Characterization of genetic variability among natural populations of wheat streak mosaic virus

A reverse transcriptase-polymerase chain reaction (RT-PCR) assay was developed to amplify cDNA from the coat protein coding region and 3'-noncoding region of the genome of wheat streak mosaic rymovirus (WSMV). AluI restriction fragment length polymorphisms (RFLPs) were found among RT-PCR products of four spatially or temporally distinct WSMV isolates. RT-PCR and RFLP analyses were then applied to examine intra- and interfield genetic variation in natural WSMV populations in 1994 and 1995. A total of 32 distinct RFLP types were found in five Nebraska counties, but most isolates could be grouped into three predominant genotypes. Chi-square analysis of the degree of sequence heterogeneity of isolates within fields, among fields in each county, and among counties indicated that there was as much variation within fields as among counties. There was, however, a significant difference (P = 0.001) in the frequencies of WSMV RFLP types between 1994 and 1995. Results of this study suggest that there are three main and many minor lineages of WSMV cocirculating in the region. The WSMV population structure is consistent with a quasispecies model. Isolates with distinctive RFLP patterns should facilitate future studies of WSMV dispersal