Why won’t my clones root, and why is my seedling stalling?

The short answer

• Clones: the biggest lever that has actually been measured is the rooting hormone. A synthetic IBA gel roughly doubled rooting success over a willow-extract gel in the one controlled trial on cannabis cuttings. Leave the leaves whole. Two or three leaves is fine. Where you cut from on the mother barely matters.
• The humidity you give a cutting is the humidity a fungus wants. Damping-off starts as a soft, dark, water-soaked patch at the base of the stem. Still air and a sodden medium make it worse; a mother plant that has been kept too long can hand it to every cutting she gives.
• Seedlings: a plant that has rooted does not want the humidity a cutting wanted. Held in seedling-level humidity for weeks it barely transpires, and the nutrients that only travel in the transpiration stream stop reaching the new growth. We did this to our own plant.

Clones: what the one real trial says

Most cloning advice is folklore passed between growers. There is one controlled study on cannabis stem cuttings specifically, from Guelph, and it tested four things growers argue about: how many leaves to leave, whether to trim the leaf tips, whether to take cuttings from the top or the bottom of the mother, and which rooting hormone. Cuttings went into a rooting chamber for twelve days and were then scored for whether they rooted and how well.

Hormone was the big one. A 0.2 % IBA gel rooted 84 % of cuttings; a 0.2 % willow-extract gel rooted 40 %, and the roots it did produce were poorer. If your success rate is low and you are using an organic willow product, that is the first thing we would change.

Trimming the leaf tips hurt. Cutting a third off the leaves — the thing almost every guide tells you to do “to reduce transpiration” — dropped rooting success from 71 % to 53 %. The intact leaf is what feeds the cutting while it has no roots; the authors saw no wilting in whole-leaf cuttings, so the water-loss argument did not hold in their chamber.

Leaf count mattered less than you would think. Two leaves rooted as often as three; three gave somewhat better roots. Position on the mother barely mattered once hormone was accounted for.

Their recommendation, in plain terms: at least three fully expanded, uncut leaves, from either the top or the base of the mother, dipped in an IBA gel. Worth knowing what their chamber looked like too, because it is what the numbers assume: 95 % humidity for the first four days, 80 % for the next four, 60 % for the last four, at 24 °C, under gentle light, with one misting at the start and none after. The humidity comes down in steps as the roots come in. That schedule is the part most home setups skip.

The fungus that lives in your humidity dome

The same conditions that let a rootless cutting survive — near-saturated air, a wet medium, no air movement — are the conditions a group of soil fungi called Fusarium likes best. The disease is damping-off, and on cuttings it looks like this: a soft, darkened, water-soaked patch low on the stem that spreads upward until the cutting folds over. Sometimes there is visible white fungal growth on the outside. Once a cutting has it, it is gone.

Three things from the disease chapter that change what you do:

• Overly wet media and poor air circulation make it worse. A dome with no vents and a soaked plug is the worst case. The trial above kept humidity high in the air and misted once — not a saturated medium.
• It can arrive inside the cutting. A mother plant carrying the fungus passes it to cuttings that look perfectly healthy when you take them. If every batch fails at the base regardless of what you change, suspect the mother, not the technique.
• Old mothers are more likely to carry it. The chapter puts the line at roughly six months. A mother you have kept for a year “because she’s a good one” is a real risk factor.

Seedlings: the humidity mistake we made

A rooted seedling is a different plant from a cutting and wants different air, and this is the one we got wrong on our own bench. The reasoning is simple once stated: water and nutrients move up a plant on the transpiration stream, and some nutrients — calcium and iron among them — travel only that way; the plant cannot pull them out of old leaves to feed new ones. Very humid air means very little transpiration. So a seedling held in cutting-level humidity for weeks keeps growing new leaves that arrive short of exactly those nutrients.

What that looks like: pale new growth with the veins staying green, on the top of the plant, while the older leaves are fine. It is easy to misread as a feeding problem and reach for the bottle, which does nothing, because the nutrient is present and not moving. On our plant it took nine days at 76–82 % humidity to show, and it cleared when we moved the air and let the humidity fall — the leaves that grew afterwards came in green without anything added. That is first-party observation, not a study, and we wrote it up in full because our own device was holding the tent exactly where we had told it to.

The controlled-environment handbook says the same thing from the other direction: faster transpiration draws nutrients to the growing points faster, and air that is too humid is also where bacteria and fungi do best. So the rule for a seedling is the opposite of the rule for a cutting: once it has roots, start bringing the humidity down. On our own device the seedling target now holds for a week and then walks toward the vegetative range over the next week; that fortnight is a choice, not a published figure, and we say so.

How to check this yourself

• Clones failing? Look at the base first. Pull one that has collapsed. A dark, soft, wet stem base is damping-off — a humidity-and-hygiene problem, not a hormone problem. A dry, pale, shrivelled cutting with a firm base died of thirst before it rooted — the opposite problem.
• Count leaves you cut. If you have been trimming tips, stop for one batch and compare.
• Check the mother’s age. Over six months and losing batches at the base: take a fresh mother from a healthy cutting and retire the old one.
• Seedling pale at the top, green below? Read the humidity at night, not noon. If it has been above the mid-70s for days, move air across the plant and let it dry down before you feed anything. New leaves that come in green afterwards are your answer.

What would show that we have this wrong

If your cuttings are failing with firm, dry bases and crisp leaves, the problem is water loss, not fungus, and the humidity advice above runs the wrong way for you — they need more, not less, and probably a vented dome. And if a seedling is pale all over, old leaves included, that is not the immobile-nutrient pattern; look at the root zone and the pH before the air.

Where our device fits, stated narrowly

Croplock does not watch your cuttings; a propagation dome is off the sensors by design, and we would not trust a camera to tell a rooting cutting from a dying one. Where it fits is the seedling half: it logs humidity at canopy height every minute, so “how long has this plant been sitting in 80 %” has a number, and on a tent it controls it walks the humidity target down after the first week instead of holding a cutting’s air over a plant that has roots. That second part exists because of the mistake above.

Sources

• Caplan, D., Stemeroff, J., Dixon, M. & Zheng, Y. (2018). “Vegetative propagation of cannabis by stem cuttings: effects of leaf number, cutting position, rooting hormone, and leaf tip removal.” Canadian Journal of Plant Science 98:1126–1132. DOI 10.1139/cjps-2018-0038 — every figure in the clones section.
• Cannabis in Controlled Environment Production (CRC Press), Ch. 8, Disease Management — Fusarium damping-off on cuttings, its appearance, the role of wet media and still air, transmission from stock plants, and the six-month line. Restated in our own words.
• Stasiak, M. & Dixon, M. (2022). “Growing Facilities and Environmental Control,” Ch. 2 in the same handbook. DOI 10.1201/9781003150442-2 — transpiration carrying nutrients to the growing points; low VPD favouring microbial growth.
• The seedling episode, the nine-day figure and the hold-then-ramp schedule are first-party and are given as such.

More of these at Answers. The device is at croplock.com.

Related: Is my pale new growth a deficiency? — the vein test for the seedling half. From the build: In band, and sick anyway.