Winter Squash Storage Rots and Their Management


Farmers in western Oregon can lose a significant portion of their winter squash in storage to storage rots. In winters 2012-2015 we collected samples of stored squash with rot symptoms from farmers in western Oregon and the OSU Plant Clinic identified the pathogens causing those rots.  The common rot diseases diagnosed were:

  1. Fusarium fruit rots (caused by Fusarium spp)
  2. black rot (caused by Phoma cucurbitacearum)
  3. gray mold (caused by Botrytis cinerea)
  4. white mold (caused by Sclerotinia sclerotiorum)

General Management Recommendations

  • Harvest squash as early as possible; do not leave them in the field exposed to fall rains. 
  • Leave a small portion of the stem on at harvest.
  • Handle squash carefully to avoid damaging the skin.
  • Dry fruit before storage.
  • Store at 50-70°F and 50-55% relative humidity with good air circulation.
  • Remove diseased fruit regularly.

Disease Diagnosis and Description


Fig. 1. Fusarium fruit rots of butternut squash.


Fig. 2. Fusarium fruit rot of delicata squash.


Fig. 3. Fusarium fruit rot of acorn squash.

Disease and Causal Organism: Fusarium fruit rots are some of the most common pre-­ and post-­harvest diseases of cucurbit crops. There are at least 10 different species of Fusarium which can cause fruit rots of winter squash. Fusarium spp. survive in soil and are more abundant in higher rainfall areas or in irrigated soils. Most Fusarium spp. infections occur in the field before harvest.        

Dispersal MethodFusarium spp. are both soil-borne and seed-borne.  Typically, soiborne propagules come into contact with the flower or fruit from splashing of soil during rain or irrigation events or when the fruit touches the soil. Infested seed can also be the cause of Fusarium rots of winter squash.

Symptoms: Fusarium spp. symptoms vary considerably as there are so many different species. In addition, symptoms change as rot lesions develop over time. Some Fusarium rot lesions are small, pitted, corky spots while others are large and sometimes corky areas covered with a white, pink, or gray mold. Lesions can occur anywhere on the fruit, but are often seen on the stem end or where the fruit was in contact with soil. If the fungal rot moves into the seed cavity, seed infestation may occur.                                            

Management: Management of fruit rot of cucurbits caused by Fusarium spp. is difficult. As most Fusarium species don't survive in soil for more than 2 or 3 years, a 3 year rotation out of cucurbits can help suppress these storage rots. Providing a physical barrier (mulch) between the fruit and soil reduces fruit infection by reducing soil contact with fruit. Infection usually occurs through wounds, and can be transmitted during harvesting if knives become contaminated with infected soil or diseased plant tissue. Avoidance of wounding during harvest and packing, storage in cool and dry conditions, and proper handling during transit and marketing will reduce losses due to Fusarium fruit rots.  Heat treatment of infested seed can reduce the likelihood of seed transmission, although in this diagnostic effort we did not find any Fusarium fruit rots that were caused by pathogens that are transmitted on seed.    


Fig. 4. Black rot of spaghetti squash.

Fig. 5. Black rot of butternut squash.

Fig. 6. Black rot of delicata squash.

Disease and Causal Organism: Black rot is an important pre-­ and post-­harvest fruit rot of winter squash. Black rot can begin in the field before harvest and continue to develop during transit and storage.            

The organism that causes Black Rot has two names: Didymella bryoniae (sexual stage) and Phoma cucurbitacearum (asexual stage).

Symptoms: Symptoms vary depending on the cucurbit infected (Figs 4-6). If contracted while still in the field, symptoms usually occur on the side of the fruit touching the ground because high moisture favors infection. Fruits develop small, water-­soaked, dark­ brown lesions. As the lesions expand, they become sunken and darken to black. Fungal fruiting bodies (pycnidia), can often be seen as black specks in a ring pattern on infected areas. On butternut, the lesions appear as bronzed, irregular patches and raised corky areas. Another appearance is a reddish-­brown ring­spot pattern that becomes bleached white (a petrified look). Severely affected fruit may collapse during or after harvest.                                       

Management: Didymella bryoniae survives between the growing seasons on diseased vines, crop debris, and seed. Another source of inoculum are the airborne sexual spores (ascospores) of the pathogen. Care should be taken to avoid rind injuries to all fruit, as the pathogen enters through wounds or injuries in the rind. Under proper curing conditions, wounded areas heal themselves by producing corky tissue. If the decay does extend into the seed cavity, the fungus may come in contact with the seeds of the fruit.


Fig. 7. Gray mold of pumpkin and delicata squash.

Disease and Causal Organism: Botrytis (gray mold) is a ubiquitous disease that affects many plant species in western Oregon.  The pathogen is spread by airborne spores.  The fungus is always present. The amount of inoculum in a field can be reduced by removing dead leaves and infected fruit, as the fungus lives on decomposing, dead organic matter of many plant species in and around the growing area. After harvest, the fungus survives in the soil as small black sclerotia. Wet, cool weather is necessary for development of this disease.          

Symptoms:  The Botrytis pathogen is soil-borne and air-borne.  It commonly infects tissue through injuries and forms gray, velvety mats of sporulating tissues (Fig. 7).

Management: General preventive measures reduce gray mold severity, such as avoiding mechanical injury and keeping fruit dry.


Fig. 8. White mold of spaghetti squash and Ambercup squash.

Disease and Causal Organism: White mold is caused by Sclerotinia sclerotiorum. This pathogen has a very wide host range - essentially, all dicots - and is an important disease of snap bean in the Willamette Valley. White mold can cause losses in the field and in storage.

Dispersal Method:  White mold survives in soil as black hardened sclerotia. Sclerotia can germinate directly and infect squash lying on the soil surface. Alternately, they can produce mushroom-like structures (apothecia) which produce spores that can land on and infect squash stems, crowns, and fruit, especially through wounds.


White mold is typically characterized by a watery, odorless rot that leads to the development of white fluffy fungal growth and the production of the very characteristic black sclerotia. The rot can easily spread in the field by fruit to fruit contact. See Figure 8.

For more signs and symptoms of white mold on vegetable crops, including pictures of sclerotia, see Photos of white mold in vegetable crops.

Management:  As white mold has a very wide host range, it is difficult to manage through rotation. However, rotation with monocots such as corn, grass family cover crops, or alliums (onions) can reduce white mold risk. Reduce the numbers of sclerotia produced on a diseased crop by incorporating diseased residues immediately after harvest. Keep foliage and fruit dry to reduce the likelihood of infection. To more rapidly kill sclerotia after harvest of a diseased crop, apply Contans™ (Coniothyrium minitans), a biocontrol fungus specific to the white mold fungus.

For more information on white mold and its management in vegetable crops, see White mold of snap bean and other vegetable crops, and for information on using Contans for white mold management, see What is Contans and how can it be used in western Oregon to control white mold?

Photo credits: Lane Selman, Melodie Putnam, and Alex Stone

Further Reading:

Bernhardt, E., Dodson, J. and Watterson, J., 1988. Cucurbit diseases: A practical guide for seedsmen, growers and agricultural advisors. Petoseed Co., Inc. Saticoy, CA.

Hawthorne, B.T., 1988. Fungi causing storage rots on fruit of Cucurbita spp.. New Zealand Journal of Experimental Agriculture 16(2):151-157. Available at:

Loy, B., 2011. Maximizing yield and eating quality in winter squash – a grower’s paradox.  Available at:

Stone, A., 2014. White mold of snap bean and other vegetable crops article.

Stone, A., 2014. What is Contans and how can it be used in western Oregon to control white mold? article.

Zitter, T., 1992. Fruit rots of squash and pumpkins. Cornell University. Fact Sheet Page 732.10 Available at

Zitter, T.A., Hopkins, D.L., and Thomas, C.E., eds., 1996. Compendium of cucurbit diseases. APS Press, Minneapolis.

Zitter, T., 1998. Fusarium diseases of Cucurbits. Cornell University Cooperative Extension. Fact Sheet 733.  Available at: