The Need as Indicated by Stakeholders:

Estimates over the last 35 years indicate that plant parasitic nematodes cause 10-14% average annual yield losses among the world's major crops [1], and within the United States, there are losses ranging from minimal in some localities to as high as 50% in other areas [2, 3]. More recent surveys of nematode-associated crop losses indicate that these estimates remain at similar levels. In economic terms, these estimated annual crop losses translate to at least $8 billion in the United States and $80 - $157 billion worldwide [4-6]. These numbers are likely to be under-estimates since plant parasitic nematodes are belowground and invisible to the naked eye, and because the disease symptoms are often non-specific, growers may be unaware of the presence of these pests [4]. Therefore, in many production systems, incipient losses are probably missed.  In addition, there are significant economic losses associated with the costs of nematicides. A recent cost estimate from a representative commercial potato farm in central Michigan, USA, indicated that nematicides can cost $1,000 or more an acre [7, 8]. The costs associated with nematode management include the price of the nematocidal products, the labor costs for application, and their efficacy [8]. In addition to the production costs incurred by nematode management, the presence of plant parasitic nematodes may be associated with trade embargos due to actual or suspected quarantine nematode infestations.

Increasingly, scientific evidence and public awareness have heightened concerns about environment quality, food quality, and human health and safety relative to pest management in agricultural production. The need for alternative and integrated nematode management has been propelled by the actions triggered by the Montreal Protocol and the Food Quality Protection Act (FQPA) of the 1990’s. The phase-out of methyl bromide and the loss of several highly effective organo-phosphate and carbamate nematicides has occurred over the last decade [9, 10]. In addition to methyl bromide, the use of fenamiphos and aldicarb have become severely restricted [11].  Moreover, the soil fumigant nematicide 1,3-dichloropropene (Telone II) is a B2 carcinogen, reviewed under FQPA and must be used under more rigorous restrictions. Together with another fumigant, metam-sodium, the fumigant nematicides have been identified by California EPA as the largest agricultural source of VOCs (volatile organic compounds) that contribute to air pollution by ground level ozone formation. US EPA Phase 2 labeling for all soil fumigants, implemented in 2012, establishes mandatory buffer zones surrounding treated fields that further restricts their use. More recently, safer nematicide chemistries have become available and can be tested as components of integrated nematode management programs [9]. Both locally and nationally, the agricultural community (our stakeholders) have a critical need for viable, sustainable alternatives to traditional chemical-based nematode control.

World travel and commerce have accelerated the dissemination of pest species, including plant parasitic nematodes. Climate change is contributing to enhanced disease severity in crops, and it is also leading to the northward migration of plant parasitic nematodes into new regions and agricultural systems [12, 13].  Development and application of new diagnostic protocols for accurate identification of nematode species are imperative for national and international regulatory and quarantine agencies [14]. For example, the presence of quarantine-status of cyst or root-knot nematodes in US potato production areas has led to restrictions on international trade and movement of potatoes within the country [15, 16].

The nematology community has repeatedly advocated the need for funding support focused on the basic and applied research required to advance agro-ecologically sustainable alternative management approaches and accurate nematode detection and diagnostic tools. Each member of this project is engaged with stakeholders (commodity boards, farm advisors, and industry experts), and a large driver of this research is the continued need from the various stakeholders for better nematode management tools. Outreach with commodity leaders, farm field days, and one-on-one meetings with growers have helped members devise the major milestones of the objectives. Our members of the grant with extension appointments will continue to gauge the stakeholder interest during these interactions. Building on advances made in the W-4186 project over the last 5 years, this proposed project renewal, called W-5186, addresses these needs directly for important groups of plant parasitic nematodes.

Importance of, and Consequences Without, the Work:

Cyst, root-knot, root-lesion and other nematode species included in this project are the most important groups of plant parasitic nematodes in the United States and globally [4]. Management of these nematodes in US agriculture has been largely via the application of broadly efficacious nematicides [17]. Nematicidal activity, especially of soil fumigants, is generally non-discriminating between nematode species and genera. Historically, growers would “spray and pray” that the chemicals they used would solve the problems with nematodes and other soil borne pathogens. But this approach also sterilized the soil of beneficial organisms [18]. A more targeted approach towards nematode control would be beneficial to soil health, and such an approach is now possible in the “omics” age. An understanding of the genetic variability and adaptation potential among nematodes will be important factors for the development of effective and target-based agrichemicals [9]. Additionally, desirable alternative nematode management approaches involve combinations of crop rotation, host plant resistance, cultural manipulations, and biological control. All of these tactics may have specific genotype-level interactions with nematodes and are influenced by production practices and environmental conditions. Preliminary evidence indicates that the promising new nematicide products show differential efficacy among main nematode groups (e.g., root-knot versus cyst nematodes). Hence, variability and adaptation in nematode populations must be considered to successfully develop and deploy new management strategies.

This multistate project was initiated because the membership recognized the increasing importance of characterizing the genetic variation in nematode populations and its influence on the success of alternative management strategies. For example, many years of research went into the development of cyst-nematode resistant soybeans and root-knot nematode resistant tomatoes, cotton, and potatoes but in some of these cases rapid selection of resistance-breaking nematode isolates has eroded their management efficacy [19]. The biological processes in nematodes are complex and ultimately will influence the development of effective management strategies. The multiple generations and interactions between nematode, host plant and environment can finally be addressed using a combination of applied and basic research. Although the effects of climate change will not be studied in this proposed research as a specific driver of nematode genetic variability and adaptation, we cannot ignore the contemporary changes in climates that may ultimately affect plant parasitic nematodes and their hosts. As a result, this multistate effort will provide a snapshot of the major plant parasitic nematodes and their current genetic repertoire that will no doubt become a resource for future genetic adaptation studies. A renewal of the project as requested herein is critical for continuing the research and application required to meet the overall project goals outlined below.

Research conducted under the current W-4186 multistate project has provided considerable evidence that genetic and parasitic variability in nematodes is important to management populations within production systems. Results from current work indicate that genetic variability and adaptation potential in nematode populations are responsible for the aberrant and inconsistent results of many experiments assessing resistance, crop rotations, host ranges, cover/trap cropping, biological control, and new nematicides. The plasticity of nematode responses to environmental factors such as the microbiome, soil structure, temperature/moisture, host nutrient status, and other biotic/abiotic factors stems from genetic variability. Greater understanding of nematode genetic response and adaptation to biotic/abiotic factors will be important in optimizing the design of cultural management tactics such as manipulations of planting and harvest times, wet or dry fallow, and soil solarization. The potential for invasive nematode pests to establish in our agricultural production systems also can be better determined from studies on genetic responses and adaptation to local environments.

Knowledge gained from our focus on cyst, root-knot and other nematodes of agricultural significance will be applied and tested between nematode groups within the project matrix (see Table 1 in Attachments). This will strengthen the overall scientific scope of the research activities and will broaden the impact of the findings to benefit agriculture in multiple states.

Strength of the Group in Technical Feasibility of the Research:

Recent advances in molecular and genetic methodologies and knowledge will facilitate the study of nematode genetic variability and adaptation. Access to genomes will promote diagnostic protocols with much greater resolution than has been possible. Some of these protocols have been developed and tested under the current project. For example, shared root-knot and cyst populations led to characterization of a mitochondrial cytochrome oxidase I (COI) gene that promises to alleviate current ambiguities in molecular species identification within these difficult-to-identify genera [20, 21]. In addition, several diagnostic tools for Meloidogyne chitwoodi were developed under the current project, including markers for a virulent, resistance-breaking pathotype [22]. Rapid advances in DNA-based diagnostics and genetic analyses generated by the current and other projects and their coupling to on-line databases and knowledge-based systems will assist in information transfer to user groups in the relevant agricultural communities.

This group of scientists has strong expertise across nematodes and applying basic and applied science approaches. Three groups of nematodes are the primary focus for this project: Group I - The warm-temperature root-knot species (Meloidogyne incognita, M. javanica, M. arenaria, M. enterolobii); Group II - The temperate root-knot species (M. chitwoodi and M. hapla); Group III - The cyst species (Globodera, Heterodera).  These nematodes are the subject of research efforts in the designated participating states. Within these groups, the quarantined nematodes in Globodera (G. pallida) and Meloidogyne (M. enterolobii) are worked on in the states and labs that are permitted to work with such nematodes (Table 1).

The project participants share strong common interests that will provide the central focus for both project members and other collaborators. In addition, parallel studies will be made by some participants on other parasitic nematodes, such as reniform nematode (Rotylenchulus reniformis), sting nematode (Belonolaimus longicaudatus), and root-lesion nematodes (Pratylenchus spp.). This will maximize both the scientific scope of the project and its multi-state impact in agricultural and natural ecosystems. 

Characterizing genetic variability – requisite for novel management strategies:

The unifying theme of this project is that genetic variability is a critical biological feature that complicates management and enhances the pest status of nematode species and populations. W-4186 participants and others have been documenting the extent of genetic variability within populations and the agro-environmental factors that influence it. Rapid developments in genomic techniques and their application through this project will continue to increase our understanding of the genetic processes involved. Failure of current nematode management practices, such as the breakdown of resistance, can be resolved through greater understanding of the underlying genetic and biological processes in parasitic nematode populations vis a vis management.

Genetic variability can impact both the effectiveness and longevity of alternative nematode-management strategies based on host plant resistance, crop rotation, cultural manipulations, and biological control.  Therefore, continuing the knowledge development in these systems should provide rational guidance for the design and development of nematode management strategies. The project focus is on understanding nematode variability and adaptation, such that it can be identified, characterized, and managed or manipulated to benefit agricultural production systems. This requires research on the genetic variability and gene frequencies, including aspects of stability and adaptability, of host range, response to resistance, response to environmental conditions, biological processes (e.g. fecundity) and morphology. This approach is being complemented and aided by the development of markers to identify variability by molecular, histochemical, and morphological polymorphisms. The development of molecular techniques with greater efficiency, predictability and ease of use will expedite nematode genetic analyses and design of management strategies.           

Current and previous work under W-4186 has allowed participants to make advances on these research goals. However, this work cannot be considered “complete,” and pressure for alternatives to existing nematicides has increased. Regarding our objectives, it is exciting that the arsenal of established and new tools used to address our applied research questions is increasing rapidly.

Below are four key nematode genetic variability-based considerations that are central to the development and deployment of alternative management strategies as proposed under this multistate project:

• Host plant resistance – The genetic composition of nematode populations is changed by the selection pressure imposed by growing resistant cultivars. The changes include shifts in species composition and shifts in presence and frequency of nematode virulence alleles matching specific resistance genes in crop cultivars [23-26]. Similar potential shifts may occur in response to nematode-resistant trap crops [27]. Little is known of the existing frequency of virulence alleles, the frequency with which new alleles are generated, or the underlying mechanisms that regulate changes in genetic variability in root-knot, cyst and other nematode populations. New genomic resources have provided information about nematode populations, the genes underlying nematode parasitism, and the molecular pathways that link the nematode and host plant [28, 29]. In addition, as more sources of resistance are bred into cultivars, knowledge of gene frequency and stability effects assumes greater importance in determining the direction and requirements of breeding for nematode resistance, and the effective long-term deployment of available resistant cultivars [27, 30-33].


• Host range for rotations and cover-cropping - The host ranges of important nematode species have been defined within general limits, but the extent of variability in host range among populations within species is not well-characterized. Much of this host range information has been compiled from numerous tests and observations based on non-standardized host testing procedures, and in most cases with only one or a few isolates per species. Standardized conditions are needed to determine whether differences are due to variability in nematode populations or to differences in susceptibility in the plant lines used.


• Cultural and Biological controls - Genetic variability in nematodes for responses to temperature and moisture has been demonstrated, but little is known about underlying mechanisms or stability. Soil amendments (compost, green manures, various bio-products) show promise for nematode suppression and improving soil health in some systems and require further study [34-37]. Potential biological control agents of cyst and root-knot nematodes are known to have specific host ranges among target nematode species [38]. Such specificity may be controlled by genetic factors, and thus, variability in Meloidogyne may influence the potential of biological control agents.


• Nematicide controls – Several new nematicides have been shown by our current group and others to have high nematicidal efficacy and are in final testing phases to support new use registrations. Active ingredients include fluopyram, fluensulfone, fluazaindolizine, spirotetramat, and cyclobutrifluram, among others. They represent important tools for integration into nematode management programs, including use as seed treatments and in combinations with bio-products and biocontrol organisms. However, nematode responses to such new nematicides may be influenced by nematode genetic factors. Research efforts in this hatch project include investigating the efficacy of new nematicide treatments while also looking at the effects of genetic variability that may underlie the efficacy.

Advantages of a Multistate Effort:

Under the current project, research to apply emerging methodologies to obtain knowledge of the variability and adaptation potential in nematode populations is in various stages of advancement. The W-4186 membership proposes to continue and extend these efforts to identify and characterize the variability in important nematode pests. The participants share research interests on primary nematode pests and bring complementary expertise and resources to the project.  

The group is a cross section of nematologists that span both basic and applied research on nematodes of major agronomic importance. Our research expertise will help to determine gene frequencies, genetic stability, and adaptation and fitness, such that genetic variability can be managed and manipulated in agricultural production systems by appropriate alternative management strategies. The diversity in cropping systems and rank of importance of nematode groups among participating states clearly provides opportunities for conducting meaningful collaborative research on major nematode pathogens. The participants utilize the opportunity to collaborate in ways that enhance the benefits accrued from the research, as opposed to pursuing individual projects within limited geographic boundaries. For example, the warm climate root-knot species will be studied by participants from a majority of the participating institutions (see Attachment Table 1) – a group effort that will pay large dividends in understanding nematode variability relative to management.

Despite retirements of key members in the W-4186 working group, this multistate project has attracted several new members. These members include nematologists asking very basic research questions about variability in nematode biology, effectors, and host resistance. In addition, several new members also have extension appointments. Their goal in the multistate effort will not only be to contribute to the excellent scientific research, but to also enhance the group’s outreach to growers and stakeholders, which is a focus of this project.

This team approach enables a pooling of scientific expertise and resources to maximize the amount and quality of the information that can be generated. This multistate project is unique in that it provides a necessary forum for rapid scientific advancement in aspects of both basic and applied research directed toward nematode diagnostics and development of management strategies. For example, some participants have programs devoted to molecular research on nematodes, which can be applied across all states for diagnosis and to assess nematode genetic variability. This project has ongoing molecular-based programs in some states (e.g. California, Hawaii, Indiana, Nebraska, Florida, Washington) that can facilitate research by other participant states. In turn, those states focusing on phenotypic differences in nematode populations can provide nematode populations and isolates for molecular analysis. This coordinated approach minimizes unnecessary duplication of research programs, and provides fertile opportunities for a seamless, interactive approach to advancing nematode management.  The end result is that the project has enhanced the quality and applicability of the research findings across geographic locations and agricultural production systems.    

Likely Impacts of Work:

The stakeholders (agricultural community) will be positively impacted by application of the project findings in expediting the development of new, environmentally benign management strategies to minimize losses due to nematodes. This in turn should help boost the international competitiveness of our agricultural production systems. The project will also benefit the diagnosis and response process required when invasive nematode pests are suspected or found in production fields or in traded agricultural products.