Identification, characterization, and genetic comparison of <i>Fusarium</i> species isolated from switchgrass (<i>Panicum virgatum</i> L.)

Fusarium spp. are ubiquitous, soilborne and seedborne pathogens that affect over 100 economically important plant hosts annually, resulting in billions of dollars in economic losses. They cause a variety of plant disease symptoms including, crown, root, and stem rots, wilts, and foliar necrosis. Furthermore, they produce harmful mycotoxins that are detrimental to the health of animals and humans. Members of this genus have been isolated from diseased tissues of switchgrass. The objective is to correctly identify and classify Fusarium isolates to species using both classic phenotypic characterization and current genetic technologies of DNA extraction and polymerase chain reaction and create microsatellite loci that will give more insight into the genetic template of Fusarium species. This will enable us to better understand the role these fungi play in agriculture systems and how to control the pathogenic ones more effectively. Whole genome sequences were developed for four Fusarium species (F. equiseti, F. graminearum, F. oxysporum, and F. sporotrichioides) isolated from commercial switchgrass seed from 11 geographic locations across the United States. From each genome, 15 dinucleotide and 15 trinucleotide (n = 30) microsatellite loci were evaluated for amplification and polymorphism. An additional 30 microsatellite loci were developed for F. graminearum. The percentage amplification of the microsatellites from each species was 93% for F. equiseti, 42% for F. graminearum, 50% for F. oxysporum and 36% for F. sporotrichioides. The sample size of F. equiseti isolates was small (n = 6), therefore this species was not included in further study. Microsatellite loci from the Fusarium species were considered polymorphic if they yielded one clear peak and the base pair (bp) length difference among individual alleles was greater than 3 bp. Polymorphic microsatellite loci were evaluated for cross amplification of F. graminearum, F. oxysporum, and F. sporotrichioides. Microsatellite loci Fg057 (from F. graminearum) and Fr006 (F. sporotrichioides) did not amplify products from F. oxysporum isolates, and Fo006 and Fo012 (from F. oxysporum) did not amplify against F. sporotrichioides. Fusarium oxysporum isolates were nonpathogenic endophytes of switchgrass, while isolates of F. graminearum and F. sporotrichioides were pathogenic on this host.