Collar rot / stem rot (Sclerotium)
A soil-line stem rot with a white cottony mat and mustard-seed-like brown sclerotia at the base — the plant wilts and dies.
- Pathogen
- Fungus (Sclerotium rolfsii)
- Spreads by
- Soil-borne sclerotia; debris; contact
- Favoured by
- Warm, moist soil + surface residue
- Main risk
- Stem girdled at soil line; plant dies
Overview
Collar rot (also called stem rot, foot rot or southern blight) is caused by the soil-borne fungus Sclerotium rolfsii, which has a huge host range — groundnut, chickpea and other pulses, tomato, chilli, potato, and many vegetables and field crops. It attacks the stem right at the soil line (the "collar"), producing a soft brown rot that girdles the stem so the plant yellows, wilts and dies, often while still carrying green upper leaves.
Its diagnostic signs are unmistakable: a white, cottony fan of fungal threads (mycelium) spreading over the stem base and nearby soil, studded with numerous small, round, brown sclerotia that look exactly like mustard seeds. These sclerotia survive for years in the soil and on debris. The fungus is favoured by warm, moist conditions and by heavy surface residue and dense planting. Management combines deep summer ploughing (to bury sclerotia), seed and soil treatment (chemical or bio-agents), and good sanitation and drainage.
How to identify it
- A soft brown rot girdling the stem right at the soil line (the collar), so the plant yellows, wilts and dies.
- A white, cottony fan of fungal threads over the stem base and the soil around it.
- Numerous small, round, brown sclerotia — exactly like mustard seeds — on the mat and stem base.
- Plants dying singly or in patches, often still carrying green upper leaves when they collapse.
What causes it and when
- The soil-borne fungus Sclerotium rolfsii, whose mustard-seed-like sclerotia survive for years in the soil and on debris.
- Favoured by warm, moist soil conditions and by heavy undecomposed surface residue and dense planting.
- Attacks from the seedling stage onward wherever the stem meets moist soil and residue.
- Spreads by growing over the soil surface and by sclerotia carried in soil, debris and irrigation water.
Cultural & organic control
- Deep summer ploughing to expose and bury sclerotia, and remove or fully decompose surface crop residue.
- Avoid heaping soil or mulch against the stem, and ensure good drainage — avoid waterlogging at the collar.
- Rotate away from susceptible hosts and rogue out and destroy affected plants with the soil around them.
- Apply a bio-agent (e.g. Trichoderma) to seed, soil or through farmyard manure as part of the package.
Chemical control
- Treat seed before sowing with a recommended fungicide (e.g. carbendazim or a carboxin+thiram type dressing).
- Drench the soil around the collar of affected and neighbouring plants with a CIB&RC-registered fungicide where recommended.
- Combine any drench with removing residue and improving drainage — chemicals alone rarely clear a sclerotia-loaded soil.
- Confirm the current seed-treatment and drench product for your crop with your local KVK.
Prevent it coming back
- Make deep summer ploughing, residue management and treated seed the routine in affected fields.
- Rotate with non-hosts, keep the collar dry and residue-free, and establish Trichoderma in the soil.
- Rogue diseased plants with surrounding soil early, before the sclerotia multiply and reseed the field.
Crops most at risk
Where this problem is called out in our crop guides — open a crop for the full package of practices.
Frequently asked questions
My plants are rotting at the base with white cottony growth and tiny brown seeds. What is it?
That white cottony fungal mat at the stem base, studded with small round brown sclerotia like mustard seeds, plus a soft rot girdling the stem at soil level and the plant wilting, is collar rot / stem rot (Sclerotium rolfsii). The sclerotia survive for years, so control is preventive: deep summer ploughing, residue removal, treated seed, Trichoderma, good drainage, and roguing affected plants with their soil.
What are the mustard-seed-like brown balls at the base of the plant?
Those are the sclerotia of Sclerotium rolfsii — small, round, tan-to-brown resting bodies, about the size of mustard seeds, that the fungus forms on the white mat and stem base. They are how the fungus survives for years in the soil, so seeing them confirms collar rot and warns you the field is now loaded with inoculum. Deep ploughing to bury them, rotation and Trichoderma help run them down.
How do I manage collar rot in an infested field?
Deep-plough in summer to expose and bury the sclerotia, remove or fully decompose surface residue, and rotate away from susceptible hosts. Treat seed with a fungicide, establish Trichoderma in the soil, keep the collar dry with good drainage, and do not heap soil or mulch against the stem. Rogue affected plants with the soil around them early, and drench with a registered fungicide where recommended. Confirm products with your KVK.
Symptoms and control measures follow ICAR, KVK and state agricultural-university package-of-practices; any named chemical is a registered use. Always read the product label and confirm the dose for your crop and zone. editorial policy.