Identification of aster yellows phytoplasmas in soybean in Wisconsin based on RFLP analysis of PCR-amplified products (16S rDNAs)

Phytoplasmas have been detected for the first time by molecular methods in soybeans in Wisconsin. Nested polymerase chain reaction (PCR) using a combination of two phytoplasma-specific "universal" primer pairs (P1/P7-R16F2n/R16R2 and R16mF2/R16mR1-R16F2n/R16R2) amplified 16S rDNA (with expected fragment size of 1.2 kilobases) in soybean leaf tissue in 48 of 121 plants tested. Restriction fragment length polymorphism analysis of nested PCR products indicated that only 2 of these samples contained phytoplasmas. Gram-positive bacterial 16S rDNA genes were detected in 46 PCR positive samples. This was confirmed by culturing bacteria and direct PCR of soybean seed. In the two soybean samples, phytoplasmas belonging to the aster yellows phytoplasma group (16SrI), subgroup 16SrI-A, and a newly established subgroup, 16SrI-O, were identified. Phylogenetic analysis using partial 16S rDNA sequences (1.2 kilobases) from representative phytoplasma strains clustered soybean phytoplasmas into two distinct phylogenetic lineages that are consistent with the two subgroups defined by restriction fragment length polymorphism analysis. No correlation between the presence of phytoplasmas and the occurrence of "green-stem syndrome" in soybeans in Wisconsin was detected.