How to Manage Pests

UC Pest Management Guidelines


Seed Rot and Seedling Diseases

Pathogens: Achlya klebsiana and Pythium spp.

(Reviewed 4/04, updated 4/04, pesticides updated 10/15)

In this Guideline:


Seed rot and seedling diseases often appear within a few days of planting. Whitish outgrowths of fungal mycelium emerge from cracks in the seed glumes or from the collar of the infected seedling's plumule. After a few days, the fungal mycelium resembles a halo that radiates from the infection point on the seed or seedling. Various algae colonize the fungal growth turning it green. In some cases the infected seed appears within a dark circular spot on the soil surface. This too may be the result of algae growth, but is most probably caused by secondary invasion of the seed and fungus by various aquatic bacteria. Early infection of germinating seeds, especially when temperatures are cool, will often result in seed rot or seedling mortality.

If seedlings produce primary leaves and roots before infection occurs, they usually survive but are typically stunted. Leaves and sheaths become yellow or chlorotic, and further development is retarded. The typical fungal halo is usually evident. If infection occurs after seedlings are well established, there is generally little apparent effect.


The disease, although prevalent throughout the rice-producing areas of California, is generally more severe when cool temperatures, which are unfavorable for rice growth, occur at or shortly after planting time. If ideal conditions for development of seed rot and seedling diseases occur, water-sown rice often is severely infected within a few days after seeding, resulting in reduced plant stands or reduced seedling vigor.


Seed treatments with fungicides provide protection against seed rot and seedling diseases, especially if seed is planted early or if environmental conditions are unfavorable to germination and seedling growth. Uneven stands caused by seed rot and seedling diseases can be partly compensated for by increasing seeding rates.

Cultural Control

Plant high quality rice seed (preferably certified seed) with 85% germination or more and a bushel weight of 44 pounds or more. Plant when water temperatures are favorable for rice seed germination and growth of rice seedlings (preferably above 70°F or 21°C). Maintain a uniform water depth of about 4 inches or 10 cm; this will also improve germination, rice stand establishment, and tillering. If the field has had severe problems in the past with seedling diseases or temperatures are expected to be cool at or shortly after planting, an increased seeding rate may be advisable.

Organically Acceptable Control Methods

Recommended cultural controls are organically acceptable.

Treatment Decisions

The benefits from fungicide seed treatment in water-sown rice are most obvious during the early planting season when environmental conditions are often unfavorable for germination and seedling growth. Chemical seed treatment increases the percent stand establishment, thus reducing the need to replant and helping to establish uniform rice stands.

Common name Amount to use per 100 lb seed REI‡ PHI‡
(Example trade name)   (hours) (days)

UPDATED: 10/15
Calculate impact of pesticide on air quality
When choosing a pesticide, consider its usefulness in an IPM program by reviewing the pesticide's properties, efficacy, application timing, and information relating to resistance management, honey bees (PDF), and environmental impact. Not all registered pesticides are listed. Always read the label of the product being listed.
(Champ Formula 2) 2–4 fl oz 48 NA
MODE-OF-ACTION GROUP NAME (NUMBER1): Multi-site contact (M1)
COMMENTS: Treat rice seed before soaking for water-sown rice. Follow label directions for disposal of soak water. Contact your farm advisor regarding specific recommendations for your area. Not all copper compounds are approved for use in organic production; be sure to check individual products.
Restricted entry interval (REI) is the number of hours (unless otherwise noted) from treatment until the treated area can be safely entered without protective clothing. Preharvest interval (PHI) is the number of days from treatment to harvest. In some cases the REI exceeds the PHI. The longer of two intervals is the minimum time that must elapse before harvest.
1 Group numbers are assigned by the Fungicide Resistance Action Committee (FRAC) according to different modes of actions (for more information, see Fungicides with a different Group number are suitable to alternate in a resistance management program. For fungicides with mode-of-action Group numbers 1, 4, 9, 11, or 17, make no more than one application before rotating to a fungicide with a different mode-of-action Group number; for fungicides with other Group numbers, make no more than two consecutive applications before rotating to fungicide with a different mode-of-action Group number.
NA Not applicable



[UC Peer Reviewed]

UC IPM Pest Management Guidelines: Rice
UC ANR Publication 3465


C. A. Greer, UC Cooperative Extension, Colusa County

Acknowledgments for contributions to the disease section:
R. K. Webster, Plant Pathology, UC Davis

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