# 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](https://genetixbay.com/knowledge/glossary/recessive.md), about three offspring show the [dominant](https://genetixbay.com/knowledge/glossary/dominant.md) 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](https://genetixbay.com/knowledge/glossary/allele.md) 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](https://genetixbay.com/knowledge/glossary/gene.md), 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](https://genetixbay.com/knowledge/glossary/chromosome.md) 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.** The two alleles of a gene separate when pollen and ovules form, so each gamete carries one.
2. **[Independent assortment](https://genetixbay.com/knowledge/glossary/independent-assortment.md).** 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 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](https://genetixbay.com/knowledge/glossary/cbd.md) 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 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