Genotypic Variability and the Occurrence of Less than Genome-Length Viral DNA Forms in a Field Population of Beet Curly Top Geminivirus

Abstract

During October 1994, a field population of beet curly top geminivirus (BCTV) from the Texas panhandle was sampled and examined for genotypic variability and the accumulation of viral DNA forms. Twelve BCTV-infected sugar beet samples collected from six fields were analyzed by Southern hybridization and found to contain typical genome-length, single- and double-stranded forms of the viral DNA. Most samples also contained less than genome-length viral DNA forms, which varied in size, abundance, and complexity among samples and were likely defective-interfering DNA molecules produced under natural conditions. The extent of genotypic variability among the field isolates was determined by restriction endonuclease mapping of 35 full-length BCTV clones directly obtained from 11 individual plant samples. A total of six genotypic variants were identified from the Texas panhandle population. All the variants were closely related to the previously characterized CFH strain of BCTV and possessed only minor variability at the level of endonuclease restriction sites. Sequence comparisons of the origin of DNA replication (ori) and 5'-proximal flanking region revealed that the six Texas panhandle variants possessed few (one to three per variant) nucleotide substitutions relative to the CFH strain, and none of the substitutions occurred within elements of the ori implicated as strain-specific determinants of replication. While minor genotypic heterogeneity was observed at all levels of population examined (single plant, field, or locality), these results indicate that CFH genotype represents the dominate BCTV strain infecting sugar beet grown in the Texas panhandle.