Research Update


Above Ground Root Collar Excavation

weedbadger for soil removal

A Weedbadger Model 2030 was acquired and modified for root collar excavation. The equipment was mounted on a tractor with the three point hitch mechanism. It has a hydraulic system with a PTO driven hydraulic pump. We fixed and confirmed the operations of the pump, valves, hydraulic actuators (cylinder and motor), and hydraulic lines. Next, we designed two paddle wheels in different sizes. The first paddle wheel had 19.5 in diameter and 4 in tall paddles. After initial testing in field conditions, we increased the diameter of the paddle to 22.5 in with 6 in tall paddles. The larger diameter and height of the paddle wheel ensured excavating the berms between the trees successfully. We are currently testing attachment of chains to increase the width of the excavation and to create a uniform spread of the excavated soil between the tree rows.

During this project term, we fine tuned the paddle wheel mechanism and integrated a safety guard. Different brush mechanisms to excavate the soil near the tree trunks for finer soil excavation with minimal disturbance to the tree roots will be tested.

levee plow demonstration to a crowdThe levee plow was presented to around 20 peach growers (SC and GA) and around 700 new acres in SC and 1,295 new acres in GA were established using the AGRCE planting system since the start of this project.

Significant lower tree death was observed on Above Ground Root Collar Excavation planting compared to grower standard. In the AGRCE orchards, tree mortality was delayed, both in an experimental and in a commercial orchard, and lower percent mortality over time was observed. No difference in disease incidence, yield, and fruit quality between grower standard and established AGRCE field trials was observed.

Tree mortality due to Armillaria Root Rot In Seneca, SC (a) and Ridge Spring (b). Different letters indicate statistical significances between treatments and years (Fisher’s LSD).Tree mortality due to Armillaria Root Rot In Seneca, SC (a) and Ridge Spring (b). Different letters indicate statistical significances between treatments and years (Fisher’s LSD).


Miller, S. B., K. Gasic, G. R. Reighard, W. G. Henderson, P. A. Rollins, M. Vassalos, and G. Schnabel (2020) Preventative root collar excavation reduces peach tree mortality caused by Armillaria root rot on replant sites. Plant Dis.

Hybrid Nursery Production

Various planting dates were applied to improve growth of the MP-29 rooted cuttings. Earlier planting helps with rootstock sizing although uniformly better sizing was not achieved.

Different grafting techniques using rooted and unrooted MP-29 cuttings, with variable planting dates and fertilization rates were also explored to improve rootstock growth. Small improvements were achieved in experimental setting and need to be tested for feasibility in nursery scale operations.

Growth tubes were used to correct for plagiogravytropic growthMP-29 tubes next to peach seedlings


Growth tubes were used to correct for plagiogravytropic growth

Antifungal Compound Identification

In vitro screening illustrationIn vitro screening protocol to assess the susceptibility/tolerance of Prunus genotypes to Armillaria was developed. Prunus germplasm in vitro screening developed by Baumgartner et al. (2018) and root microscopy confirmation of absence of fungal penetration are used in Step 1. Resistant germplasm from Step 1 is multiplied and grown in co-culture with Armillaria in Oasis® IVE phenolic resin (Step 2). Germplasm with confirmed resistance after in vitro screen 1 and 2 is multiplied and analyzed for anatomical and biochemical (Objective 1b), and transcriptomic and metabolomic (Objective 2) responses to infection. Stocks of healthy plants are maintained in vitro, in pots in the greenhouse and field for assessing optimal horticultural characteristics (Objective 3a).

Using the new resistance screening pipeline we have tested 81 Prunus spp accessions from Prunus National Clonal Germplasm Repository (NCGR) in Davis, CA and 4 from Clemson Prunus germplasm for their response to ARR infection in vitro.

Resistant response, observed in 4 accessions in vitro was confirmed by root microscopy.

In vitro screeningAntifungal activity of the compounds from the root periderm of 28 different Prunus genotypes was investigated using three-step, in vitro antifungal activity screening bioassay.

Antifungal compounds phytoanticipins were detected, specifically flavonoids, including uncommon flavonoids, alnusin and alnustinol and their precursors.

We demonstrated host’s ability to limit ARR infection by several collective nonspecific host responses acting together, such as the formation of new callus tissue on the root surface, a colored reaction zone, necrophylactic periderm, new cells, and new vascular cambium to compartmentalize the pathogen.

Mode of tolerance

Mode of tolerance/resistance in Prunus. a, c - Necrophylactic periderm (np) formation; b - Intact bark walling off; d - A. mellea infection spreading around the bark of S-37 Stribling and thin layer of newly formed cells (nc) unable to compartmentalize the fungal spread and infection; e - Healthy wounded root of P. mahaleb #1 with internal callus (ic) formation around the cambial region; f - D. tabescens infection in P. mahaleb #1 root. Bars = 200 µm (a, b, d, e, and f) and 50 µm (c) (Devkota et al., 2020)

Devkota, P., Iezzoni, A., Gasic, K., Reighard, G., and R. Hammerschmidt (2020) Evaluation of the susceptibility of Prunus rootstock genotypes to Armillaria and Desarmillaria species. European Journal of Plant Pathology.

ARR Resistant Rootstock Breeding

Newly detected resistant sources were used in breeding with standard peach and cherry rootstocks. Hybrid seeds were included in the resistance pipeline screening.

PTSL genomic regionsWe have identified genomic regions controlling peach tree short life (PTSL) tolerance in resistant rootstock Guardian®. COmaprion of genomic regions controlling PTSL response between Lovell (PTSL susceptible) and Guardian® (PTSL tolerant) shows exponential increase of number genes involved in plant tolerance to diseases in tolerant rootstock.

The DNA test for pre-screening hybrid seedlings for PTSL tolerance are in the validation stage.

transcriptomeTranscriptome analyses in ‘MP-29’ (ARR resistant) and ‘GF305’ (ARR susceptible) after co-cultivation with Armillaria spp, have detected differentially expressed genes and revealed key genes NOT encoded in peach, that appear to be critical to resistance.

One of the detected genes present in MP-29 but not GF305 was Oxalate oxidase (+chitinase). This gene naturally exists in wheat, banana, and other plant species. It neutralizes/degrades oxalic acid that is required by fungus for wood infection. Fungus is allowed to live as a saprophyte, reducing chance for evolution of resistance.

Additional Efforts

We have successfully brought to the table stone fruit industry (growers and nurseries) and researchers across the U.S. from regions affected by Armillaria root rot to discuss the present state of the research and what needs to be done.

group photo of growers and nurseries and researchers across the U.S. from regions

The three-day workshop in Clemson and round table discussion in Savannah GA were organized to gather information on what were the major obstacles to providing solutions for this replant problem. Engagement of both research community and stakeholders resulted in the development of objectives for a research proposal to advance the knowledge on Armillaria root rot and to test/provide short- and medium-term solutions to the industry.

The need for accurate socio-economic assessment of the impact of Armillaria root rot to the industry was evident. Summary of the state of the Armillaria research and short- and long-term needs of the stone fruit industry were developed and shared with commodity boards and wider audiences as presentations at the conferences and or local growers meetings.

scientists at round tables working on grant planning in teamsWe have assembled a national, interdisciplinary, multi-institutional team of researchers to:

  • identify gaps in current Armillaria root rot (ARR) research and potential collaborations to fill such gaps;
  • involved stakeholders on the project team, to ensure rootstock acceptance;
  • identified and aligned common goals to develop ARR resistance; an
  • integrated pathogen and plant collections. 

Acquired knowledge from Specialty Crop Multistate Block Grant (USDA-AMS-SCMP-2015-10.170) and other unpublished research was incorporated into Standard Research and Extension Proposal that was funded by NIFA-SCRI for next four years (2020-2024).