abstract
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NON-TECHNICAL SUMMARY: Potato is the most important non-grain food crop in the world. In the U.S., more than 1 million acres are planted to potato, with an estimated farm gate value of $4.2 Billion. The long-term economic productivity of the U.S. potato industry depends upon the ability to respond in a quick, economical, and environmentally sound way to invasive agricultural pests such as cyst nematodes in the genus Globodera. An integrated Cooperative Agricultural Project will be established at three Land Grant universities, the USDA Agricultural Research Service, and with four international partner institutions to increase the capacity of the U.S. to respond to the threat of Globodera. We will pursue four interrelated, trans disciplinary objectives concerning invasive Globodera. Objectives 1-2: enable regulatory agencies and the potato industry to make scientifically-informed decisions regarding Globodera regulation using new molecular tools; examine implications of genetic diversity on Globodera virulence and deployment of resistance; deploy potato germplasm with resistance to three Globodera species; Objective 3: engage stakeholders and provide them with information need to respond to Globodera; examine economic implications of Globodera on U.S. potato production; engage minority groups in management of invasive agricultural pests. Objective 5: employ trans disciplinary synthesis to engage students in the study of invasive pests. AFRI Priority Areas: A) plant health and production and plant products, C) food safety, nutrition, and health, D) renewable energy, natural resources, and environment, and E) agriculture systems and technology.
OBJECTIVES: GLOBAL CAP Project GoalsProject Vision and Goals. GLOBAL (Globodera Alliance) will integrate the efforts of researchers, industry, extension, and academic educators, facilitating communication and cooperation among them. We have formed a consortium of researchers, extension specialists, and educators from three land-grant institutions (University of Idaho, Oregon State University, Cornell University), USDA Agricultural Research Service (ARS) units (Corvallis, OR; Prosser, WA, Aberdeen, ID; Ithaca, NY), and international experts (James Hutton Institute, Scotland; INRA, France; Agriculture Agri-Food Canada). Our project has been developed in consultation with, and is strongly supported by, the potato industry including growers, regulators, and policy-makers. Together, GLOBAL represents the only comprehensive effort in the U.S. to tackle the threat posed by invasive Globodera. Our integrated research, extension, and education efforts will yield a model management approach to protect the U.S. potato industry from current and future introductions of these nematode pests, and will improve U.S. agriculture, food security, and stakeholders' economic interests, knowledge base, and participation in decision-making.The three main goals of this research/extension/education collaboration over the next 5 years are to (listed in priority):Long-term Goals & Objectives• Enhance the profitability and sustainability of U.S. potato production, in the face of threats posed by invasive soil borne cyst nematodes in the genus Globodera.Avoid or mitigate adverse socioeconomic and international trade ramifications such as embargoes, posed by potential introductions and spread of Globodera.Use the Extension, Outreach, and Education efforts for this proposed work to serve as a model for other present and future invasive agricultural pests.Supporting Goals & Objectives• Use a genomics approach to improve diagnostics and to characterize pathogen virulence and host resistance for development of resistant cultivars, and for detection and identification of effector genes and broader genetic variability in Globodera across its geographic range.• Identify potato germplasm conferring resistance to three species of Globodera in new breeding lines for development of economically viable potato varieties.• Work closely with stakeholders and policymakers to co-develop science-based agricultural approaches to deal with the threat of Globodera and implement sustainable, environmentally sound agricultural practices for potato production in the context of Globodera risk management.Specific Project Objectives. We will pursue four interrelated objectives, focused on Research, Extension and Outreach, and Education. Project success will depend on the integration of the diverse expertise and institutions included in GLOBAL in a transdisciplinary framework.Research Objectives 1. Genomic approaches to risk assessment of Globodera. Understanding the molecular bases underlying virulence will inform detection and diagnosis, guide the deployment of resistance, and reduce the threat of new Globodera introductions. We will genetically characterize Globodera populations from the U.S. and other countries, using cutting-edge genomics technologies, and will link this genetic diversity to virulence variants and to pathotype. Expected outcome: Development of molecular genomics tools for regulatory agencies and others to manage risks of potential Globodera introductions and spread, and for deregulation. 2. Enhance potato breeding for resistance to Globodera. We will develop molecular markers for resistance sources against Globodera and use these to accelerate the development of commercially acceptable varieties for the U.S. Expected outcomes: Development of method for identifying resistant germplasm, and development of new breeding lines with resistance to Globodera spp.Extension and Outreach Objective 3. Enhance stakeholder engagement, knowledge and action related to Globodera and consequences on the U.S. potato industry. Together with our stakeholders, we will develop and disseminate innovative extension and outreach materials and presentations on the impacts of Globodera on trade relations, agriculture policies, and potato production, to empower the potato industry to make optimal decisions to minimize adverse economic impacts to U.S. agriculture and food security. We will characterize the interrelationships between potato industry sectors and related economic sectors, and determine current and potential potato production changes due topotato cyst nematodes, so that resulting shocks to the economy can be mitigated. Also, we will develop coupled models of nematode population dynamics x potato cropping system x pest economic impacts, to predict effects of susceptible vs. resistant potato cultivars on crop loss. Expected outcomes: Co-production and promotion of regionally and nationally relevant extension and outreach materials and presentations on Globodera will lead to increased engagement, knowledge, and action by growers and other stakeholders. Dissemination of decision-making tools, in the form of predictions and recommendations for deployment of Globodera-resistant varieties, will aid in setting priorities and schedules for allocating resources to improve food system resilience and manage associated risks. Our extension, outreach and education efforts will help increase minority participation in the decision-making process.Education Objective 4. Develop educational programs, using Globodera as a model, to teach concepts of ecological, agroeconomic, and global trade aspects of invasive plant pathogens. Our transdisciplinary project will incorporate several educational priorities, including increased participation of students in the agricultural sciences to enhance understanding of how these fields benefit society. Expected outcomes: A better-trained next generation of scientists, increased understanding of agriculture, and a better understanding of the trade-offs implicit in effective but environmentally sound pest management.
APPROACH: MethodsObjective 1 - Genomic approaches.Development of molecular detection methods. Strategies will be explored to assure the development of rapid and reliable molecular tools to distinguish Globodera pathotypes. Genotyping by sequencing (GBS) will identify single nucleotide polymorphism (SNP) markers specific for each population phenotype. This will allow the comparison of numerous pathotype populations and serve to develop pathotype-specific primer sets for each species.Collection of DNA and rearing of Globodera populations We will collect a genetically diverse set of U.S. Globodera populations, which we will rear in our respective facilities. We will collaborate with international partners to obtain Globodera DNA from diverse geographic locations.Evolutionary population genetics Using high-throughput DNA sequencing technology, we will analyze evolutionary and population genomics in Globodera. Individual single-cyst lineages will be analyzed; polymorphic sites will be used to identify loci under selection within each of the three species. Evolutionary analyses will reveal loci under different forms of selection, providing candidate genes that play roles in plant interactions. Functional studies will test the hypothesis that specific genes play important roles in virulence for particular Globodera spp.Globodera virulence markers. Capture array technologies based on the effector complement of Globodera spp. will enrich for a subset of a genome prior to sequencing which will give higher read depth for individual genes and facilitate identification of sequence polymorphisms that may be associated with differences in virulence. A customized library will be generated based on the full G. pallida and G. rostochiensis effector dataset. This process will be applied to DNA from populations with differing virulence characteristics to identify virulence-associated polymorphisms.Objective 2 - Enhance potato breeding.Development and screening for resistance. Progeny of NY121 x NY115 have been genotyped with the SolCAP SNP chip and 4229 SNP markers segregated. With genotyping of these parents for G. rostochiensis, the focus will be to phenotype the population with G. pallida and G. ellingtonae. Clones of an Eden x Western Russet cross will be used for mapping and selection of agronomically acceptable resistant clones for resistance development. Subsequent population will be genotyped with the SolCAP SNP chip and phenotyped against Globodera.Rapid mapping of quantitative trait Bulked samples of the most resistant and susceptible progeny will be selected for next-gen sequencing. QTLs will be identified and compared with results obtained by screening the segregating population with the SolCAP SNP chip. Of the 8303 SNPs on the SolCAP SNP chip, 58% can be scored for dosage in tetraploid potato, and the SolCAP second generation chip with 4000 additional markers located in or near R gene clusters will also be used. Progeny from Eden x Western Russet will be screened with the available solCAP SNP chip to establish linkage associations between SNPs and characterized resistant genes. To assess the effects of dosage of known Globodera resistance genes and H3 on chromosomes 4 and 11, selfs and intercrosses will be made between clones known to contain these genes. Offspring from these will be tested for resistance, and markers identified will then be used to assess gene dosage. Clones with varying gene dosages will then be phenotypically evaluated.Exchange and screening of Globodera-resistant parent. Control of Globodera is most likely to succeed if clones with multiple resistance genes can be developed. PCR markers have been described for several Globodera resistance genes: H1, GroI-4, a chromosome 4 gene from CPC 2802, and a chromosome 5 gene from Solanum vernei. Clones containing these genes, as well as clones known to be resistant, but with unknown resistance genes, will be exchanged among breeding programs and used as parental material to pyramid resistance genes. Selection for northeastern market types will be done in NY and for western market types in Idaho. Each family evaluated will have progeny grown in the field and at harvest selections will be made based on size, shape, and type. Selected individuals will be planted the following year in hill plots and subjected to selection criteria, such as processing characteristics and number of tubers per plant. Selected clones will be saved for further nematode testing and for continued advancement in field trials which include standard varieties for comparison.Extension and Outreach Objective-Objective 3Initial and ongoing project information dissemination. Information on the situation with Globodera presence in ID, OR, and NY will be presented at the annual Potato Conferences in those states, at field tours and open houses. Current and proposed research efforts will be developed cooperatively with stakeholders and will include impact on U.S. potato production, economic sustainability, quarantine and regulatory processes, and how teams of scientists, regulators and stakeholders work to protect the U.S. potato industry and food security. Materials will include oral presentations, online postings, and bulletins.Information dissemination in Spanish at regional potato meeting. Minority groups remain underrepresented in the agricultural sciences in the U.S., as well as among decision-makers. Our efforts include addressing factors that discourage minority participation in these. A model for this type of dissemination will be the Spanish language workshops and presentations on potato production held at the annual UI Potato Conference.Dissemination of extension information on the GLOBAL website. Extension and outreach information on the website will be a repository for materials disseminated through extension channels. Material will include descriptions of ongoing research efforts and results, information about quarantine processes, impacts of Globodera on the U.S. potato industry and international trade, materials developed for the GLOBAL extension and outreach and education objectives, and a calendar of meeting dates.Coupled Models: Nematode population, potato cropping system, and potato economics. Our modeling platform will be the DSSAT (Decision Support System for Agrotechnology Transfer) software application program (34). DSSAT comprises crop simulation models for a number of crops including potato,.The DSSAT platform will be used to estimate potential damages from Globodera. The model will be linked to the Google Earth GIS system. Because assessment of Globodera economic impacts extends beyond impacts to growers alone, we will examine all other economic sectors to get a true measure of the economic impact, wage impacts, and employment impacts. This will be accomplished by constructing a Leontief Input-Output model using the Output-Based Adjustment method.Assessment of extension and outreach efforts. A technical assistant will be hired to assist the team with data collection during events for stakeholders. Stakeholder input will be used to continuously improve the efforts of the project. Surveys will be embedded in presentations using Turning Point technology - clickers will be used to determine pre- and post-presentation knowledge of Globodera.Education Objective -Objective 4Graduate research training. We will train graduate students to address critical agricultural issues, using invasive Globodera in the U.S. as a foundational system. Our graduate education model will utilize a team-based, transdisciplinary approach to train graduate students to collaborate with stakeholders and policymakers.Mapping. We will develop an online mapping and analysis application for this project, based on the widely available platform Google Earth that users can access free of charge. In this way, stakeholders will have real-time access to online interactive maps, without needing expensive or difficult GIS software.