A culture independent PCR based assay to detect the root rot pathogen Fusarium solani species complex 11 from soybean roots and soil.

Fusarium solani species complex 11 (FSSC 11) is the primary phylogenetic species of FSSC causing root rot in soybean in the north central United States. A PCR based assay was developed to identify and differentiate the FSSC 11 from less aggressive FSSC 5 and other Fusarium and Pythium species associated with soybean roots. The primer set FSSC11-F and FSSC11-R designed from the RNA polymerase second largest subunit gene yielded the expected amplicon of about 900 bp with DNA from all 22 FSSC 11 isolates tested in PCR. However, it did not produce an amplicon with DNA from 29 isolates of FSSC 5, seven other Fusarium spp., three Pythium spp., and soybean tested in PCR. Furthermore, the primer set successfully detected the FSSC 11 from a DNA mixture containing the DNA of FSSC 11, FSSC 5, other Fusarium spp., and soybean. The primer set also detected the FSSC 11 from both soil and soybean roots. Additionally, the prevalence of FSSC 11 in soybean roots was determined in five fields in North Dakota by both a culture independent PCR approach with FSSC11-F and FSSC11-R, and a culture dependent approach. Results from both the culture dependent and culture independent approach with FSSC11-F and FSSC11-R were consistent and revealed the presence of the FSSC 11 in three of five fields sampled.