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Title: Newly emerged populations of Plasmopara halstedii infecting rudbeckia exhibit unique genotypic profiles and are distinct from sunflower-infecting strains

item RIVERA, YAZMIN - Rutgers University
item SALGADO SALAZAR, CATALINA - Rutgers University
item Gulya Jr, Thomas
item Crouch, Jo Anne

Submitted to: Phytopathology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/12/2016
Publication Date: 6/14/2016
Citation: Rivera, Y., Salgado-Salazar, C., Gulya Jr, T.J., Crouch, J.A. 2016. Newly emerged populations of Plasmopara halstedii infecting rudbeckia exhibit unique genotypic profiles and are distinct from sunflower-infecting strains. Phytopathology. 106(7):752-761.

Interpretive Summary: Rudbeckia -- also known as black eyed Susan is one of the most popular flowering herbacious perennial plants, with U.S. production valued at more than $13 million each year. Since 2004, rudbeckia has been afflicted by a destructive new downy mildew disease, caused by a fungus-like pathogen, Plasmopara halstedii. The pathogen also infects sunflower and numerous other flowering plants. To understand the reasons why downy mildew is suddenly killing cultivated rudbeckia plants, we examined the genetic diversity of 232 P. halstedii samples collected over a period of 131 years. We sequenced the genome of P. halstedii, and used it to develop a new set of 15 DNA markers capable of producing DNA fingerprints of P. halstedii samples. We found that samples collected from rudbeckia and sunflower are not members of a single species, because they have unique DNA fingerprints. Samples from wild populations of rudbeckia collected prior to the downy mildew outbreaks were different from pathogen populations collected from cultivated rudbeckia, but are nevertheless members of the same species. These findings are important because they show that the recent downy mildew outbreaks on cultivated rudbeckia likely occurred due to genetic changes to indigenous North American populations originating from wild-grown rudbeckia. This information will be useful to plant pathologists, plant breeders and regulatory officials working to control the spread of these diseases, and will help scientists resolve other problems identifying related downy mildew pathogens.

Technical Abstract: The oomycete Plasmopara halstedii emerged at the onset of the 21st century as a destructive new pathogen causing downy mildew disease of ornamental Rudbeckia fulgida (rudbeckia) in the U.S.A. The pathogen is also a significant global problem of sunflower (Helianthus annuus), and is widely regarded as the cause of downy mildew affecting 35 Asteraceae genera. To determine whether rudbeckia and sunflower downy mildews are caused by the same genotypes, population genetic and phylogenetic analyses were performed. A draft genome assembly of P. halstedii was generated and used to design 15 polymorphic SSR markers. SSRs and two sequenced phylogenetic markers measured differentiation between 232 P. halstedii samples collected between 1883 to 2014. Samples clustered into two main groups, corresponding to host origin. Sunflower-derived samples separated into eight admixed sub-clusters, and rudbeckia-derived samples further separated into three sub-clusters. Pre-epidemic rudbeckia samples clustered separately from modern strains. Despite the observed genetic distinction based on host origin, P. halstedii from rudbeckia could infect sunflower, and exhibited the virulence phenotype of race 734. These data indicate that the newly emergent pathogen populations infecting commercial rudbeckia are a different species from sunflower-infecting strains, notwithstanding cross-infectivity, and genetically distinct from pre-epidemic populations infecting native rudbeckia hosts.