Diagnosing rhizoctonia hypocotyl rot in narrow-leafed lupins

Strains of the soil-borne fungus Rhizoctonia solani cause hypocotyl rot only in all lupin species, and most other crop and pasture legumes in WA. Infection incidence is generally low, but when bad can significantly reduce plant establishment.


Reddish-brown lesions on the hypocotyl
Hypocotyl totally rotted

What to look for


  • Seedling death and poor early growth, that is worst on deep sown plants on sandy soils.
  • Diseased plants occur generally as individual plants throughout the crop but may have a clumpy distribution with several seedlings in a row showing symptoms.


  • Reddish-brown sunken lesions on the hypocotyl.
  • Seedlings may rot before emergence.
  • From emergence to the 8-leaf stage, infected seedlings wilt and die as the lesions grow and eventually rot through the hypocotyl.
  • Infected plants that survive past the 8-10-leaf point often remain stunted and are less productive than healthy plants.

What else could it be

Condition Similarities Differences
Diagnosing rhizoctonia ZG6 in narrow-leafed lupins Reddish-brown hypocotyl lesions Plants also have red-brown root lesions (rare).
Diagnosing pleiochaeta root rot in narrow-leafed lupins Stunted , dying seedlings. Dark-brown rather than red-brown root lesions, no hypocotyl lesions.

Where did it come from?

Contaminated soil
Contaminated soil
  • This strain of Rhizoctonia solani infects the hypocotyls of many species of crop and pasture legume but cause negligible damage to cereals.
  • The fungus can survive in soil in the absence of legumes and can still infect lupin crops after two or more cereal crops.
  • After the break of the season the fungus grows out to infect hypocotyls of lupin plants soon after germination.
  • Plants are most susceptible in the first two weeks after germination.
  • The fungus is more active with warm soil temperatures and will be more prevalent in early sown crops.
  • Disease is worse after legume pastures that host the disease.
  • Damage to seedlings by pre-sowing herbicides can also increase incidence of hypocotyl rot.
  • Deep sowing increases the length of the hypocotyl and exposes more tissue to possible infection

Management strategies

  • Rotate crops because the disease most often occurs in lupin after a legume pasture.
  • Avoid sowing very early into warm drying soils in paddocks with known disease risk, particularly after legume pastures.
  • Avoid sowing lupins less than 24 hours after applying glyphosate in disease prone paddocks.
  • Shallow sowing reduces hypocotyl exposure to the disease.
  • Increase seed rates in disease prone paddocks by 10-25% to compensate for loss of seedlings during establishment.
  • Both iprodione or procymidone-based seed dressings, which are applied for brown spot control, can reduce the severity of hypocotyl rot.
  • Cultivation will not reduce the disease.

Where to go for expert help

DDLS Seed Testing and Certification
+61 (0)8 9368 3721
Page last updated: Friday, 17 April 2015 - 9:14am