2012 Annual Report
1a.Objectives (from AD-416):
To sequence the complete genomes of 2500 isolates of PVY representing all identified strain and phenotype groups and to correlate sequence information with biological phenotypes.
1b.Approach (from AD-416):
Recent studies have identified an explosion of genetic and biological diversity in the Potato virus Y (PVY) population leading to a widespread distribution of damaging necrotic variants that were recently considered to be absent in North America. Nevertheless, the population structure, recombination potential, and pathogenicity of PVY strains in different environments and in prominent potato varieties remain poorly understood. Two of the co-PIs were the coordinators and principle scientists for a 3-year (2004-07) survey of PVY diversity in all U.S. and Canadian seed potato production areas. More than 4,000 PVY isolates were analyzed by multiplex RT-PCR to determine a molecular phenotype, by enzyme-linked immunosorbent assays using a panel of monoclonal antibodies to determine a serotype, by bioassays on tobacco and potato to determine a necrosis phenotype. All of this information was used to categorize isolates into strain groups. Additionally, there is a growing list of collaborators willing to share representative PVY isolates from other continents. The research objective is to sequence a minimum of 2500 isolates that represent multiple individuals within each of the distinct strain groups. We will utilize both the standard bioinformatics platforms and develop unique tools to address PVY genomic diversity, phylogeny and evolution of PVY strains, and to correlate molecular phenotypes with biological phenotypes relevant to potato production and international and domestic marketing and trade. The results of the proposed research will directly result in the identification of molecular markers and sequences that can be used to develop new methods to detect and differentiate various novel PVY strains, and to quickly identify biological phenotypes. This information will also be invaluable for potato breeding programs focused on developing PVY resistance in potato and other susceptible crops.
The ordinary strain of Potato virus Y (PVY), PVYO, causes mild mosaic in tobacco and induces necrosis and severe stunting in several potato cultivars common in North America. There is, however, a growing body of evidence that PVYO strain group is not uniform, genetically or biologically. Researchers found a novel sub-strain of PVYO, PVYO-O5, spreading in the U.S. and distinguished from other PVYO isolates by its reaction with a monoclonal antibody specific to necrotic strains of the virus. To characterize this new PVYO-O5 sub-group, and address possible reasons for the continuing spread of this novel PVYO-O5 sub-type, Univ of Idaho researchers conducted a biological and molecular study of PVYO and PVYO-O5 isolates from the North American collection of PVY using whole genome sequencing and phylogenetic analysis. Forty-four PVYO isolates were sequenced, including 31 from the serologically defined PVYO-O5 group. Most of the serologically defined PVYO-O5 isolates formed a separate, PVYO-O5 lineage within the PVYO genome cluster in the whole genome phylogenetic tree. When tested on a set of potato cultivars, PVYO-O5 isolates induced a systemic HR response in cultivars Desiree and Maris Bard carrying Ny gene, like other PVYO strains. However, this HR reaction was more severe and developed earlier than for other, ordinary PVYO isolates. The PVYO-O5 sub-type, thus, represents a novel evolutionary lineage of PVY from potato.