# S1s and selfing: what happens when a plant pollinates itself

> An S1 is seed from a plant pollinated by its own pollen, usually by reversing one female clone or branch. S1s are feminised, and they are not copies of the parent: each S1 seed is a new genotype. Selfing halves heterozygosity per generation, reveals hidden recessives (good and bad), and is a fast way to test what a clone carries. Done carelessly, especially S1 on S1 from plants that herm, it is one of the main ways herm-prone lines are made; only self proven-stable females and cull every intersex offspring.

- Canonical: https://genetixbay.com/knowledge/breeding/s1-selfing.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 an S1 seed?** An S1 seed comes from a female cannabis plant pollinated by itself: one branch or clone is reversed to make pollen, which is then used on the same genotype. S1 offspring reshuffle the parent's own alleles, segregating 1:2:1 at every [heterozygous](https://genetixbay.com/knowledge/glossary/heterozygous.md) gene, so they relate to their parent much as F2s relate to an F1.

**Is an S1 a copy of the mother plant?** No, an S1 is not a copy of the mother plant. Selfing reshuffles the mother's alleles, so S1s vary: some resemble the parent, while about 25% show each hidden recessive trait. Research found genetic variation among S1 progeny similar to that among cross-fertilised progeny. Selling S1s as 'the clone in seed form' is misleading.

**Are S1 seeds feminised?** Yes, S1 seeds are feminised. The reversed female's pollen carries only X chromosomes, as do its ovules, so the S1 seeds are female, barring rare exceptions. Feminised is not the same as stable, though: S1s still segregate genetically and inherit any intersex tendency the parent carried, so only self a proven sex-stable female.

**Why are my S1s weaker than the clone?** S1s are often weaker than the parent clone because selfing halves heterozygosity in one generation, raising the [inbreeding coefficient](https://genetixbay.com/knowledge/glossary/inbred-line.md) to 0.5. That exposes harmful recessive alleles the clone carried hidden, which is [inbreeding depression](https://genetixbay.com/knowledge/glossary/inbreeding-depression.md): weaker growth, poorer fertility and deformities. Selecting for vigour and fertility over several selfed generations can gradually purge the worst.

**What is an S2?** An S2 is the next generation after an S1: a selected S1 plant pollinated by itself. Expected heterozygosity drops to about 25%, with an inbreeding coefficient of 0.75; an S3 drops to 12.5%. Stacking S1 on S1 without strict culling fixes everything the line carries, including any intersex tendency, which GenetixBay considers a main route to [herm-prone](https://genetixbay.com/knowledge/glossary/herm-prone.md) lines.

**Should I make S1s of my keeper?** Make S1s of a keeper only for a clear purpose, such as finding the recessives it carries or backing up its alleles in seed, and only if it stayed fully female for at least two runs. GenetixBay frowns on selfing as a shortcut; a proper cross with a selected male is preferred. S1s preserve the keeper's alleles, not its exact combination.

**Do S1 seeds turn hermaphrodite?** S1 seeds turn hermaphrodite mainly when the parent was unstable or was selfed from stress-herm pollen. The GenetixBay breeder position is that careless and repeated selfing is a prime source of herm-prone lines, because the tendency passes into every female seed. One S1 from a proven-stable mother, grown out with intersex plants culled, is a legitimate tool.

**Short answer.** You reverse one branch (or a clone) of a female so it makes pollen, then use that pollen on the same genotype. The seed is an S1. S1s are female (both gametes carry X) [1][2] and they are related to the parent like F2s are to an F1: they reshuffle the parent's own alleles. Expect variation, some plants close to the parent, and some recessive surprises. Used carelessly, selfing is also one of the main ways herm-prone lines get made.

> **Breeder's standard.** Only self a female that has stayed fully female for at least two runs, reversed under control (never pollen from a stress herm). Grow out the S1s, cull every plant that shows intersex flowers, and don't self again from a line that throws hermies. Never stack S1 on S1 without that culling, and disclose the [herm rate](https://genetixbay.com/knowledge/glossary/herm-threshold.md) with any S1 seed you release. Cannabis is a dioecious species; keeping it that way is the breeder's job.

> **House position: selfing is mostly frowned upon.** Real breeding needs real males, selected as carefully as the females. Males are encouraged and rewarded on GenetixBay, and a well-documented male line is a prized contribution. Selfing is mostly frowned upon: it was historically an emergency measure to save a line, not a shortcut. GenetixBay holds the best breeding standards: snobby, and proud of it.

## What's happening

At every gene where the parent is heterozygous (Aa), S1 offspring segregate 1 AA : 2 Aa : 1 aa. On average half the heterozygosity is lost per generation of selfing [4]. That does two things:

1. **Reveals recessives.** Useful hidden traits (a colour, a terpene type, [autoflowering](https://genetixbay.com/knowledge/glossary/autoflower.md)) appear in ~25% of plants. So do harmful ones (weak growth, poor fertility, deformities): this is inbreeding depression [3].
2. **Fixes faster.** A selfed line becomes uniform much faster than a sib-mated one, if you can live with the inbreeding.

Punja and Holmes (2020) found the genetic variation among progeny after one generation of selfing was similar to that among cross-fertilised progeny in their markers [1]. That is a reminder: S1 seed is not a clone in a seed.

## Numbers that matter

| Generation | Expected heterozygosity left (from a fully heterozygous start) | Inbreeding coefficient F |
|---|---|---|
| S0 (the parent) | 100% | 0 |
| S1 | 50% | 0.5 |
| S2 | 25% | 0.75 |
| S3 | 12.5% | 0.875 |
| S4 | 6.25% | 0.94 |

Single-locus expectations [4]. Real clones are not 100% heterozygous, so start values are lower.

## When S1s make sense

| Goal | S1 useful? | Why |
|---|---|---|
| Back up a clone in seed form | Partly | You preserve its alleles, not its exact combination |
| Find what recessives a clone carries | Yes | ~25% of S1s show each recessive |
| Make a feminised production line fast | Sometimes | Uniformity rises quickly; vigour may fall |
| Create a breeding parent with fewer hidden recessives | Yes, with selection over S1-S3 | Purging by selection |
| Sell "a seed version of clone X" | Only with honest labelling | Must say S1 and show grow-out variation |

## Why careless selfing makes hermies

Historically, selfing was an emergency measure: a way to save a line when no male was left, not a trait to want or a shortcut to sell. Treat it the same way today.

Cannabis has been dioecious and stable for millennia. The GenetixBay breeder position is that herm-prone lines are mainly made, not born, and repeated selfing is a prime route:

- **Selfing a plant that has already hermed** puts its readiness to make [male flowers](https://genetixbay.com/knowledge/glossary/staminate-flower.md) into every seed, and with no male parent there is nothing to dilute it.
- **S1 on S1 (S2, S3...)** without strict culling fixes whatever the line carries, the tendency included, at the same speed it fixes the traits you wanted.
- **Hermaphrodite pollen gives female seed** [1], so the defect hides inside an "all-female" pack until the buyer's [light leak](https://genetixbay.com/knowledge/glossary/light-leak.md) exposes it.

Punja and Holmes found one generation of selfing had no measurable effect on [genetic diversity](https://genetixbay.com/knowledge/glossary/gene-pool.md) in their markers and said more sequential selfing would need study [1]. That supports the point that one S1 from a proven-stable mother is a tool; it is the unselected stacking and selfing of unstable plants that does the damage.

## Step by step

1. Choose a female with **no** intersex tendency across at least two runs. Selfing a plant that hermaphrodites readily concentrates the trait. Don't self it; cull it.
2. Reverse one clone or branch with [silver thiosulfate](https://genetixbay.com/knowledge/glossary/sts.md) (see [feminised seed and sex reversal](https://genetixbay.com/knowledge/breeding/feminised-seed-sex-reversal.md) for method and safety).
3. Collect the pollen in a separate space.
4. Pollinate tagged branches on an untreated clone of the same plant.
5. Harvest seed 5-7 weeks later; record as an S1 batch with the parent's GB-IND/GB-CUT ID.
6. Grow out at least 20-30 S1s and record vigour, uniformity and any off-types or intersex plants. Cull intersex plants and never use them as parents. Publish those numbers, including the herm rate, with the seed.

## Common mistakes

- Selling S1s as "the clone in seed form".
- Selfing for several generations without selecting for vigour and fertility.
- Using pollen from a stress-induced hermaphrodite rather than controlled reversal. You can't separate "the trait" from "the tendency".
- Stacking S1 on S1 and releasing the result untested. That is how [pollen chuckers](https://genetixbay.com/knowledge/glossary/pollen-chucker.md) spread herm-prone genetics.

## Evidence

- S1 seed is female and genetically variable: *Established* [1][2].
- Loss of heterozygosity and inbreeding depression under selfing: *Established* [3][4].
- Careless and repeated selfing as a main source of herm-prone lines: GenetixBay house position (breeder experience). Risk depends mainly on the parent's own stability and on culling; one generation of selfing did not reduce marker diversity [1]. Controlled cannabis comparisons of intersex rates in S1 vs [outcrossed](https://genetixbay.com/knowledge/glossary/outcross.md) lines are lacking.

## Sources

1. Punja ZK, Holmes JE. 2020. Hermaphroditism in marijuana (Cannabis sativa L.) inflorescences: impact on floral morphology, seed formation, progeny sex ratios, and genetic variation. Frontiers in Plant Science 11:718. https://doi.org/10.3389/fpls.2020.00718
2. Flajšman M, Slapnik M, Murovec J. 2021. Production of feminized seeds of high CBD Cannabis sativa L. by manipulation of sex expression and its application to breeding. Frontiers in Plant Science 12:718092. https://doi.org/10.3389/fpls.2021.718092
3. Charlesworth D, Willis JH. 2009. The genetics of inbreeding depression. Nature Reviews Genetics 10:783-796. https://doi.org/10.1038/nrg2664
4. Suza W, Lamkey K (eds). 2023. Quantitative Genetics for Plant Breeding. Iowa State University Digital Press. https://iastate.pressbooks.pub/quantitativegenetics/