# Inbreeding depression and hybrid vigour

> Inbreeding makes hidden harmful recessive alleles homozygous, so inbred plants often lose vigour, yield and fertility (inbreeding depression). Crossing unrelated lines masks those alleles and can push F1s above both parents (hybrid vigour, or heterosis). The vigour fades in the F2 because the masking breaks down as genes segregate.

- Canonical: https://genetixbay.com/knowledge/breeding/inbreeding-depression-hybrid-vigour.html
- Category: Breeding · Level: Breeder
- Evidence: Established · Status: Draft: awaiting expert review (some figures are being checked)
- Stage: Any stage · Systems: Any system
- Updated: 2026-10-31 · Licence: CC BY-SA 4.0 (https://creativecommons.org/licenses/by-sa/4.0/), attribute "GenetixBay Knowledge Base (genetixbay.com/knowledge)"

## Questions and answers

**What is inbreeding depression in cannabis?** Inbreeding depression in cannabis is the loss of vigour, yield and fertility when related plants are mated. Selfing, sib-mating or repeated [backcrossing](https://genetixbay.com/knowledge/glossary/backcross.md) to one clone makes hidden harmful [recessive alleles](https://genetixbay.com/knowledge/glossary/recessive.md) [homozygous](https://genetixbay.com/knowledge/glossary/homozygous.md). Symptoms include slower or deformed seedlings, lower [germination](https://genetixbay.com/knowledge/glossary/germination.md), smaller plants, poorer seed set and odd mutants such as albino or variegated seedlings.

**Why are my F2 or S1 plants weaker?** F2 and S1 cannabis plants are often weaker because inbreeding exposes harmful recessive alleles that the parents carried hidden. Selfing raises the inbreeding coefficient to 0.5 in one generation, and F2s also lose the [F1](https://genetixbay.com/knowledge/glossary/f1.md)'s hybrid vigour as genes segregate. A line sib-mated from one pair for several generations will show it most.

**What is hybrid vigour?** Hybrid vigour, or heterosis, is when offspring of two different, unrelated parents outperform either parent in growth and yield. It is the flip side of inbreeding depression: the F1 carries a working allele at most genes where either parent was weak. In cannabis it shows mostly in growth and yield, not necessarily in flower quality.

**Why are F1 hybrids so vigorous?** F1 cannabis hybrids are vigorous mainly because crossing unrelated parents masks harmful recessive alleles, so each F1 carries a functional copy at most genes where a parent was weak. This [dominance](https://genetixbay.com/knowledge/glossary/dominant.md) explanation is thought to be the main cause; [heterozygote](https://genetixbay.com/knowledge/glossary/heterozygous.md) superiority at some genes may add a little. The finer mechanisms are still debated.

**How do I avoid inbreeding depression when stabilising a line?** Avoid inbreeding depression by keeping the breeding population wide, with several females and several males each generation rather than one pair. Select hard for vigour and sex stability and cull every [intersex plant](https://genetixbay.com/knowledge/glossary/hermaphrodite.md), which purges harmful recessives over time. Track germination, seedling vigour and [dry yield](https://genetixbay.com/knowledge/glossary/yield.md); a germination drop over 10 points signals a problem.

**Does hybrid vigour carry on into the next generation?** No, hybrid vigour does not fully carry on into the next generation. Heterosis is strongest in the F1 and declines in the F2 and later generations as genes segregate and harmful recessives become homozygous again. Expecting F2s to keep the F1's vigour is a common mistake; production seed for vigour is remade from two different parent lines.

**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]:

1. **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].
2. **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](https://genetixbay.com/knowledge/glossary/staminate-flower.md) 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](https://genetixbay.com/knowledge/glossary/herm-prone.md) 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](https://genetixbay.com/knowledge/breeding/s1-selfing.md) and [diagnosing hermaphrodites](https://genetixbay.com/knowledge/diagnosis/hermaphrodites.md).

## 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 approximations [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

1. **Keep the breeding population wide.** Several females and several males each generation. Avoid single-pair [bottlenecks](https://genetixbay.com/knowledge/glossary/genetic-bottleneck.md) every generation.
2. **Select hard for vigour and sex stability** in inbred generations; cull every plant that herms. This **purges** the worst recessives over time [1].
3. **Use inbreeding on purpose, briefly.** S1 or sib generations reveal recessives; then outcross the best.
4. **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].
5. **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.

## Evidence

- Inbreeding depression from recessive load and its purging: *Established* [1].
- Heterosis in crops: *Established* as a phenomenon; mechanisms partly *Contested* [2].
- Cannabis-specific inbreeding depression magnitudes: *Grower practice* (little published data).

## Sources

1. Charlesworth D, Willis JH. 2009. The genetics of inbreeding depression. Nature Reviews Genetics 10:783-796. https://doi.org/10.1038/nrg2664
2. Schnable PS, Springer NM. 2013. Progress toward understanding heterosis in crop plants. Annual Review of Plant Biology 64:71-88. https://doi.org/10.1146/annurev-arplant-050312-120145
3. Suza W, Lamkey K (eds). 2023. Quantitative Genetics for Plant Breeding. Iowa State University Digital Press. https://iastate.pressbooks.pub/quantitativegenetics/
4. Lynch RC, Vergara D, Tittes S, et al. 2016. Genomic and chemical diversity in Cannabis. Critical Reviews in Plant Sciences 35(5-6):349-363. https://doi.org/10.1080/07352689.2016.1265363