COMPLETE SEQUENCE AND DIVERSITY OF THE PVY COMPLEX
Biological Integrated Pest Management Unit
2010 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.
Research has been initiated on the biological characterization of numerous PVY isolates that represent the different strain groups. Primary focus is to determine if these PVY isolates can cause tuber necrosis on a range of potato cultivars grown in the U.S. Three different long term assays requiring 3-4 months to complete were conducted during the year. Five cultivars of potato widely grown especially in the eastern half of the U.S. and one advanced breeding line from NY were challenged by multiple isolates of PVY representing three different strains or strain variants suspected of inducing tuber necrosis. Isolates of the NTN strain reliably caused tuber necrosis or related symptoms in Yukon Gold, Norland Red and NY138. Atlantic, Red LaSoda and Snowden were not susceptible to tuber necrosis under our testing conditions. Several isolates from two variants of the N-Wilga strain of PVY, the ‘a’ and ‘b’ variants were also tested. Several of the ‘b’ isolates induced tuber necrosis in Yukon Gold and Norland Red, whereas none of the ‘a’ variants were able to induce tuber necrosis in the greenhouse assays. Isolates from these studies as well as numerous isolates of PVY collected at various field sites and characterized for biological phenotypes have been sent to the University of Idaho for complete genome sequencing. Progress is monitored through email and phone conversations.