Final report for GS22-254
Project Information
Consumer preference is growing in organic field production of vegetables, including peppers. However, a major challenge for organic production is managing diseases, including root-knot caused by the southern root-knot nematode (RKN; Meloidogyne incognita). Since chemical nematicides are severely limited in organic production, two primary methods for production involves deploying resistant cultivars and amending the soil. RKN resistant pepper cultivars are available for commercial production, but currently there is a scarce genetic diversity regarding resistance conferred against this pathogen. The objective of this work is to test RKN resistant pepper cultivars with value for improving productivity of organic operations. We propose to test the impacts of integrating an advanced inbred line of pepper (‘UFRJ107(6)A3’, named ‘Ruby’) into production in a pesticide-free system, in which compost application is used as a tool to both suppress RKNs and improve soil fertility. Gaining insight into the range of pepper host resistance as a supplement to cultural management practices involving organic amendments will be valuable for providing research-based recommendations to vegetable growers in the Southern United States.
Although soil treatments (chemical fertilizer vs. chicken manure) affected total fruit yield, all reproduction parameters and soil RKN densities were only significantly different between pepper cultivars. ‘Ruby’ displayed high levels of resistance when grown under pesticide-free conditions; however, a few ‘Ruby’ plants in the chicken manure–amended plot enabled high RKN reproduction.
1) Evaluate productivity of pepper cultivars differing in RKN resistance when integrated with soil organic amendment treatments in RKN-infested plots to measure effectiveness of genetic resistance under field conditions.
Field trials will be conducted at the University of Florida Plant Science and Research Education Unit (PSREU) located in Citra, Florida. They will be maintained in areas reserved for organic production research. Soil samples will be collected at the beginning and end of field trials to determine rate of change in RKN population density. The efficacy of organic amendments, with or without RKN resistant pepper varieties, for the management of RKN will be tested and measured through plant productivity and susceptibility to RKN. Pepper plant productivity will be measured by analysis of total fruit yield at time of harvest, fruit quality parameters, and plant nutrition during early vegetative and 50% flowering stages. Pepper plant roots will be evaluated for levels of RKN galling and rate of reproduction at the time of harvest to measure effectiveness of resistance.
2) Verify the identity of the species of RKNs isolated from roots of infected plants
3) Report the results of this research to inform BMPs and plant breeders involved in production systems dealing with RKN.
The work is intended to address issues of pepper cultivar selection with relevance to economic loss due to RKN infection. Also, it will address the effect of organic amendment on both pepper plant productivity and level of RKN disease in susceptible pepper cultivars. This objective includes dissemination of information through extension outreach, conference presentations and research publications in refereed journals.
Cooperators
- (Researcher)
- (Educator and Researcher)
Research
Materials and methods
Trial site and design: Two spring field trials (Apr–Aug 2023; Apr–Aug 2024), split‑plot with fertility as whole‑plot factor (chicken manure vs. granular fertilizer) and cultivar as subplot. Black plastic mulch; weekly fertigation with fish emulsion.
Plant material: Three resistant cultivars were tested: ‘Ruby’ (UFRJ107(6)A3), ‘CM334’, ‘Charleston Belle’. Three susceptible cultivars were tested: ‘Jimmy Nardello Italian’, ‘Early California Wonder’, ‘Yolo Wonder L’. For the first trial (2023), all cultivars were tested, whereas for the second trial (2024), three namely ‘Ruby’, ‘CM334’, ‘Jimmy Nardello’ were tested.
Preparation of inoculum and evaluation of resistance: Seedlings were inoculated with 300 J2 M. incognita race 3 prior to transplanting. RKN resistance was evaluated after harvest by counting egg mass counts/indices and gall ratings. Also, soil J2 densities were measured pre‑plant and post‑harvest.
Species ID: To identify the RKN species infecting both resistant (‘Ruby’) and susceptible cultivar (‘JNI’) qPCR/triplex assays were done to distinguish M. incognita from M. enterolobii and other tropical RKN.
Period covered by report: January 2023-August 2025
Results
Across trials, the genetic background of cultivar was the primary driver of variation in RKN reproductive rate (P ≤ 0.05). In contrast, soil‑amendment and block effects were not significant. In Trial 1 a small subset of ‘Ruby’ plants, mainly under chicken‑manure plots, showed high reproduction, a pattern absent in Trial 2. In trial 2, a small subset of ‘CM334’ plants enabled RKN reproduction in the conventional plot, but not in Trial 1. Yields favored ‘Ruby’, which consistently ranked at or near the top under both fertilizer treatments in both trials, while susceptible checks generally yielded less. At the time of harvest, cultivar ‘CM334’ was just starting to set fruit in contrast to the other cultivars, which were already fully ripened. Chicken manure was ineffective, producing no consistent main effect on RKN densities or fruit yield. Although significant differences in RKN reproductive potential were observed, they were cultivar‑specific and not sustained across both trials. Additional plant‑parasitic nematodes (sting, ring, stubby‑root, lesion) stayed low to moderate. Only ring nematode suggested a correlation with chicken manure-associated increase in one trial. qPCR-based tests on RKN isolated from infected ‘Ruby’ plant’s root identified M. incognita, not M. enterolobii,,suggesting that a sub-population of RKN could break the genetic resistance of ‘Ruby’ under the field conditions used in this study.
Chicken manure often improved yield (e.g., ‘Ruby’ +37%, ‘CHB’ +141%), but the increase did not imply nematode suppression. Host resistance remains the primary management method for the current system, whereas soil amendment mainly affects productivity, not RKN biology.
Learning outcomes
The main outcome from this research is the first-hand awareness that resistance can occasionally be overcome. Managing RKN in organic systems is highly complex, with multiple factors potentially attributable to the plant, the nematode, and the environment. One potential major factor is the high variability of nematodes present in the soil. Ensuring identification at the species level, not only at the genus level, is essential to guiding management decisions. Even more optimal would be to identify the soil RKN at the race level prior to planting and choose resistant cultivars for those races of the RKN.
Extension presentations.
- Padilla, D.P. (2025) UF Pepper Breeding Program: Developing varieties with enhanced resistance to root-knot nematodes and bacterial spot. Vegetable Seminar at the Citrus Show, Fort Pierce, FL, Mar 13, 2025. Oral presentation.
- Padilla, D.P. (2024) Root-knot resistant peppers. Pepper Field Day, Citra, FL, Oct 23, 2024. Oral presentation.
- Research manuscript Padilla, DP., Dickson, DW, Brito, J., Rathinasabapathi, B (2025) Evaluation of a Root-knot nematode chili pepper cultivar under a pesticide-free field production system. Annals of Applied Biology (MS in preparation following first review)
Educational & Outreach Activities
Participation Summary:
Extension manuscript
- Online publication on RKN resistance in pepper in the IFAS-supported EDIS Journal, a free resource for Extension program initiatives, in preparation for peer-review
Project Outcomes
Project outcomes
We are grateful for this research funding which was acknowledged in our presentations and publications. Two Extension presentations to stakeholders and one research and one extension manuscript are this project’s outcomes.
We became more cautious about assuming organic amendments provide significant suppression of RKN infection, and more confident that deploying resistant cultivars can reduce dependence on pesticides without sacrificing yield. We also became more aware regarding durability of resistance given evidence of localized infection in resistant backgrounds and potential resistance‑breaking populations. Experience in field experimental design was valuable (split‑plot, mixed models), as well as experience in data interpretation to inform BMPs. We also added isolate‑level pathogenicity testing (single‑female progeny assays) to verify virulence on resistant hosts, gaining experience in signs of resistance breakdown from the field. Species and race identification should be done prior to planting. Resistant cultivars should nonetheless remain to be prioritized when suitable for managing the isolate(s) identified in the field.