Soybean Sudden Death Syndrome Species Diversity Within North and South America Revealed by Multilocus Genotyping

Abstract

Sudden death syndrome (SDS) of soybean has become a serious constraint to the production of this crop in North and South America. Phenotypic and multilocus molecular phylogenetic analyses, as well as pathogenicity experiments, have demonstrated that four morphologically and phylogenetically distinct fusaria can induce soybean SDS. Published molecular diagnostic assays for the detection and identification of these pathogens have reported these pathogens as F. solani, F. solani f. sp. glycines, or F. solani f. sp. phaseoli, primarily because the species limits of these four pathogens were only recently resolved. In light of the recent discovery that soybean SDS and Phaseolus and mung bean root rot (BRR) are caused by four and two distinct species, respectively, multilocus DNA sequence analyses were conducted to assess whether any of the published molecular diagnostic assays were species-specific. Comparative DNA sequence analyses of the soybean SDS and BRR pathogens revealed that highly conserved regions of three loci were used in the design of these assays, and therefore none were species-specific based on our current understanding of species limits within the SDS-BRR clade. Prompted by this finding, we developed a high-throughput multilocus genotyping (MLGT) assay which accurately differentiated the soybean SDS and two closely related Phaseolus and mung BRR pathogens based on nucleotide polymorphism within the nuclear ribosomal intergenic spacer region rDNA and two anonymous intergenic regions designated locus 51 and 96. The single-well diagnostic assay, employing flow cytometry and a novel fluorescent microsphere array, was validated by independent multilocus molecular phylogenetic analysis of a 65 isolate design panel. The MLGT assay was used to reproducibly type a total of 262 soybean SDS and 9 BRR pathogens. The validated MLGT array provides a unique molecular diagnostic for the accurate identification and molecular surveillance of these economically important plant pathogens.

Comparison of inoculation methods for characterizing relative aggressiveness of two soybean sudden-death syndrome pathogens, Fusarium virguliforme and F. tucumaniae

“…Research is needed to elucidate the infection process of the SDS and bean root-rot fusaria (O'Donnell et al, 2010). It may be essential to determine whether toxins contribute to virulence and how environmental conditions influence the expression of foliar symptoms.…”

“…Isolates were identified using morphology and molecular phylogenetics (Scandiani et al, 2003(Scandiani et al, , 2004Aoki et al, 2005;O'Donnell et al, 2010) …”

“…(Aoki et al, 2005;O'Donnell et al, 2010). Fusarium tucumaniae is the dominant species in Argentina, comprising over threequarters of the SDS isolates genotyped, with F. virguliforme forming a comparatively small percentage of the SDS pathogens sampled (O'Donnell et al, 2010). Results of the latter survey revealed that these two pathogens both occur in the same soybean core-producing provinces of Buenos Aires and Santa Fe.…”

“…has been reported in North America (Rupe, 1989) and several South American countries (Nakajima et al, 1996;Wrather et al, 1997;O'Donnell et al, 2010). Prior to the recognition that four closely related Fusarium spp.…”

“…However, it is now recognized that SDS is caused by F. virguliforme within the U.S. and Canada, whereas in Argentina it is caused by at least four Fusarium species: F. tucumaniae, F. virguliforme, F. brasiliense, and an undescribed Fusarium spp. (Aoki et al, 2005;O'Donnell et al, 2010). Fusarium tucumaniae is the dominant species in Argentina, comprising over threequarters of the SDS isolates genotyped, with F. virguliforme forming a comparatively small percentage of the SDS pathogens sampled (O'Donnell et al, 2010).…”