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United States Department of Agriculture

Agricultural Research Service

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Research Project: COMPLETE SEQUENCE AND DIVERSITY OF THE PVY COMPLEX

Location: Biological Integrated Pest Management Unit

2011 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.


3.Progress Report

The ordinary strain of Potato virus Y (PVY), PVYO, causes mild mosaic in tobacco and induces necrosis and severe stunting in potato cultivars carrying the Ny resistance gene. Last year we reported on a novel sub-strain of PVYO, PVYO-O5, which is spreading in the U.S. and is distinguished from other PVYO isolates by reacting with a monoclonal antibody that is supposed to be specific for the necrotic strain of PVY. To characterize this new PVYO-O5 sub-group, and address possible reasons for its continued spread, we conducted a molecular study of PVYO and PVYO-O5 isolates from a North American collection of PVY using whole genome sequencing and phylogenetic analysis. Forty-four PVY isolates were sequenced, 31 from the PVYO-O5 group and 13 additional typical PVYO isolates. PVYO-O5 isolates formed a separate lineage within the PVYO genome cluster in the whole genome phylogenetic tree and represented a novel evolutionary lineage of PVY from potato. The PVYO sequences separated into at least two distinct lineages on the whole genome phylogenetic tree. To shed light on the origin of the three most common PVY recombinants, a more detailed phylogenetic analysis was conducted on an ca.1400 nucleotide virus fragment that is present in all PVY strains. The analysis revealed that isolates in the tobacco necrotic recombinant strains (PVYN-Wi and PVYN:O) acquired their PVYO segments from two separate PVYO lineages, while the potato tuber necrotic recombinant strain (PVYNTN) acquired its PVYO segment from the same lineage as PVYN:O. These data suggest that PVYN:O and PVYN-Wi recombinants originated from two separate recombination events involving two different PVYO parental genomes, while the PVYNTN recombinants likely originated from the PVYN:O genome via additional recombination events. This information is useful in determining the evolution of PVY and in developing stable resistance to PVY in various crop species.


Last Modified: 11/1/2014
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