almond, pistachio, walnut disease models - cover photo

Almond, pistachio and walnut disease models

Walnut Anthracnose

The disease walnut anthracnose is caused by the fungal pathogen Gnomonia leptostyla (imperfect stage: Marssonina juglandis), which infects mainly eastern black walnut trees (Juglans nigra L.), whereas also the varieties butternut, Persian or English walnut, Hinds walnut and California walnut get infected.

Walnut trees vary in their susceptibility for the pathogen, but even low susceptible ones become infected when optimal conditions for the fungal pathogen are given. Walnut anthracnose is worldwide distributed.


Leaves, nuts, and, occasionally, shoots are likely to be attacked. Tiny dark-brown or black spots, circular to irregularly circular, appear on infected leaves. These spots become more numerous, enlarge, and often merge to form still larger dead areas. Yellowish to golden leaf tissue usually borders these spots. Infected leaves and leaflets generally fall prematurely, but some infected leaflets usually remain attached to the tree for most of the season.

Premature defoliation affects the quality and growth of nuts. Nuts from diseased trees commonly have dark, unattractive, and shriveled meat. Sunken, necrotic spots, smaller than those on the leaves, appear on husks of infected nuts. Nuts that become diseased when immature do not develop normally and many drop prematurely. Lesions also appear on current shoots, which are attacked on rare occasions, and form dead, sunken areas that are oval to irregularly circular, and light, grayish-brown with dark, reddish-brown margins.

Life cycle of the fungal pathogen

Perithecia are formed during wintertime at temperatures between 7°C-10°C. To form the sexual, spore-bearing perithecia two compatible strains are needed. Within each perithecium many asci are developed, each containing eight ascospores. Ascospores are discharged from the perithecium during wet spring weather and are carried by wind to leaves. For spore discharge and dissemination, rain is needed. The optimal temperature is above 10°C. Wind and rain splash carry the spores to new green leaves, where infections take place. Symptoms are found at the beginning of May.

Infected leaves show black small asexual fruiting bodies (acervuli). At about 18°C the production of these acervuli is highest, they produce large numbers of conidia. Conidia cause the secondary infection source (in June- autumn). Rain splash is required as well as free moisture must remain on the leaf surface for more than 6 hours. The optimal temperature for infection is about 21°C. Symptoms could be found after 2-3 weeks of incubation.

Under unfavorable conditions (dry conditions) spores are able to survive some weeks. The fungal pathogen overwinters in fallen leaves (as perithecia) or on walnut twigs (spores).

FieldClimate shows the probability of infections and discharge of ascospores under favorable conditions in dependence of temperature, rain and leaf moisture.

Walnut Blight

The bacterial disease Xanthomonas arboricola pv. juglandis, is called walnut blight. The bacterium overwinters in infected buds and catkins. Buds with the highest bacterial populations are the ones most likely to develop blight. During early spring growth, bacteria spread along developing shoots and nuts. There seems to be very little secondary spread to other shoots and trees by raindrops. This results in local infection centers within a tree or orchard. Frequent, prolonged rain, just before and during bloom and for about 2 weeks after, result in severe blight outbreaks within these local infection centers. This is when nuts are most susceptible.


On leaves, infection appears first as reddish-brown spots, on the stems as black, slightly depressed spots often girdling the shoots. Young, infected leaf and catkin buds turn dark brown or black and soon die. The disease is serious on nuts, where it causes black slimy spots of varying sizes. The organism penetrates the husk, the shell, and occasionally the edible meat. The late-season infection produces black rings on husks.

The bacterial disease is favored by warm, moderate seasons with temperatures of 10-28°C, light and frequent rainfalls with heavy winds and dews. Local dispersal is possible by rain splash.

Leaf spot disease

Alternaria alternata causes leaf spot disease, rots and blights on a wide range of host plants. The fungus belongs to the opportunistic pathogens.


Alternaria leaf spot appears as fairly large brown spots on leaves, about 12-18 mm in diameter. The fungus produces spores, which are seen as black spots. Leaf spot develops most rapidly in June and July, and trees can be almost completely defoliated by early summer when the disease is severe. The disease appears to be most severe where dews form, humidity is high, and air is stagnant.

Alternaria leaf spot can occur on almond trees grown anywhere in the Central Valley, but rarely is it severe enough in the northern San Joaquin Valley to require treatment. It has been most serious on trees in the southern San Joaquin Valley and in the northern Sacramento Valley.

Disease cycle

The asexual spores of the fungus are thick-walled, multicellular, and pigmented and are able to tolerate adverse conditions like dry weather. Spores are produced on leaves and in lower numbers on fruits and twigs remaining on the tree as well as on leaf litter. When there is no susceptible tissue available, such as over the winter, the fungus survives on mature leaves, twigs, and fruit. Spore production is greatest when relative humidity is above 85%. Spores are air-borne and release into the air is triggered by rainfall or by a sharp change in relative humidity. Once the spores are released, they are moved by wind to susceptible tissue where they are able to infect. When temperatures are favorable 20-29°C, the length of the wetting period required for infection is about 8-10 hours. When temperatures drop below 17°C or rise above 32°C , the fungus requires extended leaf wetness durations (>24 hrs) to cause significant infections.

On highly susceptible cultivars, as little as 6 hours of leaf wetness can result in infections. Most of the infections probably follow a rainfall event, but dew can be sufficient to bring about infection. For example, in Israel and Spain, little rain occurs after petal fall, but they can still have a significant infection as the result of heavy dews.

Disease models

Disease model originated from UC IPM.

The model calculates a disease severity value (DSV) per day (similar model as the TomCast in Tomato).

Disease severity values depend on the average temperature during leaf wetness periods during a day. Application of fungicides is recommended if an accumulated index value of 10 DSV or higher is reached over a 7 day period.


(C) during wetness Leaf wetness duration (hours)

In some orchards, Alternaria sp. resistance to quinone outside inhibitor (QoI) fungicides (also known as strobilurins) and succinate dehydrogenase inhibitor (SDHI) fungicides have been documented; do not use FRAC mode of action Group number 7 or 11 fungicides in these orchards.


The disease occurs first and is most severe on exposed leaves. Trees trained to an open and spreading canopy usually have more severe Alternaria leaf spot. Trees planted with rows in an east-west direction also have more severe disease than do orchards with rows planted north-south. Varieties that are most susceptible include Carmel, Sonora, Monterey, Winters, and Butte. Monitor for signs of the disease in April through June. If monitoring indicates the presence of Alternaria, begin late-spring treatments about mid-April. In orchards with a history of the disease, treat in mid- to late April and 2 to 3 weeks later.


  • Dewdney M. M. (2013). Alternaria Brown Spot- Document PP152, one of a series of the Plant Pathology Department, Florida Cooperative Extension Service, Institute of Food and Agricultural Sciences, University of Florida. Original publication date July 2001. Reviewed May 2008. Revised June 2013. Visit the EDIS website at Edis.
  • Adaskaveg J. E., Gubler W. D., Duncan R., Stapleton J. J., Holtz B. A. (2012) UC IPM Pest Management Guidelines: Almond; UC ANR Publication 3431. This page.

Brown rot

Brown rot, caused by Monilia spp. (Monilia laxa, Monilia fructigena and Monilia fructicola) are among the most destructive diseases throughout Europe.


Flowers may become infected from pink bud to petal fall and are most susceptible when fully open. In almonds, stigma, anthers, and petals are all very susceptible to infection.

Symptoms of the brown rot disease are the blight of the cherry blossom as well as the green tip of twigs due to the penetration of the pathogen into the open blossom through the stigma of pistils or anthers. This usually results in wilting of the whole part of a one-year-old twig. The leaves start to hang down, later they become brown and rigid, but usually do not fall down on the soil, they remain on the tree until the spring of the next year. Sometimes, especially under humid conditions droplets of gum are visible, which are symptoms of colonization of the fungus as well as the established cankers. At high humidity, gray to tan spore masses form on diseased flower parts and twig cankers.

The infected fruits are covered by putrefactive spots, from which warty sporodochia (hyphe) with conidia of the “summer” form appear. Additionally, in late autumn and winter, the fungus produces sporodochia of the “winter” form on infected twigs. With time, severely affected fruits become mummified. The mycelium growing in such mummies gradually aggregates into sclerotia. Such fruits remain on the tree during winter.

Temperature and wetness duration are important environmental factors, determining the infection incidence of M. laxa on sweet cherry blossoms. Monilia laxa is well adapted to the relatively low temperatures during spring and causes infections at temperatures as low as 5°C within a very short period of wetness duration. The infection of the active bloom through the stima does not need very much leaf wetness. Leaf wetness is only needed for the germination of the conidia. Therefore infection of the young fruit needs longer leaf wetness periods. To infect the young fruit an appressoria has to be formed and free moisture is needed to build up the pressure to form the infection peg to enter the epidermis cell. With the maturity of the fruit, small scars on the fruits allow an infection without infection peg again and the needed leaf wetness duration becomes shorter again.

No sporulation is possible if relative humidity does not overcome 85% rel. humidity.

Brown rot model in FieldClimate

Calculates weak and severe infections. Weak infections are modeled for conditions to infect highly susceptible stages like flowers and wounded fruits close to maturity. To infect this tissue very short leaf wetness periods have shown to be sufficient.

Several studies, for example:” Phenological Analysis of Brown Rot Blossom Blight of Sweet Cherry Caused by Monilinia laxa” (L. Tamm, Chr. E. Minder, and W. Flickiger; 1994) or “Effects of wounding, fruit age and wetness duration on the development of cherry brown rot in the UK.” ( X.-M. Xu*, C. Bertone and A. Berrie ;2003) confirmed low wetness periods needed for infections. Further on, immature fruits are more resistant for infections, but close to maturity they are becoming more susceptible and conditions for severe infections are given.

Springtime dispersal patterns of Monilinia laxa conidia in apricot, peach, prune and almond trees. Canadian Journal of Botany (1974), 52: 167-176

Fieldclimate Modeling: It is probably that the time needed for infection during bloom has to be shortened. Therefore the model is shorting infections down in the area of 2000 to 4800 degree hour above 5°C.

The first graph shows a model for Styria in the year 2010, which indicates a weak infection at the 06th of April. At this time the cherry tree starts to bloom. This infection can already lead to latent infections of the fruits, which would cause severe damages. Late blossoms will be completely destroyed by infections in mid to end of April. Severe infections are determined on the 6th of April due to longleaf wetness periods and temperatures above 5 to 15°C.

Rust on almond

Rust is caused by the fungal pathogen Tranzschelia discolor.


Common symptoms of the disease are twig cankers, leaf lesions and fruit lesions. Not all symptoms may develop in each growing season.

Twig cankers

Twig cankers are the first symptoms in the spring. These cankers develop after petal fall in spring during fruit development on one year old wood. Symptoms are seen as blisters and longitudinal splits in the bark. The infection starts with water- soaked lesions, which swell and rupture the epidermal tissue of the twig. Cankers are usually found on the upper, red-ish side of the twig. Few days afterwards (depending on the temperature) the cankers mature and produce rusty brown powdery masses of specialized spores (urediniospores). These urediniospores are spiny and sharply constricted at the base. At the end of the saison old cankers could be still observed, they may persist in the following season but no longer viable spores are produced.

Leaf lesions

Leaf lesions develop usually after cankers form in spring and may continue till autumn. Defoliation can occur when high numbers of infections are on single leaves. First infected leaves are close to the twig cankers (infection source). Lesions develop as pale yellowish green spots visible on both leaf surfaces. The lesions become bright yellow and angular and with age necrotic in the center. On lower leaf surfaces numerous spore pustules (uredinia) can be found. They become rusty brown due to the production of powdery masses of urediniospores. At the end of the season leaf lesions may turn dark brown to black and they produce two- celled teliospores. These leaf lesions are angular shaped, small size and rusty brown.

Fruit lesions

Fruit lesions develop during the growing season after the symptoms of the leaves. Firstly brownish spots with green halos on mature, yellow fruits are seen. When fruit reddens, the halos become greenish- yellow. Numerous infections develop on each fruit and these can lead to secondary infections by other fungal pathogens like Monilinia, Colletotrichum, Alternaria or Cladosporium.


The fungal pathogen attacks plants of the genus Prunus, including almond, apricot, cherry, peach, nectarine, plum and prune. The fungus can be separated by special forms, based on the host where it is found. These forms are T. discolor f. sp. persicae on peach, T. discolor f. sp. dulcis on almond, T. discolor f. sp. domesticae on prune.

The fungus has multiple spore stages, which develop on two different hosts (alternate hosts). The only alternate host which is reported from California is Anemone coronaria (Ranunculaceae). The different spore stages are urediniospores, teliospores, basidiospores and aeciospores. Only urediniospores and teliospores are found on Prunus sp.

The single celled, rusty brown urediniospores are produced on peaches and can re-infect peaches. This secondary infection and additionally spore production and reinfection causes epidemic damages on peaches. The teliospores, which develop late in the season on peaches, are not able to reinfect peaches. After overwintering, the teliospores germinate and produce basidiospores that infect the alternate host Anemone coronaria.

Aeciospores that are produced on A. coronaria infect only Prunus spp. and the infection produces the first cycle of urediniospores in the spring. A. coronaria is rare in stone fruit yards and probably not the source of first infection in the yards.

The fungus probably overwinters as mycelium in infected fruit wood from the previous summer or fall. In spring these infections become the twig cankers and that are the source of primary inoculum each year. Urediniospores from twig cankers infect leaves, where more spores are produced in lesions and under favorable conditions the disease becomes epidemic.


  • Adaskaveg JE, Soto-Estrada, A, Förster, H, Thompson, D, Hasey, J, Manji, BT, Teviotdale, B. (2000) Peach rust caused by Tranzschelia discolor in California. University of California. Agriculture and Natural Resources.

Conditions for an infection – Output in FieldClimate

Urediniospores are dispersed by wind and rainfall. They germinate over a wide temperature range from 5°C to 30°C with an optimal temperature range of 10-25°C. The viability of inoculum and wetness are major factors for determining infection periods.

Leaf and twig infections can occur over a wide range of wetness periods (12 to 36 hours) and temperatures (15 to 25°C). Under controlled conditions the optimal wetness duration and temperature for infection was 18 to 36 hours at 15°C to 20°C. The incubation period after infection is 8 to 10 days, whereas the incubation period for twig symptoms is 4 to 6 weeks at 20°C.

Recommended equipment

Check which sensor set is needed for monitoring this crop’s potential diseases.