Location: Crop Genetics and Breeding Research
2025 Annual Report
Objectives
1. Deployment of root-knot nematode resistance in cotton and peanut.
1.A. Determine the economic value of growing nematode-resistant vs. a susceptible cultivar in continuous and rotated peanut.
1.B. Evaluate the economic effect of growing M. incognita-resistant cotton in fields with damaging levels of the nematode.
2. Identify and screen nematode resistant crops that can be grown in rotation with cotton and peanut.
2.A. Identify sources of resistance to Meloidogyne incognita in sorghum that differ from known sources of resistance.
2.B. Identify sorghum cultivars that are poor hosts for Pratylenchus brachyurus and Meloidogyne arenaria.
3. Increased understanding of the interactions between plant-parasitic nematodes and the soil microbiology community and how that contributes to disease.
3.A. Evaluate the interactions of nematode parasitism, the salicylic acid (SA) and jasmonic acid (JA) plant defense pathways, and Fusarium oxysporum f.sp. vasinfectum in the Fusarium wilt disease complex in cotton.
3.B. Investigate the contribution of predatory nematodes in suppressing root-knot nematodes.
3.C. Identify the host and environmental factors that influence the attachment of Pasteuria penetrans spores to Meloidogyne arenaria.
Approach
The long-term goal of our research is to develop integrated approaches for managing plant-parasitic nematodes in cotton and peanut. Host-plant resistance is the most consistent means of reducing yield losses from nematodes. Our research will investigate the most effective deployment of resistance in cotton and peanut for improving yield and economic returns. For sustainable long-term production, farmers cannot rely solely on host-plant resistance for managing plant-parasitic nematodes. Therefore, we will investigate other management options. We will identify crops that can be grown in rotation with cotton and peanut that will reduce population densities of damaging nematodes. Biological control organisms are being marketed for use in cotton and peanut, and they also occur naturally in fields. We will investigate the contribution of predatory nematodes to suppression of root-knot nematodes and the environmental factors that influence the susceptibility of these nematodes to their host-specific bacterial pathogen, Pasteuria penetrans. Nematodes commonly interact synergistically with other plant pathogens to cause greater crop losses. We will investigate how nematodes interact with cotton’s innate defense systems and whether that plays a role in the Fusarium wilt disease complex.
Progress Report
Progress was made on all three objectives, despite one of the researchers leaving the agency to retire, and the ARS researcher at Tifton, Georgia will continue to deploy root-knot nematode resistance in peanut and cotton, identify and screen nematode resistant crops that can be grown in rotation with cotton and peanut, and work to increase understanding of the interactions between plant-parasitic nematodes and the soil microbiology community and how that contributes to disease.
The field project to evaluate the economic value of resistant peanut (Subobjective 1A) completed its first field season in 2024 and the second field season is underway. Other ARS researchers at Tifton, Georgia are collaborating on this project to incorporate remote sensing to determine if Meloidogyne arenaria damage can be detected via aerial imagery during the peanut cropping season. The field experiment to evaluate the economic benefit of growing nematode-resistant cotton (Subobjective 1B) completed its final season of field testing in 2024.
Two trials phenotyping the sorghum association panel (SAP) against Meloidogyne incognita were completed in 2024, and the final two trials are underway (Subobjective 2Ab). This work contains 268 accessions per trial.
One hundred twenty sorghum lines were screened against Pratylenchus brachyurus in 2024 and the same 120 lines are being screened against M. arenaria currently (Subobjective 2B). The trials are being repeated.
Projects to evaluate interactions of nematode parasitism, the salicylic acid (SA) and jasmonic acid (JA) plant defense pathways, and Fusarium wilt in cotton (Subobjectives 3Aa, 3Ab, and 3Ac) have been delayed due to critical vacancies and issues with method development. However, progress has been made in the methods for measuring SA and JA in cotton and will result in a manuscript.
The project to investigate the role of predatory nematodes in the suppression of root-knot nematodes (Subobjective 3B) is underway and soil samples were collected at the end of the 2024 cropping season. The methods for the project are being revised due to low population densities of predatory nematodes in the initial samples and samples from the 2025 cropping season from corn, cotton, and peanut fields in both Georgia and Florida have been collected for analysis. The laboratory experiments are underway.
Regarding soil type and crop plant influence (Subobjective 3C), a field trial was established in 2024 and sampled twice during the growing season to analyze Pasteuria penetrans spores up to 90 cm deep in the soil profile. This trial is being repeated in 2025.
Additionally, ARS researchers at Tifton, Georgia are involved in the Fertilize 4 Life initiative, an agreement between USDA-ARS, Embrapa, the International Fertilizer Development Center, and the University of Florida to reduce dependence on foreign fertilizer inputs. Field and greenhouse experiments are underway to advance soil health assessments in sweet corn, cotton, peanut, and potato. Another component of this research involves collaboration with University of Georgia researchers to conduct nematode community sequencing using DNA barcoding to analyze free-living and plant-parasitic nematode populations in soil samples.
A greenhouse study involving three ARS researchers at Tifton, Georgia evaluated common winter weeds for their ability to support M. incognita and M. arenaria reproduction. The trial will be repeated.
A greenhouse study investigating a potential resistance-breaking isolate of M. arenaria is underway. This study involves testing two nematode isolates of M. arenaria along with known M. arenaria-resistant and susceptible peanut and involves collaboration with ARS researchers and University of Georgia geneticists at Tifton, Georgia.
A cotton stalk puller study was established in May 2025 that will examine if pulling cotton stalks at the end of the cropping season will reduce M. incognita population densities for subsequent crops.
As part of the OTT Pilot Initiative, the Parasight System (an automatic egg counting machine) was purchased and analyzed for its utility in counting plant-parasitic nematode eggs from root-knot nematodes. This work will result in a manuscript.
Finally, 120 microplots were installed in collaboration with the University of Georgia at Tifton, Georgia. These microplots are being maintained with irrigation and centipede grass. Long-term nematode cultures are being established in many of these microplots for future research projects.
Accomplishments
1. Previously undescribed source of resistance to Meloidogyne incognita identified in sorghum. Sorghum (Sorghum bicolor) is an important drought-tolerant grain and forage crop that is typically a good host for the Southern root-knot nematode, M. incognita. Although a few resistant genotypes have been reported, identifying additional sources of resistance could prolong the effectiveness of currently available sources. ARS scientists in Tifton, Georgia and Lubbock, Texas identified five sorghum genotypes that were moderately resistant and likely represent at least one previously undescribed source of resistance. Once genetic markers are identified, these new sources of resistance can be easily bred into desirable sorghum lines.
2. Nematode community structure in peanut is less affected by irrigation, crop, and nematicide than in cotton. Fluopyram nematicide has been available to peanut growers for less than 10 years, and its continued assessment on nematode communities is warranted. Additionally, a sustainable crop rotation using a longer rotation (i.e., peanut-cotton-bahiagrass-bahiagrass) improves crop yields and soil properties versus a shorter conventional rotation (i.e., peanut-cotton-cotton). Peanut phases of these rotations had not been studied in conjunction with irrigation and nematicide on nematode community structure and ecological indices (indicators of soil health). An ARS scientist in Tifton, Georgia determined that fluopyram nematicide application did not reduce population densities of plant-parasitic or free-living nematodes in peanut plots of either rotation. This research highlighted that in peanut production, fluopyram use did not negatively impact beneficial nematodes like it did in cotton phases of either crop rotation system. Crop rotation system is an important factor influencing soil health relative to nematode community stability and peanut is better than cotton in this regard.
Review Publications
Khanal, S., Kumar, P., Da Silva, M., Singh, R., Suasunna, N., Nichols, R.L., Davis, R.F., Chee, P.W. 2025. Time-course RNA-seq analysis of upland cotton (Gossypium hirsutum L.) responses to southern root-knot nematode (Meloidogyne incognita) during compatible and incompatible interactions. BMC Genomics. 26, 183. https://doi.org/10.1186/s12864-025-11339-w.
Schumacher, L.A., Small, I.M., Grabau, Z.J. 2024. The influence of irrigation, crop rotation, and Fluopyram nematicide on peanut yield and the nematode community. Nematropica. 54:96-110.
Poudel, N., Torres, L., Davis, R.F., Jagdale, G., Mcavoy, T., Chowdhury, I.A. 2025. Effect of non-fumigant nematicides on reproduction of recently detected Meloidogyne species in Georgia under greenhouse conditions in tomato. Horticulturae. 11(1):36. https://doi.org/10.3390/horticulturae11010036.
Schumacher, L.A., Bird, G.W. 2025. Distribution of Pratylenchus spp. and Heterodera glycines in Michigan and combined reproduction on Peking and PI 437654 soybean. Plant Health Progress. https://doi.org/10.1094/PHP-10-24-0101-RS.
Davis, R.F., Harris-Shultz, K.R., Hayes, C.M., Xin, Z., Knoll, J.E. 2025. Evaluating diverse sorghum genotypes used in breeding programs for resistance to Meloidogyne incognita. Nematropica. 54:166-176.
Poudel, N., Davis, R.F., Mcavoy, T., Dutta, B., Chowdhury, I.A. 2025. Reproduction of Meloidogyne enterolobii on onion and potential yield suppression. Journal of Nematology. 57:e2025-0005. https://doi.org/10.2478/jofnem-2025-0005.