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Differentiation of Biologically Distinct Peanut Stripe Potyvirus Strains by a Nucleotide Polymorphism-Based Assay

October 1998 , Volume 82 , Number  10
Pages  1,121 - 1,125

S. S. Pappu , Department of Entomology , and H. R. Pappu , Department of Plant Pathology, University of Georgia, Coastal Plain Experiment Station, Tifton 31793 ; C. A. Chang , Taiwan Agricultural Research Institute, Taichung, Taiwan ; and A. K. Culbreath , Department of Plant Pathology , and J. W. Todd , Department of Entomology, University of Georgia, Coastal Plain Experiment Station, Tifton 31793

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Accepted for publication 25 June 1998.

A necrotic strain of peanut stripe potyvirus (PStV-Ts) was used to design and test strain-differentiating oligonucleotides. The 3′ region of PStV-Ts, including a part of the NIb region, the complete coat protein (CP) gene, and the 3′-untranslated region, was cloned and sequenced. PStV-Ts had a high degree of sequence identity (92 to 95%) to the known non-necrotic (blotch) strains both at the nucleotide and amino acid sequence levels. Nucleotide sequence differences unique to the necrotic strain were identified when compared to the available non-necrotic isolates of PStV. Nucleotide polymorphism in the CP gene sequences was utilized in designing oligonucleotides that were specific to the necrotic strain, and were employed in an assay to differentiate the necrotic strain from non-necrotic. The 3′ end mismatch in the oligonucleotides contributed in particular to the differentiation of the strains. This approach facilitated rapid, sensitive, and reliable detection and differentiation of PStV strains.

Additional keywords: capsid gene sequence, necrotic strains, RT-PCR, strain differentiation

© 1998 The American Phytopathological Society