Single-strand conformation polymorphism analysis of RT-PCR products of UK isolates of barley yellow mosaic virus

Single-strand conformation polymorphism (SSCP) analysis of the bipartite genomes of several UK isolates of barley yellow mosaic virus (BaYMV) was done using fragments of cDNA amplified by RT-PCR. Isolates differed in their SSCP patterns in several regions, but in no case was the pattern able to distinguish between common and r resistance-breaking strains. In regions where the nucleotide sequences of UK isolates had been determined, there was no simple relationship between numbers of nucleotide differences and SSCP patterns: differences of only 2 or 3 nucleotides (nt) gave different SSCP patterns, whereas differences of as many as 29 nt did not. Although SSCP analysis has some potential as a rapid and sensitive tool for distinguishing virus isolates, differences detected do not necessarily relate to biological properties and the results are highly dependent on gel conditions.