Short answer. Every outbreeding plant carries hidden, mostly recessive, harmful alleles. Inbreeding (selfing, sib-mating, backcrossing to one clone) makes them homozygous and visible: weaker growth, lower yield, poorer seed set. Crossing unrelated parents hides them again and can give F1s more vigour than either parent. That vigour is strongest in the F1 and declines as later generations segregate [1][2].
What's happening
Two main explanations, both supported [1][2]:
- Dominance (partial dominance) hypothesis. Most of inbreeding depression comes from many mildly harmful recessive alleles. Inbreeding exposes them; crossing masks them. This is thought to be the main cause in most species [1].
- Overdominance. At some genes the heterozygote itself is superior. This is harder to prove and probably explains less [1].
Heterosis is the flip side: the F1 of two different inbred lines carries a functional allele at most genes where either parent was weak [2]. Real mechanisms also involve gene regulation and dosage effects that are still being worked out [2] (Contested in detail).
Cannabis is naturally outcrossing and dioecious, so it is expected to carry a substantial load of hidden recessives (Supported by general theory; little cannabis-specific data) [1][4].
Inbreeding and hermaphrodites. Selfing a dioecious species is only possible by forcing or tolerating male flowers on females. The GenetixBay breeder position is that repeated, unselected selfing (S1 on S1) of plants that herm is a main source of herm-prone lines: inbreeding fixes the tendency along with everything else. Inbreed only from proven-stable females, cull every intersex plant in each inbred generation, and outcross rather than self again when a line starts throwing hermies. See S1s and selfing and diagnosing hermaphrodites.
How much heterozygosity is lost
| Mating | Inbreeding coefficient (F) after 1 / 2 / 3 generations |
|---|---|
| Selfing | 0.50 / 0.75 / 0.875 |
| Full sibs | 0.25 / 0.375 / 0.50 |
| Half sibs | 0.125 / ~0.22 / ~0.31 |
| Backcross to same clone (offspring F) | 0.25 / 0.375 / 0.4375 (approx.) |
Selfing and full-sib values are standard; half-sib and backcross values are approximationsbeing reviewed [3].
Symptoms of inbreeding depression
- Slower seedlings, more weak or deformed seedlings, lower germination.
- Smaller plants and lower yield.
- Lower pollen production or seed set.
- More unusual mutants (variegation, leaf deformities, albino seedlings).
- More intersex plants, if the line was selfed from unstable parents (house position; see above).
- Sometimes more variation in performance, not less.
How to manage it
- Keep the breeding population wide. Several females and several males each generation. Avoid single-pair bottlenecks every generation.
- Select hard for vigour and sex stability in inbred generations; cull every plant that herms. This purges the worst recessives over time [1].
- Use inbreeding on purpose, briefly. S1 or sib generations reveal recessives; then outcross the best.
- Make F1s from two genuinely different, partially inbred lines if you want uniform, vigorous production seed. This is how hybrid seed works in maize and vegetables [2][3].
- Measure. Germination rate, seedling vigour and dry yield per plant tracked across generations show inbreeding depression early.
Numbers that matter
| Signal | Possible inbreeding depression if... |
|---|---|
| Germination | falls by >10 percentage points vs earlier generations under the same test |
| Seedling abnormalities | >2-5% of seedlings |
| Yield | inbred family mean consistently below both outcrossed checks |
Thresholds are GenetixBay practice suggestions, not research values.
Common mistakes
- Blaming "bad genetics" on a line you've sib-mated from one pair for five generations.
- Expecting F2s to keep the F1's vigour.
- Selfing again from a plant that hermed. You fix the defect along with the traits.
- Assuming hybrid vigour means better flower quality. It mostly shows in growth and yield.
