AAFC Research Update on Sudden Apple Decline and Fruit Tree Decline Disorders in Ontario

Research Highlights

In 2018 and 2019 researchers collected samples of dead, diseased and healthy trees from multiple orchards across the province to evaluate the disorders and identify potential pathogens. The research team identified a number of pathogenic fungi in apple and stone fruit trees in Ontario.

Researchers are investigating potential links to Sudden Apple Decline (SAD) and Fruit Tree Decline (FTD), such as:

  • Viruses and nematodes may contribute to tree disorders
  • Decline orchards often contain ambrosia beetles and identification to species level is underway
  • Reduced water pathways in dead and dying trees due to the weakened water transport capacity in the dwarfing rootstocks, particularly at the graft union.
  • To date, no single pathogen has been identified as the direct cause of these disorders.

Current research is investigating the possibility of biotic and abiotic factors working together to contribute to tree decline and death.


Rapid decline and death of apple and stone fruit trees was first observed five years ago in Canada. While the economic impact to growers has been considerable; to date the full economic impact has yet to be tabulated. To differentiate between the crops, the disorder was named SAD in apples and FTD in pears and stone fruit.

Agriculture and Agri-Food Canada (AAFC) provided funding in 2019-2022 to researchers in British Columbia, Ontario, Quebec and Nova Scotia. The research teams were to identify biological and environmental stresses that may be associated with the disorder.

Fungal and bacterial involvement in SAD and FTD

In 2018 and 2019 seven apple and nine stone fruit orchards were sampled in Ontario, Canada. Scion, graft union and root samples were collected from healthy and symptomatic trees. Fungal appearance, or morphology, was used to place the 1,500 fungal isolates into species:

  • Alternaria
  • Diaporthe
  • Diplodia
  • Paraconiothyrium
  • Cytospora
  • Fusarium
  • Penicillium
  • Epicoccum
  • Aureobasidium
  • Rhizopus
  • Ilyonectria
  • Trichoderma

Known plant pathogens in this group will be further tested in potted tree inoculations and characterized by molecular technologies to genus and species level. Thirty potential bacterial pathogens have been isolated from the woody samples, maintained in pure culture and greenhouse trials are under way to test if any of the bacterial isolates are associated with decline symptoms in peach. Similar greenhouse pathogenicity trials will follow in apple.

Fungal inoculation trials with Cytospora spp., Diaporthe sp. and Diplodia sp. showed “decline like” symptoms on fungus inoculated apple, apricot and nectarine trees.  Early research has indicated that these fungi are not the primary cause of tree fruit decline; however, they could be key components associated with the disease complexes for both SAD and FTD.

Viral involvement in SAD and FTD

Genomic-based approaches were used to identify a number of plant viruses in apple and stone fruit trees. Tomato ringspot virus was detected in approximately 30% of apricots and peaches. Peach latent mosaic viroid was identified in a number of diseased peach samples. Many other viruses were identified in diseased samples from the Niagara region including: Peach latent mosaic viroid, Prunus necrotic ringspot virus, Prune dwarf virus, and other virus types. None of these viruses were consistently identified in dead and dying trees. We are still investigating the role viruses might be playing in FTD through more targeted surveys to determine the distribution and diversity of Tomato ringspot virus in the Niagara region.

Apple leaf samples were collected from 40 trees from five farms in Ontario. Total RNAs were extracted and two mixed samples from each farm were sequenced. Preliminary data analyses identified the following viruses:

  • Apple stem pitting virus
  • Apple luteovirus 1
  • Apple chlorotic leaf spot virus
  • Prokaryotic dsDNA virus
  • Winged bean alphaendornavirus 1
  • Bell pepper alphaendornavirus
  • Bell pepper endornavirus
  • Apple rubbery wood virus
  • Pepper cryptic virus
  • Hymenoscyphus fraxineus mitovirus 1
  • Apple rubbery wood virus 2
  • Pepper cryptic virus 2
  • Ophiostoma mitovirus
  • Pyricularia oryzae ourmia-like virus 2
  • Cladosporium uredinicola ourmiavirus 1
  • Alternaria alternata chrysovirus 1
  • Citrus concave gum-associated virus
  • Apple green crinkle associated virus
  • Brome mosaic virus
  • Maize stripe virus MStV NSF4
  • Broad bean mottle virus

Nematode involvement in SAD and FTD

To understand the association of plant parasitic nematodes (PPNs) with tree fruit decline, the present study isolated and characterized PPNs from several apple and stone fruit orchards in Ontario, Canada from May-October 2019. The sampled trees from the selected fruit orchards were visually scored as three categories; healthy, moderately and severely stunted/dead. A composite sample consisting of 10 deep soil cores were collected from within 40 cm of trunks of several individual trees of each category/orchard. Nematodes were extracted from 50 g of soil sample from a mix of these soil cores using the sugar centrifuge technique at the AAFC nematology lab.

The dagger nematode (Xiphinema spp.) was present in 72% of the 29 apple samples collected from four different locations. In addition, other PPNs such as the lesion (Pratylenchus spp. 27%), ring (Criconemella spp. 10%), pin (Paratylenchus spp. 34%) and spiral (Helicotylenchus spp. 41%) were also present.

A total of 33 apricot soil samples were collected from five different locations. Presence of lesion, ring, dagger and pin nematodes were significantly high (more than 50%) within these samples. For plum soil samples, 100% of them were ring nematode positive, and 75% of them were positive for dagger. Most of the samples collected from peach and cherry orchards were positive for both ring and dagger while nectarine was positive for only dagger. All samples were positive with presence of other parasitic nematodes like lesion, pin, stunt and spiral.

The preliminary data indicates that an association exists between SAD/ FTD and ring and dagger nematode in Ontario. Thereby, research continues on these two plant parasitic nematodes. Pure cultures of ring and dagger have been initiated in AAFC greenhouses and growth chambers. In addition, a micro-plot study has been set up on the AAFC Jordan farm, Vineland Station, Ontario using Haroblush and Harlayne apricots on Krymsk 86 rootstock. This planted orchard is under observation and we will study plant growth, vigor, nematode counts, etc. to understand the pathogenicity of these nematodes for upcoming years.

Ambrosia beetle involvement in SAD and FTD

In early May to mid Sep 2019, ethanol-baited traps were set-up in nine apple orchards and five stone fruit orchards in Ontario.  Traps (six per orchard) were checked weekly; captured beetles were sorted, pinned and identified.

Over 6,600 ambrosia beetles were captured over the 14 sites.  In stone fruit orchards in Niagara, 49% of captures were black stem borer (Xylosandus germanus), a well-known, invasive pest of deciduous trees.  Fruit tree pinhole borer (Xyleborinus saxesnii) and a relatively new invasive ambrosia beetle species in Canada (Anisandrus maiche) were 30 and 12% of captures, respectively.  Captures were higher during a “second peak” (mid-July to early Sep) than in late spring/early summer.

In apple orchards (Norfolk, Middlesex and Durham regions), black stem borer was most frequently captured, at 67-75% of the total catch. Ambrosia beetles and fruit tree pinhole borer were the second and third most captured species at most sites.  Captures were typically greater later in the summer than late spring/early summer.  In many orchards, beetle captures in traps placed in an edge row were greater than in traps placed in an interior orchard row. Damage assessments in trapping blocks was not conducted.

Trapping was not conducted in 2020 due to the pandemic, and captured ambrosia beetles were not assessed for associated pathogenic fungi as planned.

Plant-water relations in SAD and FTD

A preliminary study of the area of active transporting tissue at grafted union of apple variety ‘Salish’/M.9 from a conventional orchard in Summerland, BC, showed that the declining trees had a significantly smaller area of active transporting tissues at the cross sections below, at and above the grafted union, being only 23%, 17% and 12% of the corresponding cross sections in the asymptomatic trees, respectively. In the declining trees, less than 10% of the grafted union was actively transporting, whereas in the asymptomatic trees on average, 35% of the grafted union was actively transporting. The damage around the grafted union on this site was associated with apple clearwing moth (not a pest in Ontario), woolly apple aphid and winter injury on the trunk.

In a plant-water relations study on Ambrosia/M.9 in three sites in Okanagan-Similkameen region, it was observed that in symptomatic trees, leaf stomatal conductance and plant tissue water potential decreased, and fruit dry matter accumulation also reduced, in 2019 and 2020. 

The results indicate that the water relations of the declining trees were undermined, at least partially due to the weakened water transport capacity around the grafted union.

Metabolite profiling for an early detection of FTD

Metabolomics identified thousands of metabolites with a clear distinction between FTD healthy, diseased, and dead trees. This preliminary work, based on nine trees, indicated that FTD can be identified by tree metabolite profile. Prunasin, a cyanogenic glycoside, was present in significantly higher concentrations in collapsing and dead trees compared to healthy trees. Scientific literature has linked prunasin with severe weather events and graft incompatibility​ issues. Our working hypothesis is that some compounds, like prunasin, were induced during recent severe weather events. These compounds are transported from the tree root stock to the scion, where they negatively impact the scion. This activity may initiate a graft incompatibility reaction, reducing water transport which then in turn allows pathogens to enter the weakened tree and kill the scion. Based on availability of funds, research would need to study the presence of FTD metabolites in a larger sample size (75 trees) in healthy, diseased, and dead trees.


Antonet Svircev, Tahera Sultana, Aiming Wang, Justin Renkema and Hao Xu (AAFC).

The authors gratefully acknowledge the technical assistance provided by Karin Schneider, Andrea Lofano, Lori Bittner, Darlene Nesbitt, Evgeny Ilyukhin, Jessica Prosser, Qing Yu (AAFC); Kristy Grigg-McGuffin and Kathryn Carter (OMAFRA).

Dr. Oualid Ellouz
Dr. Oualid Ellouz

Research Scientist – Plant Pathology, Agriculture & Agri-Food Canada

Dr. Jonathan Griffiths
Dr. Jonathan Griffiths

Research Scientist – Plant Virologist, Agriculture & Agri-Food Canada