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United States Department of Agriculture

Agricultural Research Service

Related Topics

Research Project: Management and Biology of Virus and Nematode Diseases of Potato and Small Grains

Location: Emerging Pests and Pathogens Research

2013 Annual Report

1a. Objectives (from AD-416):
1: Improve detection and management for potato cyst nematode (PCN) and potato virus Y (PVY). 1.1: Develop management options for emerging pathotypes of PCN (G. rostochiensis). 1.2: Reduce PVY incidence in seed stocks and the potato crop. 2: Discover and characterize genes and proteins that influence virus-vector-host or nematode-host interactions for potato and grain crops. 2.1: Characterize candidate nematode parasitism genes and their associated host proteins contributing to plant parasitism. 2.2: Develop biomarkers for circulative virus transmission competence in aphid populations. 2.3: Define how luteovirus proteins orchestrate virus movement within plants and aphid vectors. 3: Develop potatoes resistant to virus or nematode infection. 3.1: Determine the resistance of potato cultivars and clones to pathotypes of PCN (G. rostochiensis). 3.2: Determine the susceptibility of potato cultivars to potato tuber necrotic ringspot disease (PTNRD) caused by some necrotic strains of PVY.

1b. Approach (from AD-416):
Viruses and cyst nematodes present the United States potato industry with its most severe regula-tory problems. This project primarily focuses on potato cyst nematodes (PCN), Potato virus Y (PVY), and Luteoviruses including Potato leafroll virus (PLRV) and the viruses causing barley yellow dwarf disease of cereal crops. The two species of PCN (Globodera rostochiensis and G. pallida) are quaran-tine pests that cause direct crop losses, increase pest control costs, constrain cropping patterns, de-value property, and interfere with domestic and international trade of potato and many other soil-associated crops. PVY and PLRV cause crop losses, interfere with marketing and trade of potato, and are the major diseases targeted by seed potato certification programs. Additionally, management options for vector-borne viruses are extremely limited and an understanding of the mechanisms by which viruses are carried between hosts by insects will lead to new targets of opportunity to control these pathogens. In recent years, PCN and the necrotic strains of PVY have been spreading to new areas. It has been determined that the population genetics of PCN and viral pathogens are far more dynamic than previously thought, and these genetic shifts profoundly influence disease detection and management strategies. The overarching research goal is to develop an understanding of the major genetic and environmental factors that drive the dynamics of nematode and virus diseases. Multifaceted objectives needed to accomplish this research goal include: the improvement of detection and management strategies of the various pathogen populations, the identification of genetic mechanisms that regulate nematode and virus pathogenicity and pathogen movement within the crops, and the development of new sources of resistance in potato germplasm. Approaches include epidemiological and etiological studies to identify major factors contributing to the spread and diversification of these pathogens, fundamental studies of the mechanisms of pathogenesis and transmission of PCN and viruses, respectively and the collaborative development of potato germplasm with effective resistance to PCN and viruses. Rapid identification and containment, coupled with new strategies for management of nematode and virus diseases will help the U.S. potato industry remain viable and allow them to expand market share.

3. Progress Report:
Emerging strains of Potato virus Y is a priority disease issue for the US seed potato industry. Continued surveys revealed an ongoing shift from the common strain, easily controlled via seed certification, to the emerging recombinant strains that are more difficult to identify and control. We developed a diagnostic assay that rapidly identifies nine strains of PVY strains found in the US. Collaborative research developed novel transgenic resistance mechanisms that would allow quick development of PVY resistant versions of popular potato cultivars should the US industry decide to embrace GMO technology. Two reviews were published that provide a comprehensive story of the PVY situation in the US and outline current management options available to seed certification agencies and to growers. Fundamental research on virus-vector-plant interactions provided new information on the protein mediated mechanisms of virus movement through plants and aphids. Using state of the art mass spectrometry techniques a suite of plant proteins were identified that interact with the virus and then function to promote the transmission of virus through the insect vector to facilitate the spread of virus between plants. This discovery provides clues into the biochemical mechanisms regulating virus entry into aphid cells. These may be exploited to disrupt aphid-virus interactions and ultimately to mitigate virus transmission. Biomarker proteins previously shown to distinguish vector and non-vector populations of one aphid species were identified in other aphid species and in a whitefly. This creates an opportunity to use these biomarkers to identify the most efficient vector populations and target them for control prior to the spread of virus within a crop. Successful management of the golden nematode (GN) is critical to prevent a further spread of this quarantine pest and to maintain the viability of the US potato industry. Results from the first year of a four-year crop rotation management program indicated that advanced potato clones resistant to different GN pathotypes were effective in reducing nematode infestation in the field. As a root parasite, GN secrets effector proteins into host root cells to promote successful infection. Detailed functional characterization of two effector protein families confirmed that they are all required for nematode parasitism. We also discovered that some GN effector proteins play an important role in host defense suppression, thereby facilitating successful nematode parasitism. This discovery represents one of the first reports revealing a function of nematode effectors in suppressing plant immunity. Additionally, we identified receptors in potato that interact with GN secreted CLE peptides and are now utilizing multiple approaches to discover additional host receptors that may be involved in nematode CLE-mediated parasitism. We have continued our collaborations with potato breeders at Cornell University and other institutions and identified new potato clones and varieties that are resistant to GN. Following additional evaluations, some of these may be released as named varieties that would be used for controlling GN.

4. Accomplishments
1. New diagnostic assay correctly diagnoses all known PVY strains infecting U.S. potato. The number of strains of potato virus Y that have emerged recently in the U.S., including several that cause significant yield and quality losses in seed and commercial stocks, has increased drastically, while diagnostic methods to correctly identify and differentiate the virus strains has lagged. Infected seed lots need to be identified and eliminated to prevent spread of the virus, but the current diagnostic methods that use several techniques are unable to identify the emergent strains. ARS researchers at Ithaca, New York, in collaboration with university researchers, have developed a new diagnostic assay that utilizes differences in genome sequences in 9 of the 10 new virus strains. This assay, in combination with a widely used serological assay, can correctly diagnose all PVY strains currently known to infect U.S. potatoes. This assay will be invaluable for diagnostic, regulatory, and seed certification laboratories that need to quickly and accurately identify the PVY strains that will have the greatest impact on the potato crop.

2. Significant discovery of GN effector function. Study of a GN-secreted effector protein (GrUBCEP12), by ARS researchers at Ithaca, New York, revealed that this effector is processed in the plant cell to release a novel peptide that functions in host defense suppression. The study represents one of the first reports demonstrating a function of nematode-secreted effectors in suppressing plant immunity. This study was selected as a featured article and appeared on the journal cover when published in the Plant Journal, a high-profile journal in the plant science community. In addition, this research has led to two invited paper submissions (one of which has already been published) and was recommended as being of special significance in its field by Faculty of 1000 (, a publisher that supports and informs the work of life scientists and clinicians.

3. Molecular diagnostic method for identifying a new nematode species related to GN has been developed. A new nematode species related to potato cyst nematodes was recently detected in Oregon. There was no quick and reliable method for identifying this new species. By using sequence variations identified in an effector gene, ARS researchers at Ithaca, New York have developed a molecular method that provides highly reliable and rapid identification of this Oregon nematode species. This method would be useful for monitoring the potential spread of this new potato pest within Oregon and in other potato producing states.

4. Improved diagnostic method to identify tuber necrotic strains of Potato virus Y (PVY). Tuber necrotic strains of PVY are emerging in the US and have the potential to become a major quality disease issue for the US potato industry, threatening farm income and export options. In collaboration with scientists at the University of Idaho, ARS researchers at Ithaca, New York have developed new knowledge of the specificities and shortcomings of commercially available diagnostic reagents for PVY. This led to improved testing protocols that eliminate false positives and allow detection of all variants within the tuber necrotic strain of PVY. Protocols were transferred to state and federal partners that conduct product testing and regulate interstate and international commerce of potatoes.

Review Publications
Cilia, M., Peter, K.A., Bereman, M., Howe, K.J., Fish, T., Smith, D., Gildow, F., Maccoss, M., Gray, S.M. 2012. Discovery and targeted LC-MS/MS of purified polerovirus reveals differences in the virus-host interactome associated with altered aphid transmission. PLoS One. 7(10).

Karasev, A., Gray, S.M. 2011. Genetic diversity of potato virus Y complex. American Journal of Potato Research. DOI: 10.1007/s12230-012-9287-7.

Replogle,, A., Wang,, J., Paolillo,, V., Smeda,, J., Kionoshita,, A., Durbak,, A., Tax,, F., Wang, X., Sawa,, S., Mitchum,, M.G. 2013. Synergistic interaction of CLAVATA1, CLAVATA2, and RECEPTOR-LIKE PROTEIN KINASE 2 in cyst nematode parasitism of Arabidopsis. Molecular Plant-Microbe Interactions. 26:87-96.

Chronis, D.N., Chen, S., Lu, S., Hewezi, T., Carpenter, S.C., Baum, T.J., Loria, R., Wang, X. 2013. A ubiquitin carboxyl extension protein secreted from a plant-parasitic nematode Globodera rostochiensis is cleaved in planta to promote plant parasitism. Plant Journal. 74(2):185-196.

Mitchum, M.G., Hussey, R.S., Davis, E.L., Baum, T.J., Wang, X., Elling, A.A., Wubben, M. 2013. Nematode effector proteins: an emerging paradigm of parasitism. New Phytologist. 199(4):879-894. DOI: 10.1111/nph.12323.

Chen, S., Chronis, D.N., Wang, X. 2013. The novel GrCEP12 peptide from the plant-parasitic nematode Globodera rostochiensis suppresses flg22-mediated PTI. Plant Signaling and Behavior. 8(9):e25359.

Yang, Y., Jittayasothorn, Y., Chronis, D.N., Wang, X., Cousins, P., Zhong, G. 2013. Molecular characteristics and efficacy of 16D10 siRNAs in inhibiting root-knot nematode infection in transgenic grape hairy roots. PLoS One. 8(7):e69463. doi: 10.1371/journal.pone.0069463.

Ali, M., Gray, S.M., Karasev, A. 2013. An improved multiplex IC-RT-PCR assay distinguishes nine strains of Potato virus Y. Plant Disease. doi: 10.1094/PDIS-02-13-0161-SR.

Krueger, E.N., Beckett, R.J., Gray, S.M., Miller, W. 2013. The complete nucleotide sequence of the Barley yellow dwarf virus-RMV genome reveals it to be a new Polerovirus distantly related to other yellow dwarf viruses. Frontiers in Virology. doi: 10.3389/fmicb.2013.00205.

Last Modified: 05/21/2017
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