Disease Management in Organic Seed Production

eOrganic authors:

Lindsey du Toit, Washington State University

Emily Gatch, Washington State University

This is an Organic Seed Resource Guide article.


Diseases can have a significant effect on production of specialty seed crops. Seed growers must pay attention to diseases that affect the vegetative growth stage of the crop, as well as those that affect the reproductive growth stages (flowering and seed formation). Some diseases, such as Verticillium wilt of spinach, become symptomatic only when the crop enters the reproductive stage; these diseases are more important to seed growers than to vegetable growers (unless the vegetable crop also has a flowering stage, e.g., tomato or potato). While vegetable growers are concerned primarily with the pathogens that affect marketable yield and quality, seed growers must also learn how to diagnose and manage seedborne pathogens and the microorganisms that affect seed quality. Pathogens usually remain viable for longer in seed than in vegetative parts of the plant or in the soil. Seeds are a major means of survival of some plant pathogens and of introducing new pathogens to a field or region.

Disease management tactics are either preventive (actions taken to avoid or reduce the likelihood of disease problems) or curative (treatments that eliminate or reduce the effects of a particular disease after it has become established). Because there are few effective curative practices available to organic farmers, organic farmers focus their disease management efforts primarily on preventive cultural practices. Such practices include planting pathogen-free seed, planting in fields of low inoculum potential and in locations with good air movement, adopting wide row spacing, orienting the crop rows to maximize air movement between rows, and tying or staking seed crops to improve air circulation and reduce humidity in the canopy. If feasible, consider using drip or furrow irrigation instead of overhead irrigation, or irrigate earlier in the day to allow the canopy to dry before nightfall.

Some significant pathogens of seed crops are soilborne, such as Fusarium wilt of spinach. To manage soilborne pathogens, it is important to know the cropping history of the field and to adopt appropriate crop rotations. A rotation of 6 to 15 years, depending on the susceptibility of the spinach cultivar, is required to control Fusarium wilt in spinach seed crops. Some soilborne pathogens affect more than one crop, e.g., the fungus that causes Verticillium wilt of spinach can also infect potato, so it is important to avoid growing other crops in the rotation that may be alternative hosts to soilborne pathogens that affect the seed crop.

Strict management of, and screening for, seedborne pathogens of vegetable crops is critical to maintaining high seed quality. Even low levels of seed contamination can cause epidemics of some diseases when infected seed is planted in the field. For example, the tolerance level for contamination of crucifer seed with the causal agent of black rot, Xanthomonas campestris pv. campestris, is 0 contaminated seeds in 10,000 to 50,000 seeds (depending on the market or country in which the seed will be distributed).

Seeds contaminated with a pathogen can be treated physically (e.g. hot water) or chemically (e.g. bleach) to destroy inoculum or reduce the incidence of infection. Some physical and chemical treatments may reduce seed quality (germination, vigor, and/or longevity), so it may be important to test a particular seed treatment on a small sample of seed and check for possible phytotoxicity to the seed before treating an entire seed lot.  Hot water treatment can only be used on some crops, such as brassicas, carrots, tomatoes, peppers, and lettuce, but even on those crops very precise parameters must be followed for hot water treatment to avoid damaging the seed. There are a number of biological and natural disease management products coming onto the market that are approved for use on organic farms, but it must be noted that the efficacy of these biocontrol products may vary among sites, crops, and diseases, reflecting the the complexities and particulars of interactions amongst the host, pathogen and environment.  Therefore, planting pathogen-free seed, when possible, is always preferable to trying to eradicate a pathogen from seed.

When growing seed crops, the following steps will minimize the risk of disease:

  1. Learn to diagnose and manage the diseases of each crop grown.
  2. Know what seedborne pathogens are important to your crop and prevalent in your region, and ensure, through communication with your seed supplier or contractor, that the seed you are planting has been tested to be pathogen-free or has been treated preventatively.
  3. Design and manage the cropping system to minimize the likelihood of disease development.  See the related article Keys to Disease Management in Organic Seed Crops.
  4. Scout fields regularly for early symptoms of disease development.
  5. If you must apply materials to your crops to control disease, communicate with your certifier to make sure the materials are permitted for use on organic farms and labeled for that crop and disease.  See the related article Can I Use this Product for Disease Management on my Organic Farm?
  6. Screen seed lots for seedborne pathogens before sale. This is the responsibility of the seed company, and all diagnostic laboratory results should be communicated to the seed grower. Be aware that there may not be commercial seed health tests available for the particular crop of interest, particularly specialty crops grown on a small scale and for which there has been limited research on seedborne pathogens. 

Seed Disease Resources

For references on organic disease management and disease management in vegetable crops, see Vegetable Crop Disease Resources below.

Web resources

Print resources

For information on the significant diseases affecting major seed crops grown in the Pacific Northwest, consult the Extension PNW seed production publications listed in the article General Specialty Organic Seed Production Resources

  • Principles of seed pathology, 2nd ed. V.L. Agarwal and J.B. Sinclair. 1997. CRC Press, Boca Raton, FL.
  • Seed pathology. Volumes I and II. P. Neergaard. 1977. John Wiley & Sons, New York, NY.
  • Seedborne diseases and their control: Principles and practice. R.B. Maude. 1996. CAB International, Tucson, AZ.
  • WSU-Mount Vernon NWREC Seed Pathology Program reports. Research reports from the Seed Pathology Program at the WSU-Mount Vernon NWREC are available through agricultural university libraries, or you can request reprints from Dr. Lindsey du Toit, 16650 State Route 536, Mount Vernon, WA 98273-4768; phone 360-848-6120; fax 360-848-6159; e-mail: dutoit@wsu.edu
    • A real-time PCR seed assay for Botrytis spp. that cause neck rot of onion. M.I. Chilvers, L. J. du Toit, H. Akamatsu, and T.L. Peever. 2007. Plant Disease 91:599-608.
    • Bacterial blight of carrot seed crops in the Pacific Northwest. L.J. du Toit et al. 2005. Plant Disease 89:896–907.
    • Botrytis porri in onion seed crops and onion seed. L.J. du Toit et al. 2002. Plant Disease 86:1178.
    • Detection and identification of Botrytis species associated with neck rot, scape blight, and umbel blight of onion. M.I. Chlvers and L.J du Toit. Online. Plant Health Progress doi:10.1094/PHP-2006-1127-01-DG. 
    • Efficacy of hot water and chlorine for eradication of Cladosporium variabile, Stemphylium botryosum, and Verticillium dahliae from spinach seed. L.J. du Toit and P. Hernandez-Perez. 2005. Plant Disease 89:1305–1312.
    • Evaluation of Actigard, bactericides, and compost teas for control of bacterial blight in carrot seed crops, 2004. L.J. du Toit and M.L. Derie. 2005. Fungicide & Nematicide Tests 60:V046.
    • Evaluation of fungicides and compost teas for control of Botrytis scape and umbel blight in onion seed crops, 2004. L.J. du Toit and M.L. Derie. 2005. Fungicide & Nematicide Tests 60:V045.
    • Evaluation of mustard cover/biofumigant crops for management of Fusarium wilt in spinach seed crops. L.J. du Toit et al. 2004. Biological & Cultural Tests 19:V004.
    • Evaluation of yield loss caused by leaf spot fungi in spinach seed crops, 2004. L.J. du Toit, M.L. Derie, and P. Hernandez-Perez. 2005. Fungicide & Nematicide Tests 60:V047.
    • First report of leaf spot of spinach, caused by Stemphylium botryosum, in Arizona. S.T. Koike, M.E. Matheron, and L.J. du Toit. 2005. Plant Disease 89:1359.
    • Fusarium proliferatum pathogenic on onion bulbs in Washington. L.J. du Toit, D.A. Inglis, and G.Q. Pelter. 2003. Plant Disease 87:750.
    • Iris yellow spot virus in onion bulb and seed crops in Washington. L.J. du Toit et al. 2004. Plant Disease 88:222.
    • Iris yellow spot virus in onion seed crops in South Africa. L.J. du Toit, J.T. Burger, A. McLeod, M. Engelbrecht, and A. Viljoen. 2007. Plant Disease 91:1203.
    • Prevalence of Botrytis spp. in onion seed crops in the Columbia Basin of Washington. L.J. du Toit, M.L. Derie and G.Q. Pelter, 2004. Plant Disease 88:1061–1068
    • Screening for resistance to leaf spot diseases of spinach. B. Mou, S.T. Koike, and L.J. du Toit.  2008. HortScience 43:1706-1710.
    • Seedborne Cladosporium variabile and Stemphylium botryosum in spinach. P. Hernandez-Perez and L.J. du Toit. 2006. Plant Disease 90: 137-145.
    • Sequence characteristics of Iris yellow spot virus (genus Tospovirus) isolates from the western region of the United States. H.R. Pappu, L.J. du Toit, and H.F. Schwartz. 2006. Archives of Virology 151:1015-1025
    • Stemphylium botryosum pathogenic on spinach seed crops in Washington. L.J. du Toit and M.L. Derie. 2001. Plant Disease 85:920.
    • Susceptibility of storage onion cultivars to Iris yellow spot in the Columbia Basin of Washington, 2004. L.J. du Toit and G.Q. Pelter. 2005. Biological & Cultural Tests 20:V006.
    • Verticillium wilt in spinach seed production. L.J. du Toit, M.L. Derie, and P. Hernandez-Perez. 2005. Plant Disease 89:4–11.


  • National Seed Health System. 
    Link: http://www.seedhealth.org (verified 10 March 2010)
    The National Seed Health System (NSHS) is a program authorized by USDA-APHIS and administered by the Iowa State University Seed Science Center to accredit both private and public entities to perform certain activites needed to support the issuance of Federal phytosanitary certificates for the international movement of seed. NSHS develops and publishes field inspection procedures and seed health testing protocols for significant seed-borne diseases of vegetable crops, and accredits organizations providing those services.
    Iowa State University
    Seed Science Center
    Ames, IA 50010
    Phone: 515-294-6493
  • International Seed Testing Association (ISTA)
    Link: http://www.seedtest.org (verified 10 March 2010)
    Develops and publishes international seed health testing standard protocols and promotes research into all aspects of seed science and technology.
    ISTA Secretariat
    Z├╝richstrasse 50
    8303 Bassersdorf
    CH - Switzerland
    Phone: +41 44 838 6000
    Fax: +41 44 838 6001
    Email: ista.office(at)ista.ch
  • The International Seed Federation (ISF)
    Link: http://www.worldseed.org
    Conducts the International Seed Health Initiative (ISHI), which includes a manual of seed health testing reference methods for vegetable seeds.
    ISF Secretariat
    Chemin du Reposoir 7
    1260 Nyon Switzerland
    Phone: +41 22 365 44 20
    Email: isf@worldseed.org

Seed Testing Labs

See also the article Government Agencies and Regulations for Organic Seed Production for information on phytosanitary testing of seed lots for export.

  • California Seed & Plant Lab, Inc.
    Link: http://www.calspl.com/ (verified 10 March 2010)
    7877 Pleasant Grove Rd.
    Elverta, CA 05626
    Phone: 916-655-1581
    Fax: 916-655-1582
  • STA Labs
    Link: http://www.stalabs.com (verified 10 March 2010)
    STA Laboratories – Colorado
    1821 Vista View Drive
    Longmont, CO 80504
    Phone: 303-651-6417
    Fax: 303-772-4003
    Colorado Customer Service: 800-426-9124
    Email: info@stalabs.com

    STA Laboratories – California
    7240 Holsclaw Road
    Gilroy, CA 95020
    Phone: 408-846-9964
    Fax: 408-846-9954
    California Customer Service: 888-782-5220
    Email: stacalinfo@stalabs.com
  • Iowa State University’s Seed Science Center. Iowa State University Seed Testing Laboratory (tests corn, soybeans, and more than 300 other species of seeds).
    Phone: 515-294-6826
    Fax: 515-294-8303
    Email: seedlab@iastate.edu
  • Washington State Department of Agriculture Seed Program
    WSDA Seed Inspection Program
    21 North First Avenue, Suite 203
    Yakima, WA 98902
    Phone: 509-225-2636
    Fax: 509-454-4395
    Toll Free: 866-865-6137

Vegetable and General Disease Management Resources

Web resources

  • Biological control of plant pathogens: Research, commercialization, and application in the USA [Online]. B. Gardener and D. Fravel. 2002. Plant Health Progress. doi:10.1094/PHP-2002-0510-01-RV. Available at: http://www.plantmanagementnetwork.org/pub/php/review/biocontrol/ (verified 10 March 2010).
  • Microbial biopesticides for the control of plant diseases in organic farming fact sheet [Online]. 2008. R. Raudales and B. McSpadden. Ohio State University Extension Publication HYG 3310. Available at: http://ohioline.osu.edu/hyg-fact/3000/pdf/HYG_3310_08.pdf (verified 10 March 2010).
  • Determining the efficacy of disease management products in organically-produced tomatoes [Online].  A.L. Wszelaki and S.A. Miller. 2005. Plant Health Progress doi 10.1094/PHP-2005-0713-01-RS. Available at: http://www.plantmanagementnetwork.org/pub/php/research/2005/tomato/ (verified 10 March 2010).
  • Organic IPM field guide: Diseases [Online]. ATTRA. Available at: https://attra.ncat.org/attra-pub-summaries/?pub=148 (verified 14 Oct 2019).
  • Plant disease management for organic crops [Online]. S. T. Koike, M. Gaskell, C. Fouche, R. Smith, and J. Mitchell. 2000. University of California Division of Agriculture and Natural Resources Extension Publication 7252. Available at: http://anrcatalog.ucdavis.edu/Details.aspx?itemNo=7252 (verified 22 Mar 2014).
  • Pacific Northwest Plant Disease Management Handbook [Online].  Available at:http://pnwhandbooks.org/plantdisease/ (verified 22 July 2014). Control recommendations are based on the unique mix of climate, crops, regulations, and growers in the Pacific Northwest and may not be applicable in other areas.
  • Resource guide for organic insect and disease management [Online]. E. Brown Rosen, E. Sideman, A. M. Shelton, B. Caldwell, and C. Smart. 2006. Cornell University. New York State Agricultural Experiment Station. Available at: http://www.nysaes.cornell.edu/pp/resourceguide/index.php (verified 10 March 2010).
  • University of California Statewide Integrated Pest Management Project publications. Available online at: www.ipm.ucdavis.edu/PMG/crops-agriculture.html) (verified 10 March 2010). The University of California’s official guides for pest-monitoring techniques and pesticide and non-pesticide alternatives for managing pests (including insects, mites, nematodes, weeds, and diseases) in agricultural crops, including vegetables. The database is updated regularly as pesticide registrations change and new methods become available. New crops are added periodically. The PDF version of each guide is suitable for printing.
  • Vegetable diseases caused by soilborne pathogens [Online]. S.T. Koike, S.V. Subbarao, R.M. Davis, T.A. Turini. 2003. University of California Division of Agriculture and Natural Resources Extension Publication 8099. Available at: http://anrcatalog.ucdavis.edu/pdf/8099.pdf (verified 10 March 2010).
  • Pacific Northwest Vegetable Extension Group (PNW VEG) [Online]. Available at: http://mtvernon.wsu.edu/path_team/vegpath_team.htm (verified 10 March 2010).
  • Pacific Northwest VEG Resources [Online]. Available at: http://mtvernon.wsu.edu/path_team/VegCropResources.htm (verified 10 March 2010).
  • Washington State Pest Management Resource Service [Online]. Available at: http://wsprs.wsu.edu/ (verified 10 March 2010).

Print resources

American Phytopathological Society Publications. Available for purchase from www.shopapspress.org (verified 10 March 2010)

  • A colour atlas of diseases of lettuce and related salad crops (lettuce, chicory, and endive). D. Blancard, H. Lot, and B. Maisonneuve. 2005. Manson Publishing. 376 pp. 513 color photos.
  • Compendium of beet diseases and insects. R. M. Harveson, L.E. Hanson, and G. L. Hein (eds.) 2009. The American Phytopathological Society. 160 (est.) pages; 289 color images. 10 black-and-white illustrations.
  • Compendium of lettuce diseases. R.M. Davis, K.V. Subbarao, R.N. Raid, and E.A. Kurtz. 1997. American Phytopathological Society. 104 pp., 104 color photographs, 13 black-and-white illustrations.
  • Compendium of onion and garlic diseases. H.F. Schwartz and S.K. Mohan (eds.) 2008. 2nd Edition. American Phytopathological Society. 250 color illustrations, 17 black and white illustrations.
  • Compendium of pea diseases and pests, 2nd ed. J.M. Kraft and F.L. Pfleger (eds.) 2001. American Phytopathological Society. 110 pp. 107 color photographs, 14 black-and-white illustrations.
  • Compendium of umbelliferous crop diseases. R.M. Davis and R.N. Raid (eds.) 2002. American Phytopathological Society. 110 pp., 136 color photographs, 16 black-and-white illustrations and photographs. 

Other publications

  • Diseases and pests of vegetable crops in Canada. R.J. Howard, J.A. Garland, and W.L. Seaman (eds.) 1994. The Canadian Phytopathological Society and the Entomological Society of Canada. 554 pp. Excellent book, very relevant to the PNW on disease and insect pests of a wide range of vegetable crops. Excellent pictures, very good information on pest life cycles and diagnostics. Good sections on overall pest and disease management strategies. Available for purchase from CPS-ESC, 393 Winston Ave., Ottawa, Ontario, Canada K2A 1Y8. Available online at  http://phytopath.ca/publications/diseases-of-vegetable-crops-in-canada/ (verified 2 June 2015)
  • Integrated pest management for cole crops and lettuce. 1992. Publication 3307. University of California Statewide Integrated Pest Management Project, Division of Agriculture and Natural Resources. 112 pp. Available online at http://www.ipm.ucdavis.edu/IPMPROJECT/ADS/manual_colecropslettuce.html (verified 24 July, 2014).Order from ANR Communication Services, University of California, 6701 San Pablo Ave., Oakland, CA 94608-1239; phone 1-800-994-8849 or 510-642-2431; fax 510-643-5470; e-mail: anrcatalog@ucdavis.edu.
  • Publications with excellent color photos available from Seminis Vegetable Seeds (formerly Peto Seed Co., Inc.), Saticoy, CA 93007-4206; Order from 1-888-222-1272.  Available for purchase from: https://seminis-us.com/resources/download/ (verified 14 Oct 2019)
    • Crucifer diseases. A practical guide for seedsmen, growers and agricultural advisors.
    • Enfermedades de las cruciferas. Guia practica para agricultores, productores y comercializadores de semillas y asesores agricolas.
    • Onion diseases. A practical guide for seedsmen, growers and agricultural advisors.
    • Pepper and eggplant disease guide: A practical guide for seedsmen, growers and agricultural advisors.

Disease Diagnostics - University Plant Clinics

For information on how to sample and send plant or seed samples to a clinic, see The Online Guide to Plant Disease Control at http://plant-disease.ippc.orst.edu/clinic.cfm


  • Plant Pathology Laboratory
    University of Idaho
    29603 U of I Lane
    Parma, ID 83660-6699
    Phone: 208-722-6701 Ext. 218 or 217
    Fax: 208-722-6708
    Contact: Krishna Mohan

  • Nematode Testing Service
    University of Idaho
    29603 U of I Lane
    Parma, ID 83660-6699
    Phone: 208-722-6701 Ext. 237
    Fax: 208-722-6708
    Contact: Saad Hafez


  • Extension Plant Pathology at Oregon State University’s Hermiston Agricultural Research & Extension Center:
    OSU HAREC Plant Pathology
    PO Box 105/2121 S. 1st
    Hermiston, OR 97838
    Phone: 541-567-8321
  • James Young, Insect Diagnostician
    1067A Cordley Hall
    Corvallis, OR 97331-2902
    Phone: 541-737-1501
    Fax: 541-737-2412

Western Washington

Eastern Washington

  • Virus Identification
    Link: http://cpcnw.wsu.edu/virus_lab/ (verified 14 Oct 2019)
    Clean Plant Center Northwest
    Tina Vasile
    24106 N. Bunn Road
    Prosser, WA 99350
    Phone: 509-786-2226


Published January 23, 2009

This is an eOrganic article and was reviewed for compliance with National Organic Program regulations by members of the eOrganic community. Always check with your organic certification agency before adopting new practices or using new materials. For more information, refer to eOrganic's articles on organic certification.