Population Structure of Uromyces appendiculatus in North Dakota

Abstract

North Dakota is the lead producing state of common bean in the USA, accounting for 43% of national production. Bean rust is caused by the autoecious, macrocyclic fungus Uromyces appendiculatus (Pers.:Pers.). All pathogen spores stages have been observed in North Dakota, but it is unclear how frequently sexual reproduction occurs. Traditionally, genetic resistance is the preferred management method. Sixty-seven percent of the 119 U. appendiculatus single pustule isolates collected in 2015 and 2016 were classified phenotypically as race 20-3. Virulence phenotypes of race 20-3 isolates ranged from hypersensitive to small pustules (0.2-0.3mm) on Early Gallatin, PC-50, Mexico 235, and Mexico 325 rust differential lines. This variation suggests more pathogen diversity is present than is discernable via traditional race classifications. The remaining 33% of U. appendiculatus isolates belonged to 18 additional races. Genome Wide Association Studies were conducted with the advanced breeding lines from the NDSU bean breeding program, the Middle American diversity panel, and a subset of Andean diversity panel reaction to races 20-3, 29-3 and 27-7. Significant SNP markers on chromosomes Pv01, Pv04, Pv06, Pv08, Pv10, and Pv11 were identified using genome wide association mapping. RAD-GBS was performed on 84 single pustule U. appendiculatus isolates using the Ion-Torrent S5 sequencing platform. A de novo assembly was performed on a single isolate of race 20-3 to generate reference sequence tags for variant calling. The relatedness measure using an identity by state (IBS) matrix suggested the presence of diversity within and among the isolates belonging to the same race, providing further evidence that the U. appendiculatus population in North Dakota is undergoing sexual reproduction and is more diverse than virulence phenotypes suggest. Results from this research increase our understanding of population dynamics and diversity in phenotype and genotype of U. appendiculatus and will assist common bean breeding for rust resistance.