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United States Department of Agriculture

Agricultural Research Service

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2011 Annual Report

1a. Objectives (from AD-416)
The long-term objective of this project is to develop an improved understanding of how endemic and emerging pathotypes of nematodes and viruses become established and are subsequently maintained in potato and grain crops. This knowledge is critical to the development of effective and sustainable control strategies, and obtaining this knowledge has become more imperative due to recent events. The emergence of new pathotypes of the golden potato cyst nematode (GN, Globodera rostochiensis), has raised new concerns about the ability of scientists and regulatory agencies to detect the nematode and about the continued effectiveness of current quarantine and management strategies. Similarly, national surveys of Potato virus Y (PVY) in seed potato production areas indicate an increase in the genetic diversity of PVY and emergence of necrotic forms of the virus. All of these findings are restricting interstate and international movement of potatoes. Over the next 5 years we will focus on the following objectives: Objective 1: Improved detection and characterization of emerging pathotypes of the GN and emerging strains of PVY. Sub-objective 1.A. Develop molecular markers that differentiate pathotypes of the GN based on divergence in nematode parasitism gene sequences. Sub-objective 1.B. Determine the geographic and genetic distribution of PVY strains affecting the U.S. potato crop and develop improved diagnostic assays. Objective 2: Identification and characterization of genes regulating the pathogenicity and transmission of viruses and nematodes affecting potato, and viruses affecting small grains. Sub-objective 2.A. Identify and characterize nematode parasitism genes. Sub-objective 2.B. Identify and characterize aphid and virus genes regulating virus transmission. Objective 3: Development of industry and consumer acceptable potato genotypes that express novel or improved resistance to virus and nematode pathogens.

1b. Approach (from AD-416)
Genetic diversity and diagnostic studies will identify differences in nematode parasitism genes that may be involved in pathogenicity or virulence/avirulence of the nematode. This information will be used to develop molecular diagnostic tools that will distinguish these two pathotypes. Serological, biological, and molecular characteristics of PVY isolates representative of each state, potato variety and production area will be used to group virus isolates and develop improved diagnostic assays to detect the strains of the virus that are potentially the most economically damaging in terms of yield and trade. Functional studies of pathogenicity and transmission genes will focus on secretory proteins encoded by parasitism genes expressed within the nematode’s esophageal gland cells known to be the principal molecular signals regulating both pathogenicity and virulence/avirulence of the nematode; as well as on aphid genes expressed in gut and salivary tissues whose products interact with specific domains on the two virus structural proteins. Genomic and proteomic based technologies will be employed to identify and characterize nematode and aphid proteins, and determine their functional role in the host-parasite/pathogen interaction. The development of nematode resistant potato varieties will focus on conventional breeding practices to transfer known nematode resistance genes to new germplasm with improved horticultural traits. Transgenic technologies will be used to isolate potato genes required by viral pathogens for replication, modify these potato genes and re-introduce them into accepted potato varieties so the altered forms no longer support virus replication.

3. Progress Report
The golden potato cyst nematode (GN) is a quarantine and devastating potato pest that secretes proteins into the plant root to facilitate a successful infection. We have analyzed several GN parasitism genes and identified sequence variants potentially useful as diagnostic markers to differentiate different GN pathotypes. Functional characterization of GN parasitism genes revealed that proteins encoded by these genes interact with plant proteins to promote nematode infection. Some of these proteins act by mimicking plant proteins to take control of certain plant cellular functions that facilitate the formation of the feeding site that sustains the development and the growth of the nematode. Using this information we have developed new forms of nematode resistance in potato that targets these important parasitism genes. Collaborations with several university potato breeding programs have identified new potato genotypes resistant to the common GN pathotype, and from the NY program we have identified resistance to a new pathotype of GN in one advanced potato clone and in the commercially available variety Sassy. Three new GN resistant potato varieties, Red Maria, Waneta, and Lamoka, were released jointly with Cornell. The availability of these new GN resistant varieties is critical for maintaining the GN quarantine in the U.S. A majority of insect transmitted plant and animal viruses circulate through the insect digestive, vascular and salivary systems. We are finding commonalities between the transmission of all viruses by identifying insect proteins that interact with virus proteins to direct virus movement in the insect. We have refined our proteomic approaches and identified a number of insect proteins that are linked to virus transmission. Several proteins are useful biomarkers for determining whether an insect population is capable of efficiently vectoring viruses and should be targeted for control. Other proteins serve as targets for new control strategies that will interfere with the protein interactions and slow or prevent the transmission of viruses between hosts. A novel form of resistance to PVY infection was developed in potato that precisely modifies a single gene in the potato genome. This modification prevents infection by all strains of PVY and related viruses and can be made in most potato cultivars without changing other desired characteristics. A second year of field evaluations found the plants completely immune to virus infection under heavy natural inoculum pressure. Plant growth and yield evaluations indicated the genetic modification did not adversely impact the performance of the potato plant and that this trait was stable and retained at least through three generations of tuber propagation. We have also identified several genetic markers within the PVY genome that are linked to various observable disease traits and can be used to develop improved diagnostic assays.

4. Accomplishments
1. Protein biomarkers identify insects that are transmitting plant viruses. There are no treatments to cure virus infections in plants, therefore the only options are to prevent or avoid infection. Spraying insecticides can control aphids and reduce the spread of viruses, but spraying is expensive and can harm the environment, people and animals. Additionally, not all aphids transmit viruses. So, how does a grower know when and what to spray to control virus diseases? ARS researchers at Ithaca, NY, have found a way to distinguish aphids that spread viruses from those that do not by studying the aphid’s proteins. Previous work had shown that for aphids to pick up and transmit viruses, the virus must be able to interact with aphid proteins that direct movement of the virus through the insect and back into a plant during feeding. By studying populations of aphids in the laboratory, they discovered that the lab-reared insects’ ability to transmit viruses was linked to the presence or absence of different “biomarker” proteins found in the insect cells. These findings were then extended to aphid populations from the field. This is the first time that protein biomarkers have been linked to an insect’s ability to transmit viruses and this discovery is expected to lead to development of a test to rapidly identify potential disease vectors. These findings have led to an expanded effort funded through Cornell University by the National Science Foundation Basic Research to Enable Agricultural Development (BREAD) program supported jointly by NSF and the Bill and Melinda Gates Foundation. The grant will allow us to determine if we can expand the technology to rapidly identify efficient vectors of other economically important viruses affecting crops in the US and Africa.

2. Three new Golden Nematode (GN) resistant potato varieties released. Effective control and management of GN depends on the availability of GN resistant potato varieties. ARS researchers at Ithaca, NY, in collaboration with scientists at Cornell University have led to the recent release of three new GN resistant potato varieties named “Red Maria”, “Lamoka”, and “Waneta”. Red Maria is the first GN-resistant red variety released and both Lamoka and Vaneta are chipping varieties. The availability of these new GN resistant varieties is invaluable for helping maintain GN quarantine in the state of NY and ensure the viability of the U.S. potato industry. Should GN become widespread in NY or elsewhere in the U.S. it will curtail interstate and international movement of potatoes and other crops that are associated with soil, e.g. turf, container nursery stock, onions, carrots, flower bulbs, etc.

Review Publications
Cilia, M., Thannhauser, T.W., Gray, S.M. 2010. Tangible benefits of the pea aphid genome sequencing in proteomics research: enhancements in protein identification, data incorporation, and evaluation criteria. Journal of Insect Physiology. Available:

Lee,, C., Chronis, D.N., Kenning,, C., Peret,, B., Hewezi,, T., Davis,, E.L., Baum,, T.J., Hussey,, R., Bennett,, M., Mitchum,, M.G. 2011. The novel cyst nematode effector protein 19C07 interacts with the Arabidopsis auxin influx transporter LAX3 to control feeding site development. Plant Physiology. 155:866-880.

Cilia, M., Tamborindeguy, C., Fish, T., Howe, K.J., Thannhauser, T.W., Gray, S.M. 2011. Genetics coupled to quantitative intact proteomics links heritable aphid and endosymbiont protein isoform expression to polerovirus transmission. Journal of Virology. 85(5):2148-2166.

Cilia, M., Howe, K.J., Fish, T., Smith, D., Mahoney, J., Tamborindeguy, C., Burd, J.D., Thannhauser, T.W., Gray, S.M. 2011. Biomarker discovery from the top down: protein biomarkers for efficient virus transmission by insects (Homoptera: Aphididae) discovered by coupling genetics and 2-D DIGE. Proteomics. 11:2440-2458.

Mello, A., Olarte, R.A., Gray, S.M., Perry, K.L. 2011. Transmission efficiency of Potato virus Y strains PVYO and PVYN-Wi by five aphid species. Plant Disease. Available: https// 10.1094/PDIS-11-10-0855.

Guo, Y., Ni, J., Denver, R., Wang, X., Clark, S.E. 2011. Mechanisms of molecular mimicry of plant CLE peptide ligands by the parasitic nematode Globodera rostochiensis. Plant Physiology. 157:476-484. DOI: 10.1104/PP.2011-180554.

Replogle, A., Wang, J., Bleckmann, A., Hussey, R.S., Baum, T.J., Sawa, S., Davis, E.L., Wang, X., Simon, R., Mitchum, M.G. 2010. Nematode CLE signaling in Arabidopsis requires CLAVATA2 and CORYNE. Plant Journal. 65:430-440.

Wang, J., Replogle, A., Hussey, R., Baum, T., Wang, X., Davis, E.L., Mitchum, M.G. 2011. Identification of potential host plant mimics of CLAVATA3/ESR (CLE)-like peptides from the plant-parasitic nematode Heterodera schachtii. Molecular Plant Pathology. 12:177-186.

Yu, H., Chronis, D.N., Lu, S., Wang, X. 2011. Chorismate mutase: an alternatively spliced parasitism gene and a diagnostic marker for three important Globodera nematode species. European Journal of Plant Pathology. 129:89-102.

Wang, J., Lee, C., Replogle, A., Joshi, S., Korkin, D., Hussey, R., Baum, T., Davis, E., Wang, X., Mitchum, M.G. 2010. Dual roles for the variable domain in protein trafficking and host-specific recognition of Heterodera glycines CLE effector proteins. New Phytologist. 187:1003-1017.

Cavatorta, J., Perez, K., Gray, S.M., Vanek, J., Yeam, I., Jahn, M. 2011. Engineering virus resistance using a modified potato gene. Plant Biotechnology Journal. DOI: 10.1111/j.1467-7652.2011.00622.x.

Karasev, A.V., Nikolaeva, O.V., Hu, X., Sielaff, Z., Whitworth, J.L., Lorenzen, J., Gray, S.M. 2009. Serological properties of ordinary and necrotic isolates of potato virus Y: a case study of PVYN misidentification. American Journal of Potato Research. 87:1-9. Available:

Gray, S.M., De Boer, S., Lorenzen, J., Karasev, A., Whitworth, J.L., Nolte, P., Singh, R., Boucher, A., Xu, H. 2010. Potato virus Y: an evolving concern for potato crops in the United States and Canada. Plant Disease. 94:1384-1397.

Last Modified: 2/23/2016
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