W5186: Variability, Adaptation and Management of Nematodes Impacting Crop Production and Trade

(Multistate Research Project)

Status: Active

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SAES-422 Reports

Annual/Termination Reports:

[01/11/2024]

Date of Annual Report: 01/11/2024

Report Information

Annual Meeting Dates: 11/13/2023 - 11/14/2023
Period the Report Covers: 01/12/2022 - 01/11/2023

Participants

Brief Summary of Minutes

Minutes Attachment:

W4186:W5186 AnnualMeetingMinutes_2023.docx

Accomplishments

Objective 1- characterize genetic and biological variation in nematodes relevant to crop production and trade             Activities in Idaho include an initiative to explore genetic diversity within Globodera spp. Different nematode populations are classified into pathotypes based on their reproductive capacity on specific potato genotypes harboring known resistance genes. The pathotypes of 10 populations from Peru were characterized using a set of potato differential lines containing different resistance genes. One outcome of this research is that, according to the pathotype scheme, the Idaho G. pallida population is pathotype 2/3 (Pa2/3) (Phillips and Blok 2008). The continuous use of resistant potatoes may encourage the emergence of more virulent populations (Varypatakis et al. 2020). It has been shown that cyst nematode resistance derived from Solanum tuberosum spp. andigena is more readily overcome than resistance from S. vernei (Phillips and Blok 2008;  Phillips and Blok 2012). Recent evidence indicates that different individuals within a cyst may exhibit varying virulence traits, possibly contributing to the breakdown of resistance. Other ongoing activities in Idaho involve genetically characterizing samples of Bolivian Globodera spp.  The University of Idaho has set up one experiment in Bolivia to phenotype for resistance to 3 populations of Globodera. An output of this research is that it has equipped Idaho scientists with the ability to identify appropriate sources of resistance that encompass cyst nematode population diversity.             Activities on root-knot nematode (RKN) genomes/transcriptomes have led to insights on the genetic factors governing nematode parasitism and virulence. For example, work at UC Davis centers on two closely related strains of M. javanica (VW4 and VW5), which differ in their ability to parasitize tomato carrying Mi-1.  The tomato gene Mi-1 confers resistance to three commonly occurring, damaging species of RKNs (Kaloshian and Teixeira 2019). On susceptible tomato, there is a reduced egg count on VW5-inoculated plants compared to VW4, indicating reduced fitness of the resistance-breaking strain. The previous reference genome M. javanica was not sufficient to allow resolution of the homeologous genomes. An output of the research has been a reference genome for VW4 and VW5 using a combination of HiFi, Hi-C, Iso-seq, and/or NanoPore sequencing. The sequencing data suggest that M. javanica is a hypotetraploid, and VW5 is missing a substantial DNA portion in a subgenome. An outcome of this research is that it lays important groundwork for identifying an avirulence gene in RKNs, a significant breakthrough for RKN research.             Advancements in molecular methods for RKN identification within and between species have also been achieved under this objective (Bogale et al. 2020;  Powers et al. 2017;  Powers et al. 2014). Activities include work on M. chitwoodi, a nematode that infects potato tubers. Transcriptome and genome analyses of M. chitwoodi-infected potato were performed, and an output was the identification of nematode parasitism genes (i.e. effector genes) that facilitate infections of potato (Zhang and Gleason 2021). More recently, the glands from M. chitwoodi were isolated for a gland-specific transcriptome analysis, laying the foundation for novel nematode effector identification in the coming year. Additional outputs from the M. chitwoodi genome data include a LAMP assay that can provide a quick DNA-based detection method for potato-infecting root-knot nematodes (Zhang and Gleason 2019) and a molecular beacon assay that allows researchers to easily distinguish between M. chitwoodi, M. minor, and M. fallax (Anderson and Gleason 2023). Within the M. chitwoodi species, three major populations (Race 1, Race 2, and Roza) exist in the Pacific Northwest, varying in virulence and host range. An output of the research has been that PCR markers were developed based on the genetic variability between these races, allowing scientists to determine that Race 1 and Roza were the predominant strains in Eastern Washington (Hu et al. 2023).              Other major outputs include advances in nematode identification by molecular ‘barcoding’ approaches. Ongoing activities in the working group aim to refine and define the conditions and limitations of DNA barcoding using the COI mitochondrial gene. A major outcome from the group was a DNA barcoding reference database called NemaTaxa was developed as a comprehensive reference database of nematodes in US agriculture (Baker et al. 2023). Moreover, work conducted in Nebraska supports a field device for rapid identification of cyst nematode juveniles, accelerating the time of species identification and reducing diagnostic expenses. Another output from this objective involves developing a metabarcoding approach for entomopathogenic nematode (EPN) identification from soil communities. Tests are underway to convert the current Sanger sequencing approach of DNA barcoding to a community-based method applicable to numerous nematode specimens in a single analysis (Gendron et al. 2023).             Continued activities in detecting and diagnosing plant parasitic nematodes provides valuable management insights to regional agricultural communities. With regards to nematodes as environmental indicators, researchers in Nebraska are working on a set of soil samples that were affected by a major contamination event associated with an ethanol production facility. An outcome of this work is the crucial understanding of measurable disturbances in nematode communities within soil health due to environmental contamination.             Final Outcomes: Studies of the genetic diversity and virulence of nematodes led to the development of innovative molecular tools for nematode detection, offering practical solutions for managing nematode infestations and preserving crop health. Additionally, the advancements in nematode identification methodologies and their role as environmental indicators enhanced agricultural sustainability and soil management practices.   Objective 2: nematode adaptation processes to hosts, agro-ecosystems and environments              Research activities at UC-Riverside are heavily focused on developing and analyzing resistance traits against RKNs in both carrot and cowpea. One of the outputs from W-4186 researchers is that they found resistance markers against M. hapla in the carrot cultivar “Homs.” However, the specific avirulence gene(s) of M. hapla involved in this interaction still need to be pinpointed. Nevertheless, an outcome from identifying natural host resistance traits is their promise for adoption in plant breeding programs. Another outcome from the cowpea genome work in this project has been the identification of root-knot nematode resistance traits on four of the 11 cowpea chromosomes (Lonardi et al. 2019;  Ndeve et al. 2019). Specifically, single resistance traits were found for resistance to M. javanica and or M. incognita on chromosomes 1, 3 and 11 (Lonardi et al. 2019). Notably, when nematodes are cultured on resistant cowpea, there was a  rapid selection for virulence (Petrillo et al. 2006). An output of this data is the observation of fluctuation in nematode populations upon the deployment of resistant cowpea.             Activities from W-4186 scientists at UC Davis include experiments on the Mi-resistance breaking M. javanica strain VW5. The VW5 nematode is less fit on susceptible crops than the avirulent M. javanica strain VW4. This discovery indicates that the acquisition of virulence in nematodes can be detrimental in the absence of resistance. This insight bears significant implications for the strategic deployment of resistant tomato cultivars.              Nematode adaptation processes studied in this objective have also included how nematodes spread and adapt to new environments. An outcome of previous research in this project has been a demonstration of how snails and slugs were associated with at least 6 genera of plant-parasitic nematodes, potentially spreading the nematodes to new environments. In terms of finding nematodes in new environments, there have been major outcomes regarding nematode first reports. Activities in this area include surveys that have established a first report of Ditylenchus dipsaci in alfalfa in NM, alfalfa cyst nematode (Heterodera medicaginis) in KS, MT and UT, cactus cyst nematode (Cactodera cacti) in ID and Co, and Cactodera milleri from Quinoa fields in CO (Powers et al. 2019). An expansion of the NM identified an Anguinidae (new species) associated with displacement of native grasses by invasive plant species. The University of Hawaii conducted surveys on native plants in areas surrounding their campus to assess susceptibility to root-knot and reniform nematodes. Their findings suggested that the native plant Ipomoea appeared to be a good host, whereas most native plants seemed to be poor hosts for these nematodes.             Additional outputs from research in this Objective include novel data connecting changes in landscape usage,  nematode communities, and soil health across various geographical regions. It is believed that nematode adaptation within agroecosystems is influenced by a combination of agricultural practices (APs) and alterations in biophysicochemical conditions within these systems. Activities include soil health assessments that are being conducted near Mead Nebraska, at the site of a major contamination event occurred during the course of a commercial enterprise developed to extract ethanol from unsold treated seed. Ongoing studies aim to assess the impact of applying 1,900 tons of "wetcake" solid waste to fields within the Eastern Nebraska Research and Extension Center. Lastly, Michigan State University (MSU) researchers have participated in activities in which they have applied the soil food web (SFW) model to establish that M. hapla presence in mineral and muck soils was associated with either disturbed and/or degraded soil health conditions (Lartey et al. 2021), and populations with higher pathogenic variability (PV) came from degraded mineral soils (Lartey et al. 2022). Collectively, these results provide a significant outcome: a foundation for an in-depth understanding of the environment where M. hapla exists, conditions associated with PV, and designing suitable management strategies.             Final Outcomes: New data was obtained on how nematodes adapt to different hosts, agro-ecosystems, and environments. Our investigations have uncovered significant levels of nematode adaptation, particularly in their ability to parasitize resistant host plants, thrive in diverse soil conditions, and spread to new areas.   Objective 3: Developing and assessing nematode management strategies in agricultural production systems             Activities under this objective have focused on four major themes: 1) novel biotechnology, 2) resistance and cropping systems, 3) biological controls and nematicides, and 4) decision-making models that translate complex biophysicochemical changes in the oil food web (SFW) into practical application.             Biotechnology offers new approaches to nematode control and will reduce the reliance on nematicides, which are often expensive and damaging to human health and the environment. For example, activities from researchers at UC-Riverside include screening a panel of rice varieties for nematode resistance. By using ‘omics technologies, one of the outcomes is that they are able to link the expression of rice fitness/defense related genes to a nematode resistance phenotype. Using “omics” for developing nematode management has been a long-standing strategy for this working group. New molecular nematologists have joined W-4186 (now W-5186) in Indiana, Arkansas, and Wisconsin to continue to study the “omics” of plant responses to nematode parasitism.             In addition to biotechnology to generate new nematode control tools, there are several examples in the working group highlighting research in nematode-cropping systems. Researchers in Alabama have performed activities around new cotton cultivars and their responses to M. incognita and R. reniformis infections. Their studies on resistant and susceptible cotton varieties with additions of seed treatments and in-furrow nematicides have helped to determine what strategies produce the best yield responses. One of the outcomes of this specific research was that the resistant varieties showed significantly increased yield, but the addition of nematicides further enhanced yields of the resistant varieties (Turner et al. 2023).             In Idaho, cropping systems using a combination of resistant varieties and trap crops are being developed for control of G. pallida. Idaho specific activities include the assessment of the impact of Solanum sisymbriifolium and quinoa as trap crops for G. pallida. Although S. sisymbriifolium is highly effective as a trap crop, it is not widely adopted due to lack of seed availability.  Quinoa, however, is a grain crop that has commercial value, and some varieties have been found to induce hatch of G. pallida, although at a lower rate than potato or S. sisymbriifolium. The data obtained in this objective will be impactful as quinoa production expands in areas of Idaho that contain G. pallida.             In this objective, many new chemical nematicides have and are being continually tested to develop crop-location-specific management strategies. For example, New Mexico researchers have continued their activities and investigations into the seasonality of M. incognita populations in drip-irrigated, wine-grape vineyards in southern New Mexico. The outcome of this effort will be to develop a management tool tied to growing degree days to aide farmers in determining the most effective timing for chemical control applications. As climate patterns shift, such monitoring may be increasingly important for advising growers on the management of such established pathogens, especially in perennial crops such as grapes. Nematicides offer an effective means of nematode management, and as companies develop new nematicides, it is important to investigate the effectiveness of their formulations or their application methods. Working directly with local commercial producers to evaluate new nematicides in locally relevant cropping systems aids growers in making informed management decisions. For example, in 2023, researchers in Alabama performed activities that looked at the reniform nematode populations on cotton. They evaluated the effects of combining the nematicide seed treatments COPeO (fluopyram), or BIOST Nematicide 100 (heat killed Burkholderia rinojenses) or the nematicide in-furrow Velum (fluopyram) or  AgLogic (aldicarb) with resistant cotton cultivars on nematode population levels and lint yield. As an outcome of this research, it was concluded that having resistant cotton with an application of nematicide reduced the reniform populations more than resistance alone. The lowest reniform numbers were found in the resistant plant combined with the in-furrow nematicide AgLogic treatment, providing cotton growers with hard data to inform how they manage reniform nematode on cotton (Turner et al. 2023).             Organic agriculture is becoming increasingly popular and there is a critical need to study biological control of nematodes and other pests in organic cropping systems.  In organic sweet potato production, one of the major activities has been establishing field trials across the South to determine the effect of selected winter cover crops and biological products in the suppression of nematode and insect pests. The outcomes of the initial trials were varied, but in general, the cover crop mix was associated with higher yield and lower M. incognita populations on sweet potatoes. Entomopathogenic nematodes (EPNs) can control insect pests, including the sweet potato weevil. Activities on EPN in Hawaii showed that EPNs could control the sweet potato weevil in the lab. In field tests, the EPN were unable to sufficiently abate damage when there was a high sweet potato weevil disease pressure. Many EPN application methods leave EPNs exposed to UV radiation and desiccating conditions but researchers in Hawaii are developing living bombs to address these limitations. EPNs were also being evaluated in corn production systems in five fields in western Nebraska for control of corn rootworm. One of the key outcomes of the Nebraska research has been data showing a low recovery of the commercial EPN product after application in corn.             Changes that occur to soil biophysicochemical conditions due to agricultural practices (application of chemicals, biologicals, etc) can also influence soil health, nematode-host interactions, and the management decisions at many levels. MSU researchers have applied the soil food web model and shown that there are variable soil health outcomes in response to soil amendments and cover crop treatments (Habteweld et al. 2020;  Habteweld et al. 2017;  Habteweld et al. 2022;  Melakeberhan et al. 2021;  Melakeberhan et al. 2018). Two of the outcomes from MSU research have been a novel fertilizer use efficiency (FUE) and an integrated productivity efficiency (IPE) model that identify if soil health outcomes are sustainable and if not, what additional measures are needed to make it sustainable. The FUE and IPE models, the only ones of their kind, provide scientists and growers with integrated decision-making tools to develop and apply sustainable soil health management strategies.             Final Outcomes- Researchers have harnessed biotechnology for nematode control by employing 'omics' technologies, while investigations into nematode-cropping systems underscore innovative management approaches. The continual testing of new chemical nematicides, exploration of biological products, and understanding of soil biophysicochemical conditions emphasize a comprehensive strategy toward sustainable nematode management across various agricultural systems. References cited Anderson, S. D., and Gleason, C. A. 2023. A molecular beacon real-time polymerase chain reaction assay for the identification of M. chitwoodi, M. fallax, and M. minor. Frontiers in Plant Science 14. Baker, H. V., Ibarra Caballero, J. R., Gleason, C., Jahn, C. E., Hesse, C. N., Stewart, J. E., and Zasada, I. A. 2023. NemaTaxa: A new taxonomic database for analysis of nematode community data. Phytobiomes Journal 7:385-391. Dandurand, L. M., Zasada, I. A., Wang, X., Mimee, B., De Jong, W., Novy, R., Whitworth, J., and Kuhl, J. C. 2019. Current status of potato cyst nematodes in North America. Annu Rev Phytopathol 57:117-133. Gendron, E. M., Sevigny, J. L., Byiringiro, I., Thomas, W. K., Powers, T. O., and Porazinska, D. L. 2023. Nematode mitochondrial metagenomics: A new tool for biodiversity analysis. Mol Ecol Resour 23:975-989. Habteweld, A., Kravchenko, A. N., Grewal, P. S., and Melakeberhan, H. 2022. A nematode community-based integrated productivity efficiency (IPE) model that identifies sustainable soil health outcomes: a case of compost application in carrot production. Soil Systems 6:35. Habteweld, A., Brainard, D., Kravchenko, A., Grewal, P., and Melakeberhan, H. 2017. Effects of plant and animal waste-based compost amendments on the soil food web, soil properties, and yield and quality of fresh market and processing carrot cultivars. Nematology 20. Habteweld, A., Brainard, D., Kravchencko, A., Grewal, P. S., and Melakeberhan, H. 2020. Effects of integrated application of plant-based compost and urea on soil food web, soil properties, and yield and quality of a processing carrot cultivar. J Nematol 52. Hu, S., Franco, J., Bali, S., Chavoshi, S., Brown, C., Mojtahedi, H., Quick, R., Cimrhakl, L., Ingham, R., Gleason, C., and Sathuvalli, V. 2023. Diagnostic molecular markers for identification of different races and a pathotype of Columbia Root Knot Nematode. PhytoFrontiers™ 3:199-205. Kaloshian, I., and Teixeira, M. 2019. Advances in plant-nematode interactions with emphasis on the notorious nematode genus Meloidogyne. Phytopathology 109:1988-1996. Lartey, I., Kravchenko, A., Marsh, T., and Melakeberhan, H. 2021. Occurrence of Meloidogyne hapla relative to nematode abundance and soil food web structure in soil groups of selected Michigan vegetable production fields. Nematology 23:1011-1022. Lartey, I., Kravchenko, A., Bonito, G., and Melakeberhan, H. 2022. Parasitic variability of Meloidogyne hapla relative to soil groups and soil health conditions. Nematology 24:983-992. Lonardi, S., Muñoz-Amatriaín, M., Liang, Q., Shu, S., Wanamaker, S. I., Lo, S., Tanskanen, J., Schulman, A. H., Zhu, T., Luo, M.-C., Alhakami, H., Ounit, R., Hasan, A. M., Verdier, J., Roberts, P. A., Santos, J. R. P., Ndeve, A., Doležel, J., Vrána, J., Hokin, S. A., Farmer, A. D., Cannon, S. B., and Close, T. J. 2019. The genome of cowpea (Vigna unguiculata [L.] Walp.). The Plant Journal 98:767-782. Melakeberhan, H., Bonito, G., and Kravchenko, A. N. 2021. Application of nematode community analyses-based models towards identifying sustainable soil health management outcomes: A review of the concepts. Soil Systems 5:32. Melakeberhan, H., Maung, Z., Lee, C.-L., Poindexter, S., and Stewart, J. 2018. Soil type-driven variable effects on cover- and rotation-crops, nematodes and soil food web in sugar beet fields reveal a roadmap for developing healthy soils. European Journal of Soil Biology 85:53-63. Ndeve, A. D., Santos, J. R. P., Matthews, W. C., Huynh, B. L., Guo, Y. N., Lo, S., Muñoz-Amatriaín, M., and Roberts, P. A. 2019. A novel root-knot nematode resistance QTL on chromosome Vu01 in Cowpea. G3 (Bethesda) 9:1199-1209. Nischwitz, C., Skantar, A., Handoo, Z. A., Hult, M. N., Schmitt, M. E., and McClure, M. A. 2013. Occurrence of Meloidogyne fallax in North America, and molecular characterization of M. fallax and M. minor from U.S. golf course greens. Plant Dis 97:1424-1430. Petrillo, M. D., Matthews, W. C., and Roberts, P. A. 2006. Dynamics of Meloidogyne incognita virulence to resistance genes Rk and Rk in Cowpea. J Nematol 38:90-96. Phillips, M., and Blok, V. 2008. Selection for reproductive ability in Globodera pallida populations in relation to quantitative resistance from Solanum vernei and S. tuberosum ssp. andigena CPC2802. Plant pathology 57:573-580. Phillips, M., and Blok, V. 2012. Biological characterisation of Globodera pallida from Idaho. Nematology 14:817-826. Powers, T., Skantar, A., Harris, T., Higgins, R., Mullin, P., Hafez, S., Handoo, Z., Todd, T., and Powers, K. 2019. DNA barcoding evidence for the North American presence of alfalfa cyst nematode, Heterodera medicaginis. J Nematol 51:1-17. Turner, K.A., Graham, S. H., Potnis, N., Brown, S. M., Donald, P., and Lawrence, K. S. 2023. Evaluation of Meloidogyne incognita and Rotylenchulus reniformis nematode-resistant cotton cultivars with supplemental Corteva Agriscience Nematicides. J Nematol 55:20230001. Varypatakis, K., Véronneau, P. Y., Thorpe, P., Cock, P. J. A., Lim, J. T., Armstrong, M. R., Janakowski, S., Sobczak, M., Hein, I., Mimee, B., Jones, J. T., and Blok, V. C. 2020. The genomic impact of selection for virulence against resistance in the potato cyst nematode, Globodera pallida. Genes (Basel) 11. Whitworth, J. L., Novy, R. G., Zasada, I. A., Wang, X., Dandurand, L. M., and Kuhl, J. C. 2018. Resistance of potato breeding clones and cultivars to three Species of potato cyst nematode. Plant Dis 102:2120-2128. Zhang, L., and Gleason, C. 2021. Transcriptome analyses of pre-parasitic and parasitic Meloidogyne chitwoodi Race 1 to identify putative effector genes. J Nematol 53.

Publications

Impact Statements

• Biogeographic information that SFW, FUE and IPE models provide novel approaches to understanding the environment where all host-nematode interactions take place, assessing efficiency of APs in developing the right management strategy on a one-size-fits-all or location-specific basis, minimizing treatments that negatively impact the soil environment, and scaling up across ecoregions.