Author

Yu Zhang

Date of Graduation

Summer 2011

Degree

Master of Science in Plant Science (Agriculture)

Department

College of Agriculture

Committee Chair

Wenping Qiu

Keywords

high throughput parallel sequencing, bandavirus, vein clearing, viral small RNAs, genomic diversity, primer walking

Subject Categories

Plant Sciences

Abstract

A severe vein clearing syndrome was discovered on Vitis vinifera L. and hybrid grape varieties in the Midwest of USA at 2004. The typical symptoms were translucent vein clearing on young leaves, short internodes, and decline of vine vigor. To discover possible viral pathogens that are associated with the disease, small RNAs were enriched from a symptomatic vine and a grapevine that is tested free of major grapevine viruses, two cDNA libraries were constructed, and high throughput parallel sequencing was applied to acquire sequences of thousands of small RNAs from which a novel DNA virus was discovered. This is the first report of DNA viruses in grapevine. Assays of more grapevines by polymerase chain reaction (PCR) found that the newly discovered DNA virus is closely associated with the presence of vein-clearing symptom in grapevines. It was thus given a provisional name Grapevine vein clearing virus (GVCV). The whole genome of GVCV was assembled from five fragments that were amplified from the symptomatic vine LBC0903 by PCR and sequenced from both directions by primer-walking strategy. GVCV genome is a circular DNA of 7,753 nucleotides. The phylogenetic analysis showed that GVCV can be assigned in the genus Badbavirus, in the family Caulimoviridae. GVCV was also detected in wild grapevines in Missouri. Restriction length fragment polymorphism (RLFP) analysis of GVCV populations indicated existence of at least seven GVCV sequence variants in six grape varieties in commercial vineyards of three states in the Midwest region.

Copyright

© Yu Zhang

Campus Only

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