# Mendelian genetics for growers, with Punnett squares

> Traits controlled by one gene follow Mendel's rules: each parent passes one of its two alleles at random, so a cross of two heterozygotes gives a 1:2:1 genotype ratio and, for a dominant trait, a 3:1 look. In cannabis the clearest single-gene examples are autoflowering (recessive) and the THC/CBD chemotype switch (close to codominant).

- Canonical: https://genetixbay.com/knowledge/breeding/mendelian-genetics-for-growers.html
- Category: Breeding · Level: Intermediate
- Evidence: Established · Status: Draft: awaiting expert review
- 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

**How do Punnett squares work for cannabis?** A Punnett square for cannabis lists one parent's possible gametes across the top and the other's down the side, then fills each box with the resulting offspring genotype. Crossing two [autoflower](https://genetixbay.com/knowledge/glossary/autoflower.md) carriers (Aa x Aa) gives 1 AA, 2 Aa and 1 aa, so about a quarter of the seedlings are autos. Each box is one equally likely outcome.

**What does 3:1 ratio mean?** A 3:1 ratio means that in an [F2](https://genetixbay.com/knowledge/glossary/f2.md) from two carriers of a recessive trait, about three offspring show the dominant trait for every one showing the recessive. For autoflowering, 100 F2 plants should give about 75 [photoperiod](https://genetixbay.com/knowledge/glossary/photoperiod.md) and 25 autos. Check real counts with a chi-square test; small tents of 10-12 plants rarely show a clean 3:1.

**What is dominant and recessive in cannabis?** In cannabis, a dominant allele shows its effect with one copy, while a recessive allele shows only when a plant has two copies. Autoflowering behaves as recessive in mapped populations, so carriers look photoperiod. Dominant does not mean common or better; it only describes how alleles interact. [Chemotype](https://genetixbay.com/knowledge/glossary/chemotype.md) alleles are codominant, so heterozygotes are visible.

**How many plants do I need to find a recessive trait?** To have a 95% chance of finding at least one plant showing a single recessive trait in a cannabis F2, where it occurs in 25% of plants, grow 11 plants. Two unlinked recessives together (1 in 16) need 47 plants and three (1 in 64) need 191. The formula is n = ln(0.05) divided by ln(1 - p).

**Why don't my F2 ratios match the textbook?** Cannabis F2 ratios often miss the textbook because samples are small, linked genes travel together, weak seedlings die before scoring and under-count recessive classes, many traits are controlled by multiple genes, and dominance is not always complete. Autoflower heterozygotes, for example, flower earlier than pure photoperiod plants. A chi-square test shows whether a deviation is just chance.

**What is linkage?** Linkage is when genes sit close together on the same chromosome and are inherited together instead of independently. Cannabis has 10 chromosome pairs, and recombination is concentrated near chromosome ends, so large central regions pass on in blocks. The [THC](https://genetixbay.com/knowledge/glossary/thc.md) and [CBD synthase](https://genetixbay.com/knowledge/glossary/cbda-synthase.md) genes sit in one such block, which is why chemotype inherits like a single gene.

**Short answer.** Every plant carries two copies (alleles) of each gene and passes one, chosen at random, to each seed. Cross two plants that each carry one hidden recessive allele and about a quarter of the offspring will show the recessive trait. Most traits growers care about (yield, potency, flavour) are not single genes, but Mendel's rules are still the foundation: they explain why [F1s](https://genetixbay.com/knowledge/glossary/f1.md) look uniform and F2s scatter.

## What's happening

Mendel's two laws [1]:

1. **[Segregation](https://genetixbay.com/knowledge/glossary/segregation.md).** The two alleles of a gene separate when pollen and ovules form, so each gamete carries one.
2. **Independent assortment.** Alleles of different genes are inherited independently, **unless the genes sit close together on the same chromosome** (linkage).

Cannabis has 10 chromosome pairs, and recombination is concentrated near chromosome ends, so large central regions are inherited in blocks [5]. That matters: the THC and CBD synthase genes sit together in such a block [5].

## Punnett square 1: a recessive trait (autoflowering)

Autoflowering behaves as one recessive gene in the mapped populations [3]. **A** = photoperiod, **a** = auto.

F1 (Aa) x F1 (Aa):

| | A | a |
|---|---|---|
| **A** | AA (photo) | Aa (photo) |
| **a** | Aa (photo) | aa (**auto**) |

Genotypes 1 AA : 2 Aa : 1 aa. [Phenotypes](https://genetixbay.com/knowledge/glossary/phenotype.md) 3 photo : 1 auto. Two of every three photoperiod F2s still carry the auto allele, and you cannot see which by eye.

## Punnett square 2: a codominant trait (chemotype)

de Meijer et al. (2003) modelled chemotype with one locus, **B**, and alleles **B_T** ([THC synthase](https://genetixbay.com/knowledge/glossary/thca-synthase.md)) and **B_D** (CBD synthase), behaving codominantly [4]. Later work shows it is really two tightly linked genes inherited as a unit, with complications (see [chemotype inheritance](https://genetixbay.com/knowledge/breeding/chemotype-inheritance.md)).

THC:CBD F1 (B_T/B_D) x THC:CBD F1 (B_T/B_D):

| | B_T | B_D |
|---|---|---|
| **B_T** | B_T/B_T (THC dominant, type I) | B_T/B_D (mixed, type II) |
| **B_D** | B_T/B_D (mixed, type II) | B_D/B_D (CBD dominant, type III) |

Expect 1 type I : 2 type II : 1 type III. Here you **can** see the heterozygote, because both alleles show.

## Punnett square 3: two genes at once

Cross two plants that are heterozygous for both autoflowering (Aa) and chemotype (B_T/B_D). If the genes are unlinked, you get 16 combinations. The share that is **auto and CBD dominant** (aa and B_D/B_D) is ¼ x ¼ = **1/16**. Each extra fixed requirement multiplies the odds down. That is the core reason pheno hunts need big numbers.

## Numbers that matter

| Situation | Expected share | Plants to grow for 95% chance of at least one |
|---|---|---|
| Recessive trait in an F2 (¼) | 25% | 11 |
| Two unlinked recessives (1/16) | 6.25% | 47 |
| Three unlinked recessives (1/64) | 1.6% | 191 |
| [Homozygous](https://genetixbay.com/knowledge/glossary/homozygous.md) dominant you can't see (1/3 of dominant-looking F2s) | 33% of the dominant class | Needs a [progeny test](https://genetixbay.com/knowledge/glossary/progeny-test.md) |

Formula: n = ln(0.05) / ln(1 - p). With p = 0.25, n = 10.4, so 11 plants [2].

## Checking a ratio

Use a chi-square test. For 100 F2 plants with 70 photo and 30 auto against 75:25: χ² = (70-75)²/75 + (30-25)²/25 = 0.33 + 1.0 = 1.33, below 3.84 (1 degree of freedom, 5% level), so the data fit 3:1. Toth et al. used exactly this logic to call autoflowering recessive [3].

## Why real ratios drift

- **Small samples.** Ten plants rarely show a perfect 3:1.
- **Linkage.** Genes near each other travel together.
- **Selection before scoring.** If weak seedlings die first, recessive classes can be under-counted.
- **Many genes.** Height, yield and terpene totals are quantitative; see [quantitative traits](https://genetixbay.com/knowledge/breeding/quantitative-traits-heritability.md).
- **Dominance is not always complete.** Autoflower heterozygotes flower earlier than pure photoperiods even though they are not autos [3].

## Common mistakes

- Assuming "dominant" means "common" or "better". It only describes how alleles interact.
- Reading 3:1 into a 12-plant tent.
- Forgetting that a dominant-looking plant can be AA or Aa. Only a test cross (to aa) or a DNA marker tells you.

## Evidence

- Mendel's laws and chi-square testing: *Established* [1][2].
- Autoflowering as a single recessive locus: *Supported* [3].
- Chemotype as a near-codominant single inheritance unit: *Established* as a working model, refined since [4][5].

## Sources

1. Miko I. 2008. Gregor Mendel and the principles of inheritance. Nature Education 1(1):134. https://www.nature.com/scitable/topicpage/gregor-mendel-and-the-principles-of-inheritance-593/
2. Suza W, Lamkey K (eds). 2023. Quantitative Genetics for Plant Breeding. Iowa State University Digital Press. https://iastate.pressbooks.pub/quantitativegenetics/
3. Toth JA, Stack GM, Carlson CH, Smart LB. 2022. Identification and mapping of major-effect flowering time loci Autoflower1 and Early1 in Cannabis sativa L. Frontiers in Plant Science 13:991680. https://doi.org/10.3389/fpls.2022.991680
4. de Meijer EPM, Bagatta M, Carboni A, et al. 2003. The inheritance of chemical phenotype in Cannabis sativa L. Genetics 163(1):335-346. https://doi.org/10.1093/genetics/163.1.335
5. Laverty KU, Stout JM, Sullivan MJ, et al. 2019. A physical and genetic map of Cannabis sativa identifies extensive rearrangements at the THC/CBD acid synthase loci. Genome Research 29(1):146-156. https://doi.org/10.1101/gr.242594.118