are associated with a wide range of plant hosts as plant pathogens, asymptomatic endophytes, and saprobes. One of these hosts is soybean, which is one of the most important crops in U.S. agriculture. Several Diaporthe species cause important diseases on soybean in the U.S., and specifically in Arkansas. The taxonomy, genetic diversity, and pathogenicity of Diaporthe species associated with asymptomatic infection of soybean are rarely studied with accurate molecular tools. Therefore, this dissertation aimed to assess the diversity and boundaries of Diaporthe associated with soybean in Arkansas. Furthermore, pathogenicity and alternative lifestyles were assessed among Diaporthe strains originating from Arkansas. Moreover, the molecular basis of pathogenesis was dissected in the most ubiquitous Diaporthe species, D. longicolla, via forward genetic screening. Phylogenetic analyses of multilocus data identified two pathogenic Diaporthe species in Arkansas besides the most common species, D. longicolla. In this study, D. unshiuensis was reported for the first time in the U.S. and on soybean worldwide, while D. ueckerae was recorded in Arkansas for the first time. Pathogenicity tests confirmed that these species could potentially alternate between endophytic and pathogenic lifestyles on soybean. Genotyping by sequencing (GBS) utilizing microsatellites revealed that D. longicolla and D. unshiuensis had high levels of genetic variability at all study sites. Additionally, these markers successfully discriminated isolates of D. longicolla, D. ueckerae, and D. unshiuensis. Genotypes of these species did not cluster genetically based on geographical origin. However, D. ueckerae, and D. unshiuensis were not isolated from all sites sampled. According to linkage disequilibrium indices, populations of D. unshiuensis may undergoing sexual reproduction and random mating, whereas populations of D. longicolla may be largely clonal in Arkansas. Furthermore, genetic screening to identify pathogenicity genes of D. longicolla highlighted the potential role of a putative cytochrome p450 in seed colonization, stem necrosis, and asexual reproduction. Together, these findings will help inform the development of new strategies to manage soybean diseases caused by Diaporthe species and to augment host resistance